NZ786712A - Methods for improving agricultural production of fowl by administration of microbial consortia or purified strains thereof - Google Patents

Abstract

The disclosure relates to isolated microorganisms-including novel strains of the microorganisms-microbial consortia, and compositions comprising the same. Furthermore, the disclosure teaches methods of utilizing the described microorganisms, microbial consortia, and compositions comprising the same.

Description

NIETI—IGDS EGR IMPROVING LTURAL PRGDUCTIQN (IF J BY AIM‘VIINIS’I‘RA'I‘IQN (IF MICRGIEIAI; (IGNSQR’I‘IA (IR PURIEIEI) STRAINS TI—IEREGE CROSSuREFERENCE T0 RELATED ATIGNS {0001} This application claims the benefit of priority to US. Provisional Application No. 62/323,305, filed on April 15, 2016; US Provisional Application No. 62/335,559, filed on May 12, 2016, and US. Provisional Application No. ,480, filed on November 22, 2016, each of which is herein incorporated by reference in its entirety.

FIELD [0002} The present disclosure relates to isolated and biologically pure microorganisms that have applications, inter alia, in the farming of fowl. The sed microorganisms can be utilized in their isolated and biologically pure states, as well as being formulated into compositions.

Furthermore, the sure provides microbial consortia, containing at least two members of the disclosed microorganisms, as well as methods of utilizing said consortia. Furthermore, the disclosure provides for methods of modulating the fowl microbiome.

STATENIENT REGARDING SEQUENCE LISTING {0003} The sequence listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by nce into the specification. The name of the text file containing the sequence listing is ASBI___003___03 \I‘V’O___S'I"25.txt. The text file is 165 kb, was created on April 13, 2017, and is being submitted electronically Via 1:}S—Web.

BACKGRGUND [0004} The global population is ted to increase to over 9 billion people by the year 2050 with a concurrent ion in the quantity of land, water, and other natural resources available per capita. tions indicate that the average domestic income will also increase, with the WO 81203 projected rise in the GDP of China and India. The desire for a diet richer in animal—source proteins rises in tandem with increasing income, thus the global livestock sector will he charged with the challenge of producing more animal products using fewer resources. The Food and Agriculture Organization of the United Nations predict that 70% more food will have to be produced, yet the area of arable land available will decrease. It is clear that the food output per unit of resource input will have to increase considerably in order to support the rise in population. {0005} Over recent decades the farm industry has seen fast growth in the meat sector, which has been inned by rising demand for poultry meat, which has consistently increased at about three times the rate of tion growth over each of the past five decades. {0006} Poultry meat, eggs, and components thereof are predominantly utilized in the ation of foodstuffs in many different forms. There have been many strategies to improve poultry and egg production through nutritional modulations, hormone treatments, changes in animal management, and selective breeding; however, the need for more efficient production of edible poultry foodstuffs per animal is required, {0007} Identifying compositions and methods for sustainably increasing y and egg production while balancing animal health and ing have become imperative to satisfy the needs of eveiyday humans in an expanding population. sing the worldwide production of y by scaling up the total number of fowl on farms would not only be economically infeasible for many parts of the world, but would further result in negative environmental consequences as the poultry sector’s growth and trends towards intensification and concentration have already given rise to a number of environmental concerns, led predominantly by the production of far more waste than can be 11131121ng by land disposal, [0008} Population densities of poultry in large farms are often accompanied by an increased incidence of microbial pathogens that place the poultry yield at risk, and r place the ultimate consumer of the poultry at risk in instances of zoonotic pathogens such as those of Closz‘rm’ium and Salmonella. Considering the widespread occurrence of many zoonotic pathogens, it is unlikely that y can be completely protected from re. Research has d on investigative means of increasing resistance to colonization in poultry exposed to these pathogens, {0009} Thus, meeting global poultry yield expectations, by simply g up current highminput agricultural systems-------utilized in most of the developed -----is simply not feasible. {8010} There is therefore an urgent need in the art for improved methods of increasing poultry and egg production, while also mitigating the colonization and spread of ial pathogens.

SUMNEARY OF THE DISCLOSURE {0011} In some embodiments, the at least two microbial strains or the at least one microbial strain present in a ition, or consortia, of the disclosure exhibit an increased utility that is not exhibited when said strains occur alone or when said strains are present at a naturally occurring concentration. In some embodiments, compositions of the disclosure, comprising at least two microbial strains as taught herein, exhibit a synergistic effect on imparting at least one improved trait in an animal. In some embodiments, the compositions of the sure------- comprising one or more isolated microbes as taught herein------exhibit markedly different characteristics/properties compared to their closest naturally occurring counterpart. That is, the compositions of the disclosure exhibit markedly different functional and/or structural characteristics/properties, as compared to their closest lly occurring counterpart. For ce, the microbes of the disclosure are structurally different from a microbe as it lly exists in a fowl gastrointestinal tract, for at least the following reasons: said microbe can be isolated and purified, such that it is not found in the milieu of the gastrointestinal tract, said microbe can be present at concentrations that do not occur in the gastrointestinal tract, said microbe can be associated with acceptable rs that do not occur in the gastrointestinal tract, said microbe can be formulated to he shelf-stable and exist outside the gastrointestinal tract, and said microbe can be combined with other microbes at concentrations that do not exist in the gastrointestinal tract, Fuither, the microbes of the disclosure are functionally different from a microbe as it naturally exists in a gastrointestinal tract, for at least the following reasons: said microbe when applied in an isolated and purified form can lead to tion of the gastrointestinal bioine, increased weight gain, increased feed utilization, decreased s of microbial pathogens, decreased pa‘thogen—associa‘ted GI lesions, said microbe can be formulated to be shelf—stable and able to exist outside the gastrointestinal environment, such that the microbe now has a new utility as a supplement capable of administration to a fowl, wherein the microbe could not have such a utility in it’s natural state in the gastrointestinal tract, as the e would be unable to survive outide the intestinal tract without the intervention of the hand of man to ate the microbe into a shelfnstable state and impart this new utility that has the aforementioned onal characteristics not possessed by the microbe in it’s natural state of existence in the fowl gastrointestinal tract. {0012} In some aspects, the present sure is drawn to a method of decreasing feed conversion ratio, increasing fowl weight, and or decreasing pathogennassociated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a stable fowl supplement comprising: i) a ed microbial population of Lactobacz’ilus bacteria comprising bacteria with a 168 c acid sequence that is at least about 97% identical to SEQ ID NO:l, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier le for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an se in feed conversion ratio, an increase in weight, or a decrease in patliogen~associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. {0013} In some aspects, the present disclosure is drawn to a method ofdecreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen~associated lesion formation in the gastroii'itestinal tract of fowl, the method con'iprising: a) administering to a fowl an effective amount of a shelf—stable fowl supplement comprising: i) a purified microbial population that comprises a bacterium with a l6$ nucleic acid sequence, and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOS: l 685, and said ium and/or fungus have a h/IIC score of at least about 0.2; and ii) a shelfustable carrier suitable for fowl administration; wherein the fowl administered the effective amount of the shelfustable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and / or a se in pathogenuassociated lesion formation in the gastrointestinal tract, as ed to a fowl not having been administered the supplement. {0014} In some aspects, the present disclosure is drawn to a method of treating poultry for necrotic enteritis, the method comprisinga) administering to a bird an effective amount of a shelf~stable poultry supplement sing: i) a purified microbial population that comprises a bacterium with a 163 nucleic acid sequence, and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ II) NOS: 1—385, and said bacterium and/or fungus have a MIC score of at least about 0.2; and ii) a shelfnstable car‘r‘ier suitable for poultry stration, wherein the bird administered the effective amount of the shelf—stable poultry supplement exhibits a decrease in the number of necrotic enteritisncausing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement. {0015} In some aspects, the t disclosure is drawn to a method of treating poultry for necrotic enteritis, the method comprising: administering to a bird an ive amount of a shelf~stable poultry supplement comprising: i) a purified microbial population oflaaohacillus ia. comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID N011, and said bacterium has a MIC score of at least about 0.2; and ii) a stable carrier le for poultry administration, wherein the poultry administered the effective amount of the shelfvstable y supplement exhibits a decrease in the number of necrotic enteritis~ causing bacteria in the gastrointestinal tract, as ed to a bird not having been administered the supplement, {@616} In some aspects, the present disclosure is drawn to a method of decreasing feed sion ratio, increasing fowl weight, and or decreasing pathogen-associated lesion formation in the gastrointestinal tract of fowl, the method sing: a) administering to a fowl an effective amount of a shelf—stable fowl supplement comprising: i) a purified microbial population of Lactobacillus ia, comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID NO:374, and said bacterium has a MIC score of at least about 0.2, and ii) a shelfustable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelfustable fowl supplement ts an decrease in feed conversion ratio, an increase in weight, or a decrease in pathogenmassociated lesion formation in the gastrointestinal tract, as ed to a fowl not having been administered the supplement. {8017} In some aspects, the present disclosure is drawn to a method of sing feed conversion ratio, increasing fowl weight, and or decreasing pathogen—associated, lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelf~stable fowl supplement comprising: i) a purified, microbial population of LilCl’ObflCi/Tlus ia comprising bacteria with a léS nucleic acid sequence that is at least about 97% identical to SEQ ID NO:382, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf~stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf~stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in weight, or a se in pathogennassociated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. {0018} In aspects, the aforementioned microbial species—that is, a purified microbial population that comprises a bacteria with a 168 nucleic acid sequence, and/or a fungi with an ITS nucleic acid sequence, which is at least about 97% identical to a nucleic acid sequence selected from the group ting of: SEQ ID NOs: I~385—are s of a hilai'kush group, as the present disclosure illustrates that the members belong to a class of microbes characterized by various physical and functional attributes, which can include any of the following: a) the ability to convert a carbon source into a volatile fatty acid such as acetate, butyrate, propionate, or ations thereof; b) the ability to degrade a soluble or ble carbon source; 0) the ability to impart an increase in weight gain to fowl administered the inicrobe(s); d) the ability to te the microbiome of the gastrointestinal tract of fowl administered the microbe; e) the ability to be formulated into a shelf—stable ition; f) the ability to exhibit a decrease in feed conversion ratio in fowl having been administered the inicrobe(s); g) the y to impart a decrease in pathogen—associated lesion formation in the gastrointestinal tract; h) the ability to impart a decrease in pathogenic microbes in the gastrointestinal tract; and/or i) possessing a MIC score of at least about 0.2 if a bacteria and possessing a MIC score of at least about 0.2 if a fungi. Thus, the members of the Markush group possess at least one property in common, which can be responsible for their on in the claimed relationship. {0019} In some aspects, the fowl is a broiler. In some aspects, the fowl supplement is stable under t conditions for at least one week. In some aspects, the fowl supplement is formulated as an: ulation, tablet, capsule, pill, feed additive, food ient, food additive, food preparation, food supplement, water additive, water—mixed additive, heat— ized additive, moisterurenstabilized additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, or combinations thereof. {8020} In some aspects, administration comprises feeding the fowl supplement to a fowl or spraying the fowl supplement onto a fowl. In some aspects, the purified microbial population is present in the fowl ment at a tration of at least 102 cellsIn some aspects, the purified microbial population comprises a bacterium with a 168 nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:ln50 and 59385. In some aspects, the purified microbial population comprises a fungus with an I'I‘S nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence ed from the group consisting of: SEQ ID NOs:51—58. In some aspects, the purified microbial population comprises a bacterium with a 168 nucleic acid sequence that is at least about 99% identical to a nucleic acid ce selected from the group consisting of: SEQ II) 50 and 59—385. In some aspects, the purified microbial population comprises a fungus with an ITS nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ II) NOs:SIm58. In some aspects, the purified microbial population comprises a bacterium with a 168 nucleic acid sequence selected from the group consisting of: SEQ ID NOs:l—50 and 59—385. In some aspects, the purified microbial population comprises a fungus with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID N()s:51—58, } In some s, the purified microbial population comprises a ium with a l6S nucleic acid sequence and a fungus with an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOszl— 385, In some aspects, the purified microbial tion ses a bacteria with a I68 nucleic acid sequence that is at least about 97% identical to SEQ ID NO: I. In some aspects, the purified microbial population comprises a bacterium with a 163 nucleic acid sequence sing SEQ ID NO: I, and wherein the bacterium is as deposited as PA’IEN1201703004. [0022} In some aspects, the purified ial population only contains organisms that are members of a group ed from: Lactobacillus, Clostridium, Faecalibacter, I-Iydrogenoanaerobacterium, Acrocarpospora, Bacillus, Subdoligranulum, ostoc, Lachnospiracea, Anaerofilum, Mici'obacterium, Verrucosispora, filum, Blautia, Pseudomonas, Sporobacter, Coiynebacterium, Streptococcus, Paracoccus, Cellulosilyticum, Ruminococcus, Rosebura, oides, Filobasidium, Gibberella, Alatospora, Pichia, and Candida.

WO 81203 {0023} In some aspects, the fowl administered the effective amount of the fowl supplement exhibits at least a 1% decrease in feed conversion ratio, at least a 1% increase in weight, and or at least a 1% decrease in en—associated lesion formation in the gastrointestinal tract. In some aspects, the fowl administered the effective amount of the fowl supplement exhibits at least a 10% decrease in feed conversion ratio, at least a 10% increase in weight, and or at least a 10% decrease in pathogennassociated lesion formation in the gastrointestinal tract. {0024} A shelf—stable fowl supplement e of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen~associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a ed population that comprises a bacterium with a. loS nucleic acid sequence and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% identical to a. nucleic acid sequence selected from the group consisting of SEQ ID NOS: l 685; and b) a. shelf—stable carrier suitable for fowl stration, wherein the purified population of bacteria and/or fungi of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, and / or decrease pathogen-associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the ment. In some aspects, the fowl administered the supplement exhibits a decrease in feed conversion ratio as compared to fowl not having been administered the supplement, In some aspects, fowl administered the supplement exhibits a, decrease in feed conversion ratio as compared to fowl not having been administered the supplement, {0025} In some s, the purified tion of bacteria, and/or fungi comprises bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID NO: 1. In some aspects, the purified population of bacteria and/or fungi ses bacteria with a 163 nucleic acid sequence that is at least about 99% identical to SEQ ID N01 In some aspects, the purified population of bacteria and/or fungi comprises bacteria with a 168 nucleic acid ce comprising SEQ 1]) N01 In some ts, the ed population of bacteria and/or fungi comprises bacteria with a 168 nucleic acid sequence comprising SEQ ID N01, and n the bacteria are as deposited as PA'I'ENT201703004. {0026} In some aspects, the slielfnstable fowl ment further comprises: (i) a purified, population of bacteria comprising a 16s nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence ed from the group consisting of: SEQ II) NO:1n50 and 59—385, and/or (ii) a purified population of fungi that comprise fungi with an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ II) N’O:51n58. {0027} In some aspects, the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOzl—SO and 59385. In some aspects, the purified population of fungi comprises fungi with an I'I‘S nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group ting of: SEQ II) NOSI—SS. In some aspects, the purified population of bacteria comprises bacteria with a 168 c acid sequence selected from the group consisting of SEQ ID NO:l—50 and 59—385. In some aspects, the purified tion of fungi comprises fungi with an ITS nucleic acid sequence selected from the group ting of: SEQ ID NO:51~58 In some aspects, the purified population of bacteria comprises bacteria with a l6S nucleic acid sequence that is at least about 97% identical to SEQ ID NO:3 In some aspects, the purified population of bacteria. comprises bacteria with a 16S nucleic acid sequence that is at least about 99% identical to SEQ ID NO:3 In some aspects, the purified tion of bacteria comprises bacteria with a 168 c acid sequence comprising SEQ ID NO:3. In some aspects, the purified population of bacteria comprises SEQ ID NO: I and n the bacteria. are as deposited as ZOI’703OOIIn some aspects, both a purified population of bacteria (i) and a purified tion of fungi (ii) are present in the supplement. [0028} In some aspects, the fowl supplement is formulated for administration to a broiler, In some aspects, the supplement is stable under ambient conditions for at least one week.

In some aspects, the supplement formulated as an: encapsulation, ulation, tablet, capsule, pill, feed additive, food ingredient, food additive, food preparation, food supplement, water additive, mixed additive, heatustabilized additive, moisture—stabilized additive, able solution, consumable spray additive, consumable solid, consumable gel, injection, itory, i, or combinations thereof. [0029} In some aspects, the purified population of bacteria and/or fungi is present in the fowl supplement at a concentration of at least 102 cells. In some aspects, the fowl administered the supplement exhibits an increase in weight as compared to fowl not having been administered the supplement. In some aspects, the fowl administered the supplement exhibits a decrease in pathogenuassociated lesion formation in the gastrointestinal tract as ed to fowl not having been stered the supplement. {@930} In some aspects, the fowl administered the supplement exhibits a decreased incidence of C[ostrz’dium gens—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. in some aspects, the fowl administered the supplement exhibits a 1% sed incidence of Closrrtdz'um perfi‘z’ngensm associated lesion ion in the gastrointestinal tract as compared to fowl not having been administered the ment. in some aspects, the fowl administered the supplement exhibits a % decreased nce of Closm'dium ‘ngens—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. In some aspects, the fowl administered the supplement exhibits a 20% decreased incidence of Ciostridz’um peifiingens—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement {0031} In some aspects, the shelf—stable supplement further comprises: (i) a purified population of bacteria comprising a 168 nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ll) NO: 1-50 and , and/or (ii) a purified population of fungi comprising an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOz51—58. [0032} in some embodiments, the present disclosure is drawn to a method for decreasing feed conversion ratio, increasing fowl weight, or decreasing en-associated lesion ion in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelfustable fowl supplement comprising: i) a purified microbial population that comprises a ium with a 168 nucleic acid sequence at least about 97% identical to SEQ ID NOstl3, 346, 19, or 22, and said bacterium has a MIC score of at least about 0.2; and ii) a stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogenmassociated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement {@933} A shelf—stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogennassociated lesion formation in the intestinal tract of fowl, comprising: a) a purified population that comprises a bacterium with a 16S c acid sequence at least about 97% identical to SEQ ID NOs: l 3, 346, 19, or 22; and b) a shelfnstable carrier suitable for fowl administration; wherein the purified population of ia of a) is present in the ment in an amount effective to se feed conversion ratio, increase fowl weight, and or decrease pathogen-associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement. {0034} A method for decreasing feed conversion ratio, increasing fowl weight, and / or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelf~stable fowl supplement sing: i) a purified ial population of Bacillus, Lactobacillus, or Eubacferium bacteria comprising bacteria with a 168 nucleic acid sequence selected from SEQ ll) NOs:l3, 346, 19, or 22, and said bacterium has a MIC score of at least about 02; and ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in weight, or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. [0035} A shelf—stable fowl ment capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population of Bacilius, Lacmbacillus, or Eubaclerizmz bacteria comprising bacteria with a res nucleic acid sequence that is at least about 97% identical to SEQ ID NOszl3, 346, 19, or 22; and b) a shelfustable carrier suitable for fowl administration, wherein the purified tion of Bacillus, Lacfobaciiius, or Eubacterz’um bacteria of a) is present in the supplement in an amount effective to decrease feed sion ratio, increase fowl weight, or se pathogen—associated lesion formation in the gastrointestinal tract of fowl, as ed to a fowl not having been administered the supplement. {0036} A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a stable poultry supplement comprising: i) a purified, microbial population that comprises a bacterium with a res nucleic acid sequence at least about 9 % identical to a nucleic acid sequence selected from SEQ ll) NOs:l3, 346, 19, or 22, and said bacterium has a MIC score of at least about 0.2; and ii) a shelfustable car'r'ier suitable for poultry administration, wherein the bird administered the effective amount of the shelfnstable poultry supplement exhibits a decrease in the number of necrotic eriteritismcausing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement. {0037} A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an ive amount of a shelf—stable poultry supplement comprising: i) a ed microbial population of Bacillus, Lactobacz’llus, or erz'um bacteria comprising bacteria with a 168 nucleic acid sequence selected, from SEQ ID NOs:l3, 346, 19, or 22, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf-stable cai‘i‘ier suitable for poultry administration, wherein the poultry administered the effective amount of the shelf—stable poultry supplement exhibits a decrease in the number of necrotic enteritis~causing ia in the gastrointestinal tract, as compared to a bird not having been administered the ment, {0038} In aspects? the aforementioned microbial species that is? a ed microbial tion that comprises a bacteria with a 168 nucleic acid sequence, and/or a fungi with an ITS nucleic acid sequence, which is at least about 97% cal to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1—385-------are members of a Markush group, as the present sure illustrates that the members belong to a class of es characterized by various physical and functional attributes, which can include any of the following: a) the ability to convert a carbon source into a le fatty acid such as acetate, butyrate, pi'opioi'iate, or combinations thereof; b) the y to degrade a e or insoluble carbon source; c) the ability to impart an increase in weight gain to fowl administered the microbe(s); d) the ability to modulate the niicrobionie of the gastrointestinal tract of fowl administered the microbe; e) the ability to be formulated into a shelf—stable composition; f} the ability to exhibit a decrease in feed conversion ratio in fowl having been administered the microbe(s); g) the ability to impart a decrease in pathogenuassociated lesion formation in the gastrointestinal tract; h) the ability to impart a decrease in pathogenic microbes in the gastrointestinal tract; and/or i) possessing a MIC score of at least about 0.2 if a bacteria and possessing a MIC score of at least about 0.2 if a fungi. Thus, the members of the h group possess at least one property in common, which can be responsible for their function in the claimed relationship.

BUDAPEST TREATY ON THE TN'I‘ERNATTGNAL RECOGNITTGN OF THE DEPOSIT OF MTCROGRGANISMS 1701?; THE PURPGSE 0F PATENT I’RGCEDURES {0039} Some microorganisms described in this application were deposited with the United States Department of Agriculture (USDA) Agricultural ch Service (ARES) Culture Collection (NRRL®), located at 1815 N. University St, Peoria, IL 61604, USA. Some microorganisms described in this application were deposited, with the Bigelow National Center for Marine Algae and iota, located at 60 Bigelow Drive, East Boothbay, Maine 04544, USA. Some microorganisms described in this application were deposited with the American Type Culture Collection (ATCC), located at 10801 University Boulevard, Manassas, Virginia 20108, USA. {00401 The deposits were made under the terms of the Budapest Treaty on the International Recognition of the Deposit of rganisms for the Purposes of Patent Procedure. The NRRL® , A'l‘CC, and Bigelow National Center for Marine Algae and Microbiota accession numbers for the aforementioned Budapest Treaty deposits are provided in Table 3. The accession numbers and corresponding dates of t for the rganisms described in this application are tely provided in Table 45. {00411 The strains ated in the below table have been deposited, in the labs of Ascus Biosciences, Inc. since at least March 1, 2016. {00421 1n Table l, the closest ted hits for taxonomy of the microbes are listed in columns 2 and 5‘ Column 2 is the top taxonomic hit predicated by BLAST, and column 5 is the top taxonomic hit for genus + s predicted by BLAST. The strains designated in the below table have been deposited in the labs ofAscus Biosciences, Inc. since at least March 1, 2016. {0043} Table 1 lists strain designations of the bacteria and fungi of the present disclosure. If a letter in parentheses follows any of the strain designations, then that indicates that each of those strains have variants that share at least 97% sequence identity with the reference strain with the (A) parenthetical. Aiscusbbr_5796(A) has two variants, Ascusbbr_5’.796(B) and Ascusbbr_5796(C) that share 97.8% and 98.2% ce identity, respectively, with Ascusbbr'_5796(A). br_14690(A) has two variants, Ascusbbr_l4690(B) and Ascusbbr_14690(C) that share 97.8% and 982%: sequence identity, respectively, with br_l4690(A). Ascusbbr_38717(A) shares 98.6% sequence identity with Ascusbbr_387l7(B). Ascusbbr_33(1-\) shares 982% sequence tity with Ascusbbr_33(B).

Ascusbbr___409(B), Ascusbbr__409(C), Ascusbbr___409(D), share 98.2%, 97.3%, and 97.8% sequence identity, respectively, with Ascusbbr___409(B). Ascus___331885(B) and Ascus___331885(C) share 97.8% and 97.3% sequence identity, respectively, with s___331885(A). Ascusbbr___247(A) shares 97.8% sequence identity with Ascusbb1'___247(B).

Ascus’b’br___10593(A) shares 996% sequence identity with Ascusbbr___10593(B).

Ascusbbr___32731(A) shares 97.3% sequence identity with Ascusbbr__fl3273l(B).

Ascusb’bi___1436(A) shares 978% sequence identity with Ascus’b’br___1436(B). Ascusbbr___265(A) shares 996% sequence ty with Ascusbb1*___265(B).

Table I: Microbes of the present sure, ing ia ('1 —97) and fungi ).

Sequence Predicted t 14x4. s BLAST BLAST Taxnnomic BLAST identifier ‘ 1 .f , BLAST hwnemus. .‘ v -. Qucrg. 7 l’/0 , , , Tap Hit w/ Genus 0/'1) Strain Designatien fur of isolated Micmbes Top Hit Cover Idem. + Species Associated Marker acflius Lac/tobaciilus 4 100%/ ,Lacttobacii’us , Ascusobr 4729. , SFVQ,11) (Genus) , crispams crzspams_ 7 - N0,1 Lachnospiraceae giqgjfifll‘f‘f‘"‘ *' P1731135?1,1" 5:31)"":‘ ‘ Bacterium mugs" /' V , 91% '5, Ascusbbr_339 Clusfier} Lactobacflius Lac/tobaciilus Lacttobaciilus SFQ U) 100% ‘ ' Ascusbbr 5796A ‘ K ) Z ‘ (Genus) crispams crzspams_ , — NO:3, Lactobacflius Lac/tobaciilus 100% .

‘ 'Lacrtobaciilus SFQ U) , br 579613 : ms ‘ ) _ - (Genus) ms N036?) Lactobacflius Lactabatiiilus (lac/fanacmusr I "1 SEQ ID> 7 100% Ascusbbr 579610. _ (Genus) crispams crzspams_ s, ‘ - 30:3, /0 Lactobacflius Lactabatiiilus Lactabaciilus SFQ 1D 100% , 0.59229 (Genus) vaginaiis vaginaiis J N04 Lactobacflius Lactabatiiilus Lactabaciilus , , n \ SFQ 1D 100% 0.59229 (Genus) vaginaiis vaginaiis J ' NO'3'7’3 Lactobacflius Lactabatiiilus (lac/fanacmusr I > 7 , . "1 . 11.) , SF , " J 1/0211n _ _ 98% _ ,. Ascusbor. 0.58403 (Genus) mgmaizs vaqmaus - NONVQ‘ Lactobacflius Lactabatiiilus Lactabaciilus , SFQ 1D Ascusbbr 1(86 S rw ‘ . .. _ ._ J ._ J 0.57845 ) Ohmic/211 Ohnswm — N06v vascalzbawerzmrz1" I U ’ * ., ’:‘ , .

. F'aecaz’ibacfermm Faecalibacferium 5p. , . SF 1789 0 _. Ascusobr Q,"11.) _ (Genus) . 50099 ,razzsmz‘zzi — N0./ Lactabatiiilus Lactabaciilus . Lactobacflius , SFQ 1D Ascusbbr_3820 (Genus) 'Ohrzswzz‘i 'Ohrzswzz‘i NO:8 . Hydro ensanaerr) Bufyrivibrio SFQ 1].) Closh'idimn 5p. bacterium (Genus) Ascusbbr_173 I’zunggafei N09 COCCQCEHE ‘ ' [7112) ('cf'ermm 7 Closmdium Cluster Ciosfria'ium Sp 92% 100% . _ ‘ J 91% 98% br_3089 053548 4 7 name h XI (Family + . Acrocarpospom Aficmbispara Nanamzzraea 57), 99% ‘01‘_ 1 67 0 {Genus} . 54 42 FUSGQ 13' f-‘JC‘O‘J "J" ‘ r b/c:"1 v Lucio/b zciilus ‘. J Lactob zciilus J ‘7 , ‘ , \Crenus) halveficus 99% 98%4 ‘. 99%,\ 98% Ascusbnr 301508. . hehiencusV 0,53% ' LN7 Baciilus sublii 99% 100% Baciilus sublil 99% 100% Ascusbbr__33(A) 99% 1 00% Bar 7213 szibl'ilis Lactabacillus Lactabacillus coleoho ' ' ++++++++++++ coleohomiifl 'S .........................................................

Anaerofi.um Faecalmactermm 99%, , 100% . . . .........................................prammtzn.............................

Eubactermm (L’Zosfir'idium Sp. 95% 100% fissicatena Lactobacillus Lactobz [fins ' 99% 95% Ascusbbr_ coleoho coleohon" ...............................1........................

La ,tobacllms ,Lacttobaciilus I"€ZIZE.'"i 100% 100% 100% 100% bbrm409iiA) reuter.’ ......................................................

Lawobaulws Lactobaciilus I"€ZIZE.'"i 100% 100% E 00% 10:2 % Ascusbbr__409(L's." Lucio/b: Illus 100% 101 % br___409(C) reu teri 36. Lactr‘haflzllus‘ ’ "f a , Lucio/b: [fins . Lactobacz/Zus I"ellt&?l‘i 100O .. 100% . l{reams , reu ter: 100% 100% Ascusbbr__127 masenr’eroides -----4 Lacimospz’mceae 100% 10:101 Ascusbbr__l4834 bacterium acillus reuter! (; ‘mdza. bacterium 33. Laclznuo‘pz m: a ae 59112;? 34 [Jaclznuo‘pz m: .519 idmm Closindlum Cluster. . . Closlridium SEQ {D 1 0/ 0, ,. \ Mvarcnam": ’icum Wm 4 / . ’f/I!), L. ’. "L. , )E /o 100 /r) AspusbbrnA/(A)1 )EIVa (Family + ciostrz‘diqforme N025 ........................................................................ _______________________________l______________________________________________________________________ '35. . . .' zmum (,l-stmdlum Llus‘ter1 fl Closlridium 1 0/ 0, w SEQ {D "varcimm": ’icum XIVa (Family + ‘ ’ ' ’7)" " "’ike’ )E m 100/0 ‘lebr 24 (B) ciostrz'diqforme NO:38() Cluster) udoclaw‘ba er PS 2 ; Verrucosmpnra Sp.

Faecalibacteri m Faecaliba-cterium . 4mm"70/1114m (Genus) ansmizn i __________________________________i7." ________figmsnitzii Liamzflmm aensu C JdL'llllS Sm 'f (Genus) +++++++++++++ lifgigzgw 0 Ascusbln 351000 4-1. Lactobacfllus 1)9 /00,, 100 /00 , Nil} / L). . 0/ rIXSCqule} 43608). _ ‘ -. SEQ ID 11460. ,7 {Genus} NOZ31 I 6 100% 10:91) Ascx"‘bbr___1436(B-) $33? 046076 salivarz‘N{S . Lac/mos: raceae Clusmdium Cluster Roseburia 93 0 N"., Raseburia , SEQ {D bbrmzs @4602;. o o 100/0 Asa X1Va(Family + muzmmrans ummmmns M132 Clusle1‘) Ruminococcus 44f. Blautia (Genus) Ruminococeus 022mm 100% 10:2 % Ascusbbr__144 045742 obeum 45. acz'llus 0.43682 Ifacl‘abacilius acilz’us 'l‘ " _______________________________________E51?}?! ___________EE{§B£"" Q 48. Lactohaflzllus’ 2‘" .: . 94%, , ,1 acilz’us €1.30 11') Obdc‘l/ZZIS1"QZIZEl‘i 88%,, ' ‘ 0143348 16613115);I. T X , _ reuter:. NO ___________________________ Pseudomomm ‘ , {Joeudomond SEQ ID chengdue/zsi x‘ ‘ ' Syntraphomonad bacterium no ___9Pk?! ____________________________ 51. Lactabaczllus Ifacl‘auaczlzz Lactabactlm ‘ SEQ ID w, , 0" . _ 9,, 00,; 8 ' _ 'Genu" ‘‘ , _ , 041),,35 cmspvm x‘ crlsgpym V IN 0:40T 52. Lactabaczllus Lactobacillus Lactobacillus SEQ ID 98"", , 82%, , a, T 0140/ ’5 (C nus) salivarius salivarius , . Laclanaczllus "Gem" A Imus, ra‘ 31/121 . . mcerlae Sédzs hydrogenafrophica Ascusbbr 0140128 55. L ctobacfllus obac 11,15 100% 100 ' Ascusbbr__252028 {Genus} vaginaii, . Peptostrepm coccaceae Ramboutsm Closiridlum Clustet 100% 100 Ascusbbr___2158 039816 [ituseburensis XI (Family + Cluster) . Lactobacfllus 9690 96% Ascusbbr_3 ‘73 037614 {Genus} . Luclobaclfim 9890 98% Ascusbbr_1802 037123 {Genus} . Lactobacfllus 9690 96% Ascusbbr_107 037123 {Genus} ,1! . Luclobaclfim LQCfObL‘lCl-ZZLIS 9390 93% AscusbbL172?" 036309 {Genus} crigmtzh ' crispatzi, ' . acierium Coryl'zebacterimn Coryl'zebacterimn 100% 100% b1‘_226 0758977 {Genus} gluiamicum ,g/ummicum . Strepmcocczts‘ Strepmcoccus Streptococcus 97% 97% Ascusbbl; 1 7' 062924 {Genus} hyovagmaii‘s hyovagmaiis . Luclobaclfim Lalstobacillzyls acilius mliarius 9990 99% obr_ 1469091) 060061 {Genus} us . Luclobaclfim Lalstobacillzyls Lactobacilius mliarius 9990 99% Asc*us’bbr_l4690(B) 060061 {Genus} aviarius Luclobaclfim ,Lacrtobaciilus Lactobacilius mliarius 9990 99% ’bbr_l4690(C} 060061 {Genus} aviarius . ijvnebacierium Coryl'zebacterimn Coryl'zebacterimn 100% 100% Ascusbbgl 8 058366 {Genus} xerosz's xerosz's . Peploslreplo coccaceae Ramboutsia R ,mboutsia (Clostridium Cluster 9890 AscusbbL7363 057242 Zitusebzzrensis [fluxebzzremis XI) (Family + Cluster} . ijvnebacierium Caijynebactwium Corymrbacterium SEQ ID 0.49929 ) nii alse‘nii NO:343 0;:Vnebacierz'z m Coryl'zebact Caryn ,a e; 'Hn 97% Ascusbbr___7779 (Genus) ammoma 461%35 a 4mes . Lachnfispiracezie (Clostridium r Closmdium L‘resuljnmmaculum Sp, . 100% Ascusl)br___1t}593(A) XlVa) (Family + , , Spl’ZQfiOIaES Cluster) . Lachnfispiracezie (Clostridium Cluster Closmdium L‘resuljnmmaculum Sp, 96% l (N)/o XlVa) (Family + , . 100% , Ascusbbr__lt}593(B) Spl’ZQfiOIaES Cluster) . Lac/mospimcea Ezyibacrermm incertae sedis 98% 100% Ascusbbr__3273 } (A) A bLtbaclerz‘zmz . ’t)8/00' , SEQ ID Wl P"/,0 ASCW’h 73 1(8)_ ‘ - / V l)4 fissicatel'za 7 E24 ' M1382 ________________________________ .l Rummococcaceae (Clostridium Cluster "4 ' -,:,I\f.'J; , S‘ 89% 78% "TWO""W'" 79% Ascusbbr 359892 F9 "3 0.3935;- a III) (Family, triermoce’71m: IVO,34/ (ClOSlIlCll‘uEEl Cluster Lacknospiraceae a) y, baitermm VO:3~O ______________________________________________________________________+ SEQID g . v, 7,, NC): 35} ‘ Lactobacillus :1)"/ ‘ ' . l _ L)_ .i 7 TM, E I 7/ whelvencus‘ _ ____________________________________ ffii:3:?331____‘f§}:f:___________:~:O:_i§§______l_?;_i__f§____ lard/0'3, . . ,V nLd i 99% M 2 F SEQ ID to" 2') '~ - : 3 (1/6alinhilus _____ff:TE________::_‘;:__'i_‘f___________:~_:9:_5__2_______iiiifffg I ‘1 i 01."! i/fiicum SEQ ID ccus Si), 1 00% aerobacferi‘zmz Ascusbbr__36257 NO:353 SGCCII’ZGFOVUFGI'ZS SEQ ID ‘Iamm (Genus) Biaufia glucerasea 100% Biaufia glucerasea Ascusbbr_6957 N01354 . Corynebactermm Cmfmebacferium Cmmebacierium SEQ [D 100% Ascusbb r___3 8 0.35488 (Genus) ‘iavescms WESC‘BK'S NO:355 . Zachnospiracea Ezytbacferiaceag mcerme sedls 92% {W"Of/I’UL/OCCI/[S4. ,1 .y. /ti;.‘ 99% 0.3477 baitermm . Corynebactermm 1 00% 100% (Genus) . Corynebactermm Calynebaclerium 1 00% 100% (Genus) Sfatmnis ' .Rummocaccus 96% Blauiia la 96% Lactobacz . Lactobachus 1 00% intestinahs inahs Bacferiu‘m A L 99% . Lachnospiraceae (Clostridium Cluster Eubaclerium SEQ ID C!05tfidium Sp, XEVa) (inmfly + vgnh'iosum NO:362 C ‘ . I chnospiraceae (Clostridium Cluster Clastridiaies Clasfrid!um SEQ ID X1Vb"; (Family + bacterium [acidfI'JIIB/i‘IVZEI’il‘GI’iS NO:363 Cluster) mm sensu SEQ ID 1 00% sine/o (Genus) NO‘ 1 Bacteroia'es dare! 100% 100% 100% Bacteroides dorei Lactobaciilus . Lactobacfllus Ascusbb (".21 E69 (Genus) Lactobaci/lus reuteri 100% reuteri 95% 100% NO:366 '"""""""""""""""""""""""""""""""""""""""""""""""""""""""T """"""""""""""""""""""""""""""""""""""""""""""§EQ":"""" LatTObGCI"us 0?"1,8 98 PUWE 0‘0 ________________________________11-.(I.Eieéar-flEy§_:§y_t§fl____E_____9_§_°_/_é____ aciiius E Lactobaciilus i SEQ 1]) E E ‘ V E - - . . i I5c501151)‘ F bi‘ 830 saerimnen E 100% saenmnen a 100% 100% N036?) E E Fusarjum E E E i 15 . , , AS"usfbrL" E 0.42(22y Fusarmm annuiatum 100% annulatum E 100% 100% E Cryptococcus Ascusi‘m- __131 23 042622 Un‘EUitUEEd fungus E____1_9_9_°c’?____ 105 ______________(3199.05%____________1.399%_____.1.99°43" i ' E__________________ Gibbercflazme Fusarl'um 0 36913 (cams + 993C335" FEE-WW"? 05 " E11993:_____l99%_____________{7.SEEK?__________LEE-9.92"?___________________ ____________ 101. ra Uncuitured SEQ ID I’kscx""br‘ "616 {Genus} Gymnoascus 83% Gymneascus reesii‘ i 83% 81% .__- N054 102‘ Hypocreaccae E chum E . E : 12 . .. E , AscusEbr E (Family) Geamcnum 3,0. 100% 10 % sand/dam 100% 100% E 103‘ chhz'a E E fprme‘ntzms (Genus E Ascusflir __53 ‘05, E ' ______Ei€tzi9_f;€:m€{3£9££_____E____1_99_°c/?____10__Ei€éfflf;€fiil€fifi€ifl£__E____199‘f/_é_____.1.9.0.1.____________________________________________________________:3_______E__________________ 1040 Candida E E E E railenensz's (Genus + Candida Ascusibr ___1379 35351? 0,285}? 115) _____£9525!£€49_{EILEEEESQEELE railenensifi ..914.______-_1_997... _____'____________E__________________ 105. vaocrcaccac E chum i , , SEQ 1D E . U i Amusfm 122 .

. E Uncuitured fungus ,_ . b" ("111110") ROM;E -. E 0. 68011‘ L E 100% 100% cana/dum E 100% 100% — E 30045} m some embodiments, the isolated microbial strains of the present disclosure further encumpass mutants therecf. in some embodiments, the present disclosure further contcmpiates microbial s having all of the. idéntifying characteristics of the presentiy disclosed microbial strains.

Table 2: Microbial Deposits Corresponding to the Microbes of Table l quenee : Identifier Predicted Taxa Identifier i ted Taxza of Strain = = i for Deposit #. of Isolated‘ Strum Designation, . . for‘ Deposnt #_ i Isolated Microbes‘ Designation. 5 5 Associate g Microbes Associated g d Marker Marker PATENT201703004 Papifiostrepm PTA-424039 : : macaw/:2 Lacfabacu’lus Ascusbbr_47 SEQ ID Clostridium SEQ ID i Ascusbbr_2158 , _ r XE7 N0467 g (Genus) 29 N01} {Famiiy (ifiuster) ......................................................................................... ...............................................................................................................................................................................

Lacimospz’mcea e Clostiidiutii P'E‘An124039 Ascusbbrm?) 3 SEQ ED : Latitobacilius KEQ u) Cluster XiVa Ascusi)br___373 9 N02 (Genus) N047 (Féamliy.

Cluster) PATEN'E‘ZG E 70300} PATENTZO1703003, Lacmbauillus Ascusbbl‘___57 SEQ [D g Lactobacillus SEQ ID br_1802 (Genus) 90(A), g PATENT201703004, NOB (Genus), _ g N048 i B ~672(37' ""M'EEEEO'EQEHZ'I'zE"""""IKEEEéEEIBE"""éEQE)""" EEKIEEEE""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""" (Genus) 06(3) No:369 Lacmbafiill’us SCqubl‘___57 SEQ ID PATENTZOWOSOOZ (Genus) 96(C) N0:370 PATENT201703002, PATENTZONO PATENT201703003, 3002, Lactobacillzyls Ascusbbr_38 SEQ ID i Laciobacilius SEQ ID i i PATENT201703004, Ascusbbl‘_107, (Camus) 71'7(A) N014 i (Genus) N049 8—67268 Lacmbaiillus Ascusbbl‘_38 SEQ ID PATENT201703001 (Genus) 71703) 'No:3'73 Lactobaciilus Ascusbbr__17 SEQ ED PATENT20170300'2 Lactobacflius SEQ 1D i Ascusbbr_l727 (Gsnus) 0211 N015 (Genus) NOISO . . 4016> PATENTZE} 3 7:1) PTA-124039, 3003 PATENT201703001, Lactobaciiius AscusbbLlé SEQ ED I’A'E‘EN'1‘201'7’03002, ijmebacte SEQ H) i Ascusbbr_226 s) 86 NO:6 201703003, _ rimn (Genus) NOI338 PATENT201703004, 13—67270 litre/calibacferiu Ascusbbrflj7 SEQ ID PTA-{24016> Strepmcnccu brfli 7 SEQ ID PATENTZMWI} iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii m (Genus) N533753002 PA‘I’EN'I‘ZO l 703 ()0 } PA‘I’EN’I‘ZO 170 3003, PATEN’E‘ZE} 1 7:1) P'E‘An124039, PTA—124039, PATENT201703002 PATENTZOIT/O 3001, PA‘I’EN’I‘ZO 170 Lactobacil/us Aseusbb (".3 8 SEQ ID LacmbczCi/ius SEQ ID 3002, Ascusbbr___l 469nm) (Genus) N08 (Gems) N0134i} E‘ZE} 1 7:1) 3003, PATENTZO 170 3004.

Laciobaci lius PTA-124016, Ascusbbr_l4690(]3) (Genus) Lactabacillus SEQ ID PATENszm Ascusbbr»__l4690(C) (Genus) N02372 E3004 Hydrogenoumae‘ Ascusbbrm 1 7 SEQ ED PTA—124016, Cnljwebacte SEQ ED ZOUU Ascu.sbbr__18 r0 ium PTAul24039 rium ) _______________________L___________________________________________ ____________________________________ fx) L15 """"""E55%}"""""""""""""""""""""""""""""""""""":r"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""":r""""""""""""""""" Peptasl’repta PTA-124016 Peptosuepto PTA-124036 coccaceae caccaceae Clostridium br_30 SEQ ID (Clostridium SEQ ID i AscusbberGS Cluster X1 89 N0110 g Cluster XI) N034 2 y (Family + Ciuster) Cluster) . -----------------------------------------------------------------------+-----------------------i-------------------------------------------------------------------------------+------------------------------------------------------------------+—---------------------------- i 5 PATENT20170 3002, a PATENTZE} 3 7:1) .r4c:r‘ocar]_7asp0ra br___} 6 SEQ [D g Cozfimebacr’e SEQ ID ; g Ascusbbr__35 g 3003, (Genus) 7 NO: 11 g rium (Genus) NO:343 g i g PATENTZO 170 3004.

PATENT20170 3002‘ PATENTZE} 1 7:3 . i Lactobacil/us brfififl SEQ [D Carynebacl‘e. g SEQ H)_ g g .AXscxlsbtar__7779 g 3003, (Genus) 1568 N012 g rium (Genus) N0:344 g i g PATENszm E3004 Bacillus Ascusbbr__33 SEQ ED PATENT20170300'2, Lachnospirac A5cusbbr__10593(A) SEQ ED PTA—1,2403% """""E """"""""" """ 'E/Slfifiiéfi'éfifiéi" """"""""""""""""""""""""""""""""""""N53213""" 'fiéfifiifififim Salim) 1A1 I\6713' Lac 367266 (Clostl‘idium 3001‘ Chm: PATENTZE} 1 7:3 .XWa) 3:302, (Famjiy PATENTZO170 Cluster) 3003 PATENT201703001, Lachmspil‘ac PTAu124016, E : I (Clostridium _ _ , g us Ascusbbrjié SEQ ID SEQ {D» i (Muster Ascusbbr___li}593(}3) i (Genus) (B) NO: 374 NO: 3 81 .XWa) (Famiiy Cluster) : .

PA’E‘ENTZONOEOOL 131151424016, PATENT20170300'2, ZOIT/O i i i ‘ Laclmaspira g Lactabacillzyls Ascusbbr_25 SEQ ID i PATENT201703003, SEQ ID i 3001, i i cea incerlae Ascusbbr_32731(A) i ,, _ , ,, _ , g (Genus) 200 N014 i PA‘IEN’I‘ZOE’iiBOiM NO:346 1 11120170 1 sedis (Genus)_ 1 i 4 ~11? ‘ Ascus‘obr_3273 1(8) 0:20 incerme N01382 Ix) \J _______________________r------------------------------------------- ____________________________________ ___________________________________________________________________r--'----'-------------------------- I sedis (Genus) I PTA-124039, Ruminacocca PTA-12403 9 PATENT2m703003 we Subdalid‘rmmlu SEQ ID (Clostridium SEQ ID Ascusbbr_84 Ascusbbr_359892. g m (Genus) N0115 Cluster 1H) N013 17 g (Family + Cluster) ___________________________________________________________________l.I.

Suhdaligranulu TA~ E24016 Laclobacz'lius br_257’2 E m (Ge nus) {Ge (in s) N01348 PATENT201703004 PTA-124039, I’A'l‘EN'l‘201‘7’0 300 E, Lacrhnaspimcea PATENTzom e Clostridjum br__12 SEQ ED ISlfrepl'ocroccu SEQ lD 3002., Cluster XlVa Ascusbbr__72076 8 N011? 5 (Genus) N01349 PATENT20170 (Family + Cluster) PATENTZE} 1 7:1) ’A'l‘EN'l‘ZO 1 703 00 l . Laclmfispirac PTA—mam, Lac:t0baciilus SEQ ED €216 Ascusbbgfléfifi PTAn124039, (Genus) N018 (Clo stn' dium ZOIT/O I I _______________________L___________________________________________ ______________________________ ___________________________________________________________________L__________________________________ : r r Cluster 3002., xwa) PA‘I’ENTZOE’ZO {Famiiy 3003, Cluster) PATEN'E‘ZEHW P'E‘An124039, PATENT20170 PATENT20170300'2, 300L Lactobacillzyls Ascusbbr_40 SEQ ID i Laciobacilius SEQ ID i : PATENT201703003, Ascusbbr_265 (A) : PATENT20170 ) 9(A) NO: 19 i (Genus) NO} 5 1 i i 3002 Lacrabacz'zlus Ascusbbr_40 SEQ ID PATENT201’703004 PATENT20170 (Genus) 9(3) 'N0:3'75 3004.

Lactobaciilus Ascusbbr__40 SEQ ED PATENT201703001 (Genus) 9(6) N013’7r3 PATEN’E‘ZG 1 7:33am PATEN’E‘ZE} 1 7:1) 3001, g PATENT20170 LactobaciiL’m_ bl‘_4U» SEQ ID _ i Lactobacillus SEQ ID i i Ascusbbrfiéfi (B) i 3002, 7 (Genus) 9(D) N037? g (Genus) N01385 g a g PA'E‘EN'I‘201‘70 """""""""""" B6"263 ATENT2017O Leuw/zostoc Ascusbbrj 2 SEQ ID Paraceccus SEQ ID .

(Genus) N012fi (Genus) N01352 PTA-124016, PTA-124039 PTA-124039, Lacimospz’mcea Puscusbbrmldr SEQ ED PATENTZOUOEOOI, Ceiiuz'osilynt: incertae sedis Ascusbbrfi6 834 NO:2E PATENT201703002, um (Genus)- PATENT201703003 PTA- £24032 PTA- £24032 PATENTZMWBOOZ, ATENszm Lacmbaiillus Ascusbbr_ 3 PATENT2017030035 Blazyttz'a br_69 5’7 (Ga 11115) {885(A) 13—67269 (Genus) N'F201‘7’0 ........................................................................>-____________________________________________________________________________________________________.<_______________________________________________________________+ Lactoiiacillus Ascusbbr_3 3 SEQ ID PA‘I’EN’I‘ZO l 703 Oi) } (Genus) 188.5(8) N02378 Lacmbalsillus SEQ ID PATENT201703004 (Ga 11115) 1885(C) 'N0:3'79 PTAJ24039, PATENT20170 Anaerofilum SEQ ED Corynebacte SEQ 1D br_3 1 PATENT201703002 Ascusbbr 38 53003 (Gsnus) N0123 rium (Genus) NOz355 """"""""""""""""""""""""""""""""""" $f§3§163§mm i PTA-12403 9 Lacknaspiracea i Lacimospiru Ascusbbr_2 3 SEQ ID SEQ ID N’I‘ZOH’ZO incerlae sedis ‘ cea incerlae Ascusbbr_13398 07 NO :24 N013 56 3003 (Genus) ‘S‘C’ditr (Genus) ' Lac/mospzracea PTA—124039, I’A'E‘EN'1‘201‘7’0 e Clostfidjum PA’E‘ENT201703004 3003 Ascx:sbtar__24 SEQ ED g Cnljwebacte (IfiusterXWa ba 57 7(A) N025 rium (Genus) N01357 (Féamlly.

Cluster) spiracea PTA-{24016 e Clostn'dium Ascusbbr_24 SEQ [D r XIVa 7(B) N02380, (Family + Ciuster) PATENT201703001, PTA-124039, 367264 PA‘I’EN’I‘ZO 170 3:301, Microbacieri‘um SEQ ID Cozfimebacr’e PATENTZE} E 7i) Ascusbbr___} 9 Ascusbb£285 160 ' (Genus) N0 :26 rium (Genus) 3002, PATENT20170 3003, PA’E‘ENTZONO """""""""""""""""""""""""""""""""""""""""""""""""""" 3064"""""""""""" Veri‘ucosispora SEQ ID Ruminacoccu SEQ ID i Ascusbbr_69 Ascusbbr_37385 (Genus) NOIZ7 , _ - _ S (Genus) N023}? . .

PA’E‘ENT201703001, PA’E‘ENTZO 1 70 g Anaerofi/um SEQ ED i Lactabacilius SEQ 1D i g Ascusbbr__§)4 i PATENT201703004 Ascusbbr__118124 i 3001 g (Genus) NOIZS i (Genus) NOz360 i (limiridzum PATEN'E‘Zi} 1 703003, PATEN'E‘20170 i Ascusbbrfil SEQ [D g ria SEQ ID i i sensz: stricr’r) g PATENT201703004 Ascu.sbbr__3 2,592, g 3002 i 3454 N029 i (Genus) N01361 ' (Genus) -sgnrac PA'E’ENTZO 1 70 eae 3004 n'dium _ , i Lactabacillus Ascusbbr_35 SEQ ID SEQ ID i Ciuster Ascusbbr_110856 W ,, i (Genus) 1000 N030 1402362 1 Xl‘v’a‘) (Famiiy Cluster) 1 13115115210535:""""""""""""""f.36111103 MAE-52101535:"""" PA’E‘ENT201703001, eat: PA’E‘ENTZO 1 70 Lactobacih’us Ascusbbr_14 SEQ ED i SEQ 1D i i PATENT201703002, (C105mduma_ _ Ascusbbr__185064 i 3 001, (Genus) 36(A) N031 i NOE-63 i PATENT201703003, Cluster 20170 PA‘IENTZO1703004 XlV‘o) 3002 """"""""""""""""""""""""""""""""""""""""""""""""""'r (131th Ciuster) Lacmbalsillus Asc1‘:sbb1‘___} 4 SEQ ID 4016 (Genus) 36(8) N02383 ,Lachnaspimcea PTA—1 24016, e Clostridium PTAul24039? Gastric/tum SEQ ID i SEQ ID Cluster XIVa Ascusbbr_28 i PATENT201703002 1 Szrzcto Ascusbbr _3 3 15 NO_ I 3 2. 5 NOI 3 64 (Family + (Genus) Clusier) PTA-124039, PTA-124039 br_14 Bacteraides Biaulm (Genus) PA'1‘EN'1‘201'7’03002 Ascusbbr_5’78 4 dorei PTA-124039, PATENTZO 170 i 20 l 703002 . 3001 Lactaiiacillus Aseusbbrjz SEQ ID i Laclobac‘z’ lius SEQ ID _ i PATEN'I‘20 l 703 003 . Ascusb‘orj E 169 (Genus) 760(A) N034 ‘ (Geuus) N01366 PATENT20 E 703004 L______________________________________________________________________ Lacitobaciilus 1X59115bt3r__42 SEQ ED : PATENT201703001 (Ge nus) 760(B) N0384 ________________________________________________________________________ ________________.%___________________________________________ ___________________________________ A‘I'EN'I‘ZO l 70 Lactaiiacillus Ascusbbrj 3 SEQ ID Laclabacilius SEQ ID g 3004 (Genus) 4994 N095 (Geuus) N01367 """"'EEL?5535&E}?22}E"""""IKEEEéEEEES""""éEQiE""" """"""""""""""""""""""""""""""EéEEHEiEEéiE""' """r"""""""""""""""""""" SEQID i Ascustbglfi (Genus) 7 8773 N036,, (Fanniy)_ ‘ N015}7 PATENTZOUOSOM Filobasidmm Pseudamanas Ascusbbl‘_25 SEQ ID flariforme SEQ ID i Ascusfbr _13 1 (Ge nus) ()3 N013?" g (Genus + NO: 52 : species) i PATENT201703002 Gibberella Spombacter Ascusbbr_3 1 i zeae (Genus Aseusfhr _26 (Genus) 2 . spectes) Lacmbaiillus Ascusbbl‘_l4 SEQ ID Alaiospora SEQ [D g Ascusfln _2616 (Genus) 09 E4 N0140 g (Genus) N054 Lactobacillm Ascusbbr__25 SEQ ED Hypocreacea SEQ 1D i Ascusfbr _12 (Genus) 762.7 N0141_ _ e (Fanuly) N055 Pichia Lacr’abaci‘llus Ascusbbr___3l SEQ ID zez'zI/‘az'zs SEQ ID i Ascusfbr 5__3 (Genus) 0088 N0242 g (Genus + N056 PTAu124016, i Candida Lachnaspiracga i PTA-124039, SEQ ID i milmenszs SEQ ID A , incerlae sedis Ascusbbr_9l_ i PA‘IENT20 l 703002._ bl‘ E 379 N043,, i (Genus + _ N02577 ) _ PA‘I’ENT201703003_ _7 i s) .. ___________________________________ Lactobacillus Ascusbbr_15 SEQ ID Hypocreacea SEQ ID : n _122 (Genus) ,, ()lfii) N044 C (Family) N0158 Lacmbalsillus Ascusbbl‘___25 SEQ ID Lactabacillus SEQ ID PTA-124039 Ascusbbr_830 i (Genus) 2028 N0245 (Genus) N01368 Table 3: Bacteria of the present diseiusure.

Sequence Sequence Predicted t Taxa 0f Igeflated Identifier fer Predicted Closest 5 of Edeutifier for Strain Designatiqm gtrain Designation Micmbes Associated ‘ Isolated Micmhes Assuciated Marker Marker SEQ ID Am; .r 2.. - Clostridium XIVb (Cluster) Asmwbrfi """’t_’_‘_i:_2_3__f_________________r_~;_<_2_:_3__9__9:V ________ SEQ ID Lacmbaciz’ius (Genus) Ascusbbrfij, l6 Ascusbbrw’ L 9 N061 Beijermckia ( kilns) N020: SEQ u) ,A , SEQ ID ASCUsbbrfiizx.’, -. 2.3.

Clustridium Xi (Cluster) Hosea (Genus) Aseusbbn N020). 7,, q SEQID Asvusbmfi265.

SEQ ID ASWBerJ‘J.

N063 Sporabacter (Genus) NO:2')3 , n SEQID SEQlD Aswusborj{P m , 5 Ascmbbrjhl" Facklamia ) N0204 br77343 ‘ Ascusbbr772266 3 Av‘membacter (Genus) Lactobacilius (Genus) AscusbbrfiSt'SS Brevundz’monas ) Ascusbbr772284 NO:206 SEQ ID Ascusb'nr 7’99 4 Ascus’b’br "1285 .Jeoigalicnccus ((Jenus).. -. ‘ L "3 Oc/zrobaclrum 115). a "1 N010?" . l orfim . » SEQ LD ‘1‘ e . ASL qubtnfl"..... K _ ' Aanli 491765 (Genus) NO;2-’JS Pseudachmbacflmm Ascusbbr 498 ASWI’LLJI77, SEQ ID ‘ ‘ ‘ 1 1 <~ " N069 (Genus) N0209 . .jeoiga/icaccr‘s (Genus) SEQ ID br 542MIE Agnew-17229;‘‘‘‘‘‘‘ n SEQ ID ..LaCf0[7aCIZ!li.§ (GenuS)7 < , \ , NO:7{ NO;210 SEQ ID """"§EQ"I"D""""" 117229,,.I e 2 _ __________________________________E_(_2_i2__1__1_________+ SEQ ID SEQ ID A Seixubbr":a c '. 'W/ J AscusbbrmZZw . Laciabacilius (Genus) N072 acinetahacter (Genus) NOZJ 2 E SphmgabaCtelmm SEQ 1]) As usbor 610, SEQ7)ID Ascnsbbr -2H p : " 9S E (Genus) NO:213 SEQ ID NO:214 ...................................................1 SEQ ID Ascusbbrfi' Lacmbau/lus (Genm) Ascusbbrw 23 E3 ‘. Jeolgaliwecus (Getius) E1023 6 ASVUsbbr"(1 » '7 SEQ-ID SEQ ID 1 93 br 2.320 E 9.(11’1COWWCB? (GenusE NO-,. (Jm’ibacter (Genus)- NO: 2 j, '7 Clostridimn XIVa SEQ LD , \ br 795 was (Genus) " E (Clusier) Ascusbbr_2324 NO:213 ; " 1 Clostridimn XIVa SEQ LD 1. Sacc'Earn 0113mm (Genus).. _ Ascusbbr 796 " :2) E (Clusier) Ascusbbr_2325 NO;219 SEQ ID SEQ ID oj. .

,.. BIevibartemum ) NOS-LE E Lacmbacillus (Genus) br_2328 N0220- C . Clostridium XIVa SEQ ID . N081 4 "1115160 Ascusbbr_2331 N022} . {Micr.bacterium ) . SEQ ID {F I, 2180‘"be "3312 SEQ 1D A5usbor 840 " .j 24. Acinefobacfer (Genus) NO:82 E Bacillus (Genus) NO:222 SEQ ID Ascusbbr 846 Ascusbbr ‘23 J Ascusbbr7786’7 AscusbbrfilEéE . Cloacéz‘bacterium (Genus) Mailmcmrium (Genus) NO:‘224 SEQ H) AscusbbrfiZ‘) 27, M" cubacterium (Getius) FAIRS Breach 'bacierium (Genus)- Ascus’b’brfiZSGS E23923: ASCllebrfiM 28. acr’er (Genus) Eli—23323161) chqub1‘ 37) Fackiamza (Genus) £13233} AscusbbrfiEPSO 29. Lactobacillus (Genus) 311%)? (CGOSEEEJEmm XIVEI Ascusbbr7772378 £13321}? AscqubI"951 . Raf/2m (Genus) Eggs) féoggeium XEVa Ascqubr**'2380 £13321; _§__1_;_£9§}?£Q:i3£€___]___§JEEEEEE____________________1"MW________Eggs?.3:_______E.522K222522923516192195221252__________éffEEEEEi____3_§i_______ $20212!) ________ .32- Ciaviba€£22;£§£§}1§l_______________________i_____f.ifffff:f§__5______________EC(>2);________Bewd’wCemS‘ __________________A:ffflffffi_______________$0233________. is] gcC 3ND ________i_____;':::‘:?f:*i_:;lfiii_____________ ________Lam)________________iiififriffifiiz‘fffl_______________ ________. _if!_-fiQEZEQIiEEQiQEEE-AQ_______________________j._____fEififPET:_j§§_____________if((3292;_________lanai/MGM") Aswbbrflm TEFOQZB ________ . (l'ia.~:zridium (Genus) bbTJ'Ow bNfigf); Lacmbacillus (Genus) br___2395 1:02:13 Ascus’bbrfillzg 36. $83? T;::;:l)(irld’ldu Ascus’bbl'771363 Ascus’b'br772421 , Clostridium XlVa (Cluster) :VloQi'g a??? ASCHSbbr’JMZ 46. ClostridiumXIVa (Cluster) 12333133 Ruminobacmr (Gena) Ascusbbi‘fi24-23 Egg?! Aswgbbrimm ASCHSMHJMH’ __4___7__._£195gigggggyig‘gggtgg_______________j, iffh?‘ Giveamyces (Gangs)- 1:292: 48 idium XIVb er) i Aswsbbr71433 1331;)? Ascusbbg2428 Psychrabacrer (Gsnus) TEES: .............................................................................................................................................................................................4 Bug/mm ".rzielia (Genus) I (H ID A SGHSbbrWMXS .

‘. Smmbacter (Genus) 130308 CInstridium IV (Cluster) Ascusbbrm2431 No;24g SEQ 3’ SEQ ID .Bmyrzczwecus ((Jetius)‘ _ _ , - - \ Ascusbbr _ _ ‘ ‘ NO:109 E (,Zosmdzmn (Genus) ASCUSbb!‘___2434 NO:24-9 .. Hydrogem'nanaerobdeterium Ascuebbr SEQ ID Clostridium XIVa SEQ ID (Genus) ‘ " N01 IO E (Cluster) Ascusbbr___2435 NO:250 SEQ ID / \ -. Ascusbbr .Anaerafilum s) .

NO:111 . . ‘ I SEQ ID " E Llosfl-zdzmn (Genus) Ascusbbrw2436. N023}, SEQ ‘D . . , , ‘ br ClostridIum XIVa SVEQ LD ’* N01 12 NO:2.‘>2 . Chasmdmm XIVa ICIusEer) E (\CIusEer) Ascusbbr_2437 Closuidium XIVa (CIuster) AscqubL $301112 coma)!" (Genus) 12133213 SEQ ID SEQ ED Ascusbbr ’- Lélcmspiracea (Emily) " N01" Chymn252195293_<_§§9_9§)______ m44l N654 ________ SE( 1]) Streptophyta {Unranked SEQED " NO:115 , , m(:-spiracaa(Family)- E Clade) br__2445 NO:255 $1:Q ID SEQ ED Ascusbbr " NO:}16 N02256 . Butwicz‘mccus (Genus) E Acinetobacrer {Genus} AscusbberASZ E SEQ ED Ascusbbr (Genus) " Cmrwumxwhssbbmm N657 ________E SEQ 1D SEQ ED Ascusbbr anaembacierium (Genus) " M1118 E . 'eisseria Ascusbbr__2465 NO:258 . SEQ ED . Hydmgenaanaerobacierium Ascusbbr SEQ ID : (Genus) " NOJU‘ E Butyriciwccus Ascusbbrw247l N02259 SEQ ID SEQ ED Ascusbbr Buyrcachcms>______________ " N012" Smobme‘rhswbbrm"? NCUC ________E ShQ ID SEQ ED 63. Lachms )iracea iv) A5cusbbr___ NO:121 E Sporobacz‘er Ascusbbr__2476 NO:261 SEQ ID SEQ ED 64. Equpelutrjchacsae (Family)- Ascusbbr__1634 NOJ22 Syntrophomonas Ascusbbrw2477 N02262 SEQ E D EEEEBQEEEEEEEESEEE 023 ___________________________________________________________________Eifiiiééfmgflg______________T)! ________ SEQ i D 66. Ascusbbr___2482 N02264 SEQ ID SEQ ED NO:125 N01265 E SEQ ED NOIJZG T102266 . SEQ ID : SEQ ED '. Bulyriciwecus (Getius) Ascusbbr___16'74 NOLIZ7 Erysipelofrichaceae Ascusbbr___2493 N02267 ; SEQ ID SEQ ED NO:128 . Bu 'ricricoccus (Genus) br 1678 Jeatgaiicaccus Ascus;bbr‘_2496 NO:268 £§E§E§9§£§T3 i Q * a delia (Genu) Ascusbbr___1684 NO;130 i Howardelia Ascusbbr___2498 N02270 ; SEQ ID SEQ ED . 1..achms Hausa (Fami‘i 7)- Ascusbbrwl685 NO:131 idium Xfl/a Ascusbbr_2500 NO:271 SEQ 1D SEQ ED N013?- ' ASCUSbbLZSOl NO:272 , SEQ ID SEQ ED Bmyricicaccus (Genus) Ascusbbr___1695 NO;133 Laclmospiracea Ascusbbr___2504 N02273 . {jvdragénoanagrabacterizyim SEQ ID SEQ ED (Gangs)- i Ascusbbrwfll NO:134 Ciostridium Xfl/a AscusbbrMZSOE NO:274 : SEQ 1D SEQ ED wror’asmuGe'wAswst_17201\0"‘_______iffiflflfl-‘ifl’ifififiéfl___________________________AEEEEEEQEEQE______________E!9.1.2.15.________ i SEQ ID SEQ ED i. Closiridium XIVa (Cluster) Ascusbbr___1722 NO;136 Bacilius Ascusbbr___2509 N02276 ‘ SEQ ID SEQ ED 79, .Jemfigal’icnccus (Genus) i Ascusbbrwl723 NO:137 Paenibacillus AscusbbrMZSlO NO:277 """"""""""""""""""""""""""""""""""""""""" .];ng SEQED A5w5bbt1743 "E0333 N0278 _______~_.553;’11.?ZQEEEQKYIEZ/EEEEEQ‘EEEBSE______________E ______A§_£ii§§_ér:%§_ll______ _- SEQED NO;139 N02279 . CEOSil‘idEum IV (Cluster) Ascusbbr___l746 Ascusbbr___2512 SEQ ED SEQEL‘: Lachnos jracsa {Fami‘i 7)- As;c:usbbr_l748 N0140- Staphylocaccus Ascus;bbr‘_2513 NO:280 : SEQ ED . Hydrogenaanaembaclerium "10281 _____________________________________________________________________A?.£E§PEL§§_1€______ SE; D SEQED NON-2 N02282 . Osciflibactazr (Genus) br___l756 E Ciostridjum IV br___2515 SEQ ED I SEQEL‘: AscusbbLfiSS M1143 Prevotei/u . Clostridium EV er) Ascus;bbr‘_2516 NO:283 JEQEDC Ascusbbr 181?. ______‘_it" A'sous'bbL[8‘1‘ No.14:V _ 87. Pediocaccus (Genus) E ClostridjumXiVa Ascusbbr___2519 No:285 , SEQED , SEQ ID I f M1’8," : E Ebbr'"E824 M11496Y 4 _ _ NO:286E . Sparabacter (Genus) g Ciosmdlum Xfl/a brflZSZO , , SEQ ED SEQ ED Aw . , _bb'I" m18 ( ,,NOW . . 'hngefig_________________________________________A:222E22;§§.?41______________[:1 0287 ________ SEQ ID SEQ ED A"bb1882scus V ‘. lomonas (Genus)w", _ I" E NOMS . a Laclmosplracea Ascusbbr___251_2 N02288.

SEQ ID I SEQED As: 5m.5w W’1887 : _ V Y i ‘ .b}wtr¢yMamanas(Genus)E , M11499 g Leucobacter Ascusbbrfl2523 NO:289 , ., SEQ ED ' SEQ ED AWW", 192.8 ,,NOE-‘0 _ "WC?"______A§_2_L:§E2_Ezr_:_2_§£fi______________E!9.1.2.29.________ SEQ ID SEQ ED A' ' bb scus I"1932 ‘ : ,. acier (Genus) NOLISI E Laclmospiracea Ascusbbr___2525 N02291 94. I’lva'rogenoanaerabactterium SEQ ID SEQ ED 1 ‘7 Ainst,wl W’1933 : .

(Genus)- M1152Y g Succmidasticum_ A A AscusbbrflZSZG NO:292 SEQED bl 1GI 3'7 A5cusbbr__2‘" NO: 2.93 ‘ SEQ ID .

. I;dr.)gemnanaelabacleriu‘m SEQED A:scqubri195" ‘ J E NO;154V (Genus) aAcmetobacter. Ascusbbr___2530. .. N02254.

SEQED " SEQ 1D f Ml’3, sbbr'"1955 : M3153Y , E Comamcmas Ascus;bbr_2531 NO:295 SEQ 1D SEQED AscusbbrfllQS‘é N0:156E._Prevoteiia A5cusbbr__25.13102296 SEQ ID SEQED 99.1335211dufiavwiifi‘aclnr(Geuus) Ascusbbr___1957 NOLIS7 Ciostridjum IV Ascusbbr___2534 N02297 SEQ 1D SEQED 100. ClostridiumXIVa (Cluster) As;c:u5bb.r_1967 NO:158 Ciosi'ridium Ascus;bbr‘_2535 NO:298 ‘bacrerz'um (Genus) i Ascusbbr 1969 102,"‘ "fact" "' um "muI" "i")1 \L CHM)‘ .‘ E Ascusbbr___19'73 NO 160 E Laclmospiracea Ascusbbrm538 N02300 SEQ 1D SEQED . . idium EV(C1usi,er) AscusbberOZO NO:161 crer brfl2539 NO:301 : , 51'; ID E SEQED bY 2023 104. C’m'abacrer (Genus) J\O(?162Closmumel! A5cusbbr__2‘"340 13102302 105. H y'droUenaanaerobacl‘erium i . bf: 111) E (Gemis) SEQ ED a Ascqubf'"203)7 . 3 EFiavobacterium Ascusbbr___2544 N02303 SEQ 1D SEQED ClostridiumXIVa(Cluster) i Ascusbbrw2047 NO:164 Eciostridium Ascusbbr_2545 NO:304 ‘ SEQ 11’) SEQED Ascusbbr_2049 N:O 165 " A5cusbbr_2547 NO:305 SEQID i SEQED Ascusbbr___2057 NURSES Arthrobacter Ascusbbr___2548 N02306 SEQ ID AscusbberOSQ NO:167 Flavobatterium Ascusbbrfl2549 N030? SEQ ID SEQ E D ____________________________________________________________________________________________________________________Wigflowv SEQ ID SEQ ED Ascusbbr___20'76 NO;169 N02309 SEQ ID SEQEL‘: A scusbbrwl 10 1 NO:170 OliviJacter ' . N0231G SEQED . SEQ 1D AscusbbyleR, NO: 1 ,7 i. ‘ _ T402311 ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ chusbbr 2127 5.130- ID SEQED ,Slnmngammms (Genus) , NO;172 E obacterjum. Ascusbbr___2555 N02312 : SEQ ID SEQEL‘: ClostridiumXIVa(Cluster) As;c:usbb.r_2131 NO:173 ESpiiingabactserium bbr‘_2556 NO:313 ClosiridiumXi‘v’b (Cmsicr) g Ascusbbr___2136 ‘ , §C105tridjumXil Ascusbbr___2560 ClostridiumXIVb (Cluster) Ascusbbrw2137 Ciostridium Xi! Ascusbbrfl2561 : SEQED Ascusbbrw2149 NOV/7'7 . A5c1;sbbr__2562 NOz3l7 ________________A_{wig/0i? 'z1:m(Genus) i A"bb 217/. , SEQ m i SEQED _ scus I" g. a . 120, Sula/w (Genus) g NOJ/S. . a i’edobacter Ascusbbr___2553 N02318 E SEQ ID SEQED i A:SW‘. 178 : P‘elrobacr’er (Genus) A.

E Mil/9Y 7 g Batillus Ascusbbrfl2564‘ NO:319 SLQ J):' 1 i Ascusbbrfizlsg : JEQ EDc .....e...........73:athcm............................................595.159....... Herod!" ......A§.2.L:§§£zr:..2.§§§..............E!9.1%39.........

SEQ-ID SEQED . a Ascusbbr 2183 Thermovibrio (Genus) i NOLISI E PrevoteI/a Ascusbbr___2566 N02321 7' 'Deélofrzchaceae SEQ ID SEQED Ascusbbrj 18:3 M1182 Lachnospiracea y) Ascusbbrfl2567 NO:322 SEQ 1D SEQED ""0183 E Lafifl‘flfliflffifififlfi‘iflfilfl 0?? ___________Aaaaazéérfiéfi______________E)! ________ A; bb 219" , A Escherichia/Shiae/laJ SEQ ED "Gus If .

, NOWV , E :26, (J-Zaciecma(Genus;.. - ‘ "Genus),. Ascusbbr___2594. - i SEQ ID E . SEQED f ’Xsmsbbr 2195L" E , i L’tl’obacz’lius(Genus), M1183Y , .1. ‘ i E Lacmbucmusflenuy bbr‘_2603 N02325 JEQ EDc i br 2200 .

T E . . . . 1‘0"" 0?? .....e...........E.’vcthGenuv .......EEQCZQEEQEEEEmainféfiayiz.........A§.2aa§§£r:.2§39§..............E)! ........

SEQID E SEQED i - . . A;sousbbI’2201 F a Yhermamicrabium (Genus) N018! _, . . Ascusbbr___2615, . . _ i a Lactobacu/us (Genus; N02327 SEQ ID : i f’XsmsbbrL" 29.04 .

Addams/term(Genus). , , V .1. ‘ i M1188 ELacmbucmuHGenuy bbr‘_2625 NO:328 E Escherichia/Shigella Ascusbbr 2205 Ascqubf"’2208 Rothia (Genus) NOSE?" Lactobacii/us (Genus) Ascusbbr___2644 N02330 A scusbbrWZRlO Seienommzas (Gangs)- 1:231: Lactobacillus (Genus) Ascusbbrfl2665 E5121: ClosmdlmXIVafCL-vtr)Aswbb17m.:10Q3?_______il-Gctobaciilus {GENE/5i Aswsber-584 Via: Ascqubf"’2216 Virgibacilius (Genus) Sigll‘g acii/us (Genus) Ascusbbr___2694 Digiié‘: Aswgbbr’zzlg Sphingamonas (Genus) 1:23;; Lactobacillus (Genus) Ascusbbrfl2699 E51212: 5th *9:' E E JEQ EDc Ascusbbrfizm E Cztwcoccumfienus)____________________________________________J\Oi9‘_______LLr'ctobacii/us } Ascusbbr_2709 N02335 SEQ ID SEQ ED Cal'enibmlerium (Genus). _ i Ascusbbr 2220 i NO;196 E Lactobacii/us (Genus) Ascusbbr___2710 N02336 SEQ ID : SEQ ED Ascusbbr72224 13 9. Arrzycalampsis (Ge nus) NO:197 Enterococcus (Genus) Ascus b bru27 14 N033? 140. @hil'zgobz‘um (Genus) NO:198 __________________________________________________________________.L_____________________________________ .............................L.................................................... ___________________________________ ______________________________ {0046} FIG. I shows a general worqulow of one embodiment of the method for determining the absolute abundance of one or more active microorganism s. {0047} shows a general workflow of one embodiment of a method for determining the conoccurrence of one or more, or two or more, active microorganism strains in a sample with one or more metadata (environmental) parameters, followed by leveraging cluster analysis and ity detection methods on the network of determined relationships. {0048} is a graphical representation of the timeline of actions/events which occurred over the 21 study days of the Phase I study which ed, Cobb 500 broiler chickens. {0049} is a cal representation of the timeline of s/events which occurred over the 21 study days of the Phase II study which utilized Ross 708 broiler chickens. {0050} is a graphical representation of an exemplary pen and cage setup for use in the phasel or II studies described in e I. {0051} is a graphical representation of an exemplary cage setup for use in the phase I or II studies described in example I. {0052} FIG. ’7 is a graphical representation of the summarized, data trating the statistical outcomes of treatment 1 vs treatment 2 in the Phase I study described in e I. {0053} is a graphical representation of the summarized, data demonstrating the statistical outcomes of treatment 1 vs treatment 2 in the Phase II study described in Example I. {0054} is a cal representation of an exemplary pen setup for use in the study described in Example II, wherein the birds are challenged with Clostrz'um perjjfringens. {0055} depicts an undegraded carbon source (Day 0) and a degraded carbon source (Day 7), as ed in the insoluble carbon source assays. {0056} A and FIG. IIB depict the shared percent similarity (percent identity) among the bacteria (A) and fungi (B) of Table I. The data points represent the greatest percent similarity pairing for each strain. {0057} is a cartoon depiction of an exemplary chicken’s anatomy. {8058} is an image of a dissected gastrointestinal track of a chicken from the beak to the cloaca. {0059} s the x microbial interactions occurring in the gastrointestinal tract. A wellubalanced commensal microbial load is involved in maintaining multiple homeostatic systems. {(9060} depicts the lVIlC score distribution for intestinal bacteria and broiler weight with three species of bacteria and their MIC scores, in which the species have been evaluated in 3 rd party studies. The lower the MIC score, the less likely the species/strains are capable of positively modulating broiler weight. } depicts the MIC score distribution for gastrointestinal bacteria and broiler feed sion ration with three species of bacteria and their MIC scores, in which the species have been ted in a rd 3. party studies. The lower the h/IIC score, the less likely the species/strains are capable of positively modulating broiler feed conversion ratio.

DETAILED DESCRIPTION {(9062} While the following terms are believed to be well understood by one of ry skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subiect matter. {0063} The term "a" or "an" may refer to one or more of that entity, 116. can refer to plural referents. As such, the terms ""a or "an", "one or more" and "at least one" are used interchangeably . In addition, reference to "an element" by the indefinite e "a" or "an" does not exclude the possibility that more than one of the ts is present, unless the context clearly requires that there is one and only one of the elements. {(9064} Reference throughout this specification to "one embodiment)9 <6 an embodiment", "one 39 (C 39 ' ’ ’ ’ ‘ aspect o1. an aspect means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present disclosure. Thus, the appearances of the phrases "in one embodiment" or "in an embodiment" in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics can be combined in any le manner in one or more ments. 0065 As used herein in articular embodiments the terms "about" or "a telv" when 7 3 .J , preceding a numerical value indicates the value plus or minus a range of l %. {0066} As used herein the terms "microorganism" or "microbe" should be taken broadly. These terms are used interchangeably and include, but are not limited to, the two yotic s, Bacteria and, Archaea, eukaryotic fungi and protists, as well as viruses. In some embodiments, the disclosure refers to the "microbes" of Table 1 and/or Table 3 or the "microbes" incorporated by reference. This characterization can refer to not only the predicted taxonomic microbial identifiers of the table, but also the identified strains of the microbes listed in the table. {0067} The term "microbial consortia" or "microbial consortium" refers to a subset of a microbial community of individual microbial species, or s of a species, which can be described as carrying out a common function, or can be described as participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of interest (eg. increased feed efficiency in poultry). The community may comprise two or more species, or strains of a species, of microbes In some instances, the microbes t within the community symbiotically. {0068} The term "microbial community" means a group of microbes comprising two or more s or strains, Unlike ial consortia, a microbial community does not have to be carrying out a common function, or does not have to be participating in, or leading to, or correlating with, a recognizable parameter, such as a phenotypic trait of st (erg, increased feed efficiency in poultry), {0069} As used herein, te," "isolated," "isolated microbe," and like terms, are intended to mean that the one or more microorganisms has been separated from at least one of the materials with which it is associated in a particular environment (for example soil, water, animal tissue), {0070} Microbes of the present disclosure may include spores and/or vegetative cells. In some embodiments, microbes of the present disclosure include microbes in a viable but non—culturable (VBNC) state, or a quiescent state. See Liao and Zhao (US Publication 1.382015267163A1). ln some embodiments, microbes of the present disclosure include microbes in a m. See Merritt et al. (US Patent 7,427,408). {0071} Thus, an "isolated microbe" does not exist in its naturally occurring environment; rather, it is through the various techniques described herein that the microbe has been removed from its natural setting and placed into a non—naturally occurring state of existence. Thus, the isolated strain or isolated microbe may exist as, for example, a biologically pure culture, or as spores (or other forms of the strain) in association with an acceptable carrier. {0072} As used herein, "spore" or "spores" refer to structures produced by bacteria and fungi that are adapted for survival and dispersal. Spores are generally characterized as dormant structures; however, spores are capable of differentiation through the process of germination.

Germination is the entiation of spores into vegetative cells that are capable of metabolic activity, growth, and uction. The germination of a single spore results in a single fungal or bacterial vegetative cell. Fungal spores are units of l reproduction, and in some cases are necessary ures in fungal life cycles. Bacterial spores are structures for surviving conditions that may ordinarily be ductive to the survival or growth of vegetative cells, {0073} As used herein, "microbial composition" refers to a composition comprising one or more microbes of the present disclosure, wherein a ial composition, in some embodiments, is administered to animals of the present disclosure.

{W74} As used herein, "carrier", "acceptable carrier", or "pharmaceutical carrier" refers to a t, adjuvant, excipient, or vehicle with which the compound is administered. Such rs can be sterile liquids, such as water and oils, including those of petroleum, , vegetable, or synthetic origin; such as peanut oil, n oil, mineral oil, sesame oil, and the like. Water or aqueous solution saline solutions and s dextrose and glycerol solutions are preferably employed as carriers, in some embodiments as injectable solutions. Alternatively, the carrier can be a solid dosage form carrier, including but not limited to one or more of a binder (for compressed pills), a glidant, an encapsulating agent, a llavorant, and a colorant, The choice of carrier can be selected with regard to the intended route of adn'iinistration and standard pharmaceutical practice. See Hardee and Baggo (1998. Development and Formulation of Veterinary Dosage Forms. 2"" Ed. CRC Press. 504 pg); EW, Martin (l970. Remington’s ceutical Sciences. l7Th Ed. Mack Pub. Co); and Blaser at a]. (US Publication US$201 l0280840Al). {8075} In some aspects, carriers may be granular in structure, such as sand or sand particles. ln further aspects, the carriers may be dry, as d to a moist or wet carrierln some aspects, carriers can be itve substances and/or prebiotic substances selected from fructon oligosaccharides, inulins, isomalto—oligosaccharides, lactitol, lactosucruse, lactulose, pyrodextrines, soy oligosaccharides, transgalacto—oligosaccharides, xylo~oligosaccharides, and vitamins, In some aspects, carriers can be in solid or liquid form. In some aspects, carriers can be zeolites, calcium carbonate, magnesium carbonate, trehalose, chitosan, c, n, starch, ilk powder, sweet—whey powder, maltodextrin, lactose, and inulin. In some aspects, a carrier is water or physiological saline. {0076} In certain aspects of the disclosure, the isolated microbes exist as ed and biologically pure cultures. It will be appreciated by one of skill in the art, that an isolated, and biologically pure culture of a particular microbe, denotes that said culture is substantially free (within scientific reason) of other living sms and contains only the individual microbe in question. The culture can n varying concentrations of said microbe. The present sure notes that isolated and biologically pure es often "necessarily differ from less pure or inipure materials." See, eg. In re Bergstrom, 427 F2d 1394, (CCPA 1970)(discussing purified prostaglandins), see also, In re Bergy, 596 F.2d 952 (CCPA l979)(discussing purified microbes), see also, Par e~Davis (E Co. v. HK il/Iulffbrd (K; Ca, 189 F. 95 (SDNY, l9l1) (Learned Hand discussing purified adrenaline), ajf’d in part, rev’d m part, 196 F 496 (2d Cir, l9l2), each of which are incorporated herein by reference. rmore, in some aspects, the disclosure provides for certain tative measures of the concentration, or purity limitations, that must be found within an isolated and biologically pure microbial culture. The presence of these purity values, in n embodiments, is a further attribute that distinguishes the presently disclosed microbes from those microbes existing in a natural state. See, ag, M'erck & Co. v. Olin Mathieson Chemical Corp, 253 F.2d 156 (4th Cir. 1958) (discussing purity limitations for vitamin BI 22 ed by microbes), incorporated herein by reference. {0077} As used herein, "individual isolates" should be taken to mean a composition, or culture, comprising a predominance of a single genera, species, or strain, of rganism, following separation from one or more other microorganisms. The phrase should not be taken to indicate the extent to which the microorganism has been isolated or purified. However, "individual isolates" can comprise ntially only one genus, species, or strain, of rganism. {0078} As used , "microbiome" refers to the collection of microorganisms that inhabit the digestive tract or gastrointestinal tract of an animal and the microorganisms" physical environment (Ila, the microbiome has a biotic and, physical component). The microbiome is fluid and may be modulated by numerous naturally ing and, artificial conditions (eg change in diet, disease, antimicrobial agents, influx of additional microorganisms, etc.) The tion of the gastrointestinal microbiome can be achieved, via administration of the itions of the disclosure can take the form of: (a) increasing or decreasing a particular Family, Genus, Species, or functional grouping of a microbe , alteration of the biotic component of the intestinal microbiome) and/or (h) increasing or decreasing gastrointestinal pH, increasing or decreasing volatile fatty acids in the gastrointestinal tract, increasing or decreasing any other physical parameter ant for gastrointestinal health (118,, tion of the abiotic component of the gut microbiome). {0079} As used herein, "probiotic" refers to a substantially pure microbe (113., a single e) or a mixture of desired es, and may also include. any onal components that can be administered to poultry for restoring microbiota. Probiotics or microbial inoculant compositions of the invention may be administered with an agent to allow the microbes to survive the environment of the gastrointestinal tract, ie., to resist low pH and to grow in the gastrointestinal environment. In some embodiments, the present compositions (6g, microbial itions) are probiotics in some aspects. {0080} As used herein, "prebiotic" refers to an agent that increases the number and/or activity of one or more desired microbes. Non—limiting examples of prebiotics that may be useful in the methods of the present disclosure include fructooligosaccharides (6g, oligofructose, inulin, inulin—type fructans), galactooligosaccharides, amino acids, alcohols, isomalto—oligosaccharides, lactitol, lactosucruse, lactulose, pyrodextrines, soy oligosacclrarides, transgalacto~ oligosaccharides, xylo—oligosacclrarides, vitamins, and mixtures thereof. See Ramirez~Farias at a]. (2008. Br. J. Nutr. 4:l~lO) and Pool~Zobel and Sauer (2007. J. Nutr. 137:258lJ—2584 and supplemental).

WO 81203 2017/028015 {0081} The term "growth medium" as used herein, is any medium which is suitable to support growth of a microbe. By way of example, the media may be natural or artificial including n supplemental agar, LB media, blood serum, and tissue culture gels. It should be appreciated that the media may be used alone or in combination with one or more other media. lt may also be used with or without the addition of exogenous nts. {0082} The medium may be d or enriched with additional compounds or components, for example, a component which may assist in the interaction and/or selection of specific groups of microorganisms. For example, antibiotics (such as penicillin) or sterilants (for example, quaternary ammonium salts and ing agents) could be present and/or the physical conditions (such as salinity, nts (for example organic and inorganic minerals (such as phosphorus, nitrogenous salts, a, potassium and micronutrients such as cobalt and magnesium), pH, and/or temperature) could be amended. {0083} As used herein, the term "fowl" and "poultry" are used interchangeably to include both domesticated and non—domesticated birds belonging to the orders of Galliformes and formes. Fowl e chickens (broilers/fryers/roasters/capons/roosters/'stewing hens), turkeys, grouse, New World quail, Old World quail, partridges, ptarmigans, junglef’owl, peafowl, ducks, geese, swans, emus, and ostriches, {0084} Broiler chickens of the present disclosure include: Cobb 500, Cobb 700, Cobb Avian ~48, Cobb Sasso, Ross 308, Ross 708, Ross PM3, Jersey Giant, Cornish Cross, Delaware, Dorking, Buckeye, Campine, Chantecler, Creyecoeur, Holland, Modern Game, Nankin, , Russian, Orlof’f’, Spanish, Sultan, Sumatra, Yokohama, Andalusian, Buttercup, Cubalaya, Faverolles, Java, Lakenvelder, Langshan, Malay, Phoenix, Ancona, Aseel, Brahma, Catalana, Cochin, Cornish, Dominique, Hamburg, Houdan, La Fleche, Minorca, New I-lanipshire, Old English Game, Polish, Rhode Island White, Sebright, Shamo, Australorp, Leghorn, Orpington, th Rock, Rhode lsland Red, Sussex, Wyandotte, Araucana, lowa Blue, Laniona, Manx Rumpy, Naked Neck, Asil, Kadacknath Bursa, Hubbard, l-lubbard, Cobb, Hubbard, , Anak 2000, Avian— 34, Starbra, Sam Rat, Bowans, Hyline, BV—300, H & N Nick, Dekalb Lehman, lLl—SO, Golden~ 92, Priya, Sonali, Devendra, 13—77, o~91, Varna, Caribro naked necked, Caribro multicolored, n, Ross, Arbor Acres, Indian River, Peterson, CobbuVantress, Avian Sasso, Hybro, Groupe Grimaud, Grimaud Frere, Ameraucana, Silkie, Marans, Rosecomb, Welsummer, Barnevelder, , Asil, Chantecler, Croad, Houdan, Pekin, Frizzle, Serama, Orloff, Ac, Aseel, Baheij, Bandara, and hybrids f. {8085} Egg—laying chickens of the present disclosure include: Ameraucana, Ancona, Andalusian, Appenzeller, na, Australorp, Barnevelder, Brahma, Buckeye, Buttercup, Canipine, Catalana, cler, Cochin, Cornish, Crevecoeur, Cubalaya, Deleware, Dominique, Dorking, Faverolles, i, g, Holland, Houdan, l’aerhon, lava, Jersey Giant, La Fleche, Lakenvelder, Lamona, Langsham, Leghorn, Marans, Minorca, Nacked Neck, New Hampshire, Orloff, Orpington, Penedesenca, Phoenix, Plymouth Rock, Polish, Redcap, Rhode Island, h, Sultan, Sussex, Welsumer, V ’yandotte, Yokohama, and hybrids f. {0086} While distinctions are made between broiler chickens and egg—laying chickens, embodiments of the t disclosure e broiler chickens, eggmlaying chickens, and/or multipurpose chickens. {8087} As used herein, "improved" should be taken broadly to encompass improvement of a characteristic of interest, as compared to a control group, or as compared to a known average quantity associated with the characteristic in question. For example, "improved" feed efficiency associated with application of a beneficial microbe, 0r consortia, of the disclosure can he demonstrated by comparing the feed efficiency of poultry treated by the microbes taught herein to the feed efficiency of poultry not treated. ln the present disclosure, "improved" does not necessarily demand that the data be statistically significant (ifl. p < 0.05); rather, any quantifiable difference demonstrating that one value (eg. the average treatment value) is different from another (eg the average control value) can rise to the level of "improved." {0088} As used herein, "inhibiting and suppressing" and like terms should not be construed to e complete inhibition or ssion, although this may be desired in some embodiments. {0089} The term "marker" or e marker" as used herein is an indicator of unique rganism type, microorganism, strain or activity of a microorganism strain. A marker can be measured in biological samples and includes without limitation, a nucleic ased marker such as a ribosomal RNA gene, a peptide- or protein-based marker, and/or a metabolite or other small molecule marker, {80%} The term "metabolite" as used herein is an intermediate or t of metabolism. A metabolite in one embodiment is a small molecule. Metabolites have various functions, including in fuel, structural, signaling, stimulatory and inhibitory effects on enzymes, as a cofactor to an enzyme, in defense, and in interactions with other organisms (such as pigments, odorants and ones). A primary metabolite is directly involved in normal growth, development and reproduction. A secondary metabolite is not directly involved in these processes but usually has an important ecological function. Examples of metabolites include but are not limited to antibiotics and pigments such as resins and terpenes, etc. Some otics use primary metabolites as precursors, such as actinomycin which is created from the primary lite, tryptophan. Metabolites, as used herein, include small, hilic carbohydrates; large, hydrophobic lipids and complex natural compounds. {0091} As used herein, the term ype" refers to the genetic makeup of an individual cell, cell culture, tissue, sm, or group of organisms. {0092} As used herein, the term "allele(s)" means any of one or more alternative forms of a gene, all of which alleles relate to at least one trait or characteristic. In a d cell, the two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes. Since the t disclosure, in emhodiments, relates to QTLs, ze genomic regions that may comprise. one or more genes or regulatory sequences, it is in some ces more accurate to refer to "haplotype" (116. an allele of a chromosomal segment) instead of "allele", however, in those instances, the term "allele" should he understood to comprise the term "haplotype", Alleles are considered identical when they express a similar phenotype. Differences in sequence are possible but not important as long as they do not influence phenotype, {@693} As used herein, the term "locus" (loci plural) means a specific place or places or a site on a chromosome where for example a gene or genetic marker is found, {@994} As used herein, the term "genetically linked" refers to two or more traits that are co- inher'ited at a high rate during breeding such that they are difficult to te through crossing {@695} A "recombination" or "recombination event" as used herein refers to a chromosomal crossing over or independent assortment. The term "recombinant" refers to an organism having a new genetic makeup arising as a result of a recombination event. {0096} As used herein, the term "molecular marker" or "genetic marker" refers to an indicator that is used in methods for izing differences in characteristics of c acid sequences.

Examples of such indicators are restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPS), insertion mutations, atellite markers (SSRs), sequencemcharacterized amplified regions (SCARS), cleaved amplified polymorphic sequence (CAPS) markers or isozyme markers or combinations of the markers described herein which defines a specific genetic and chromosomal location. Markers further include polynucleotide sequences encoding loS or 188 rKNA, and internal transcribed spacer (ITS) sequences, which are sequences found n small—subunit and largevsubunit rRNA genes that have proven to be especially useful in elucidating relationships or distinctions among when ed against one another Mapping of molecular s in the vicinity of an allele is a procedure which can be performed by the ' verage person skilled in molecular~biological techniques {0097} The primary structure of major rRNA subunit lfSS comprise a particular ation of conserved, variable, and hypervariable regions that evolve at ent rates and enable the resolution of both very t lineages such as domains, and more modern lineages such as genera The ary structure of the 168 subunit include approximately 50 helices which result in base pairing of about 67% of the residues These highly conserved secondary structural features are of great functional importance and can be used to ensure positional homology in multiple ce ents and enetic analysis. Over the previous few decades, the 168 rRNA gene has become the most sequenced taxonomic marker and is the cornerstone for the current systematic classification of bacteria and arcliaea (Yarza er al. 2014, Natur ’ Rev. A/Iz’cm. l2:635~45). [0098} A sequence identity of 94.5% or lower for two 168 rRNA genes is strong evidence for distinct genera, 865/6 or lower is strong evidence for distinct families, 82% or lower is strong ce for distinct orders, 785% is strong evidence for distinct classes, and ’7 Jr,% or lowerI is strong ce for distinct phyla. The comparative analysis of 163 rRNA gene sequences enables the establishment of taxonomic thresholds that are useful not only for the classification of cultured microorganisms but also for the classification of the many environmental sequences.

Yarza er a]. 2014. Nature Rein M’icm. l2:635—45).

U3 U1 {0099} As used herein, the term "trait" refers to a characteristic or phenotype. For example, in the context of some embodiments of the present sure; quantity of eggs produced, efficiency of feed utilization, amount of feces produced, susceptibility to gut pathogens, and a decrease in mortality rates; among others. Desirable traits may also include other characteristics, including but not limited to: an increase in weight; an increase in egg production; an increase of musculature; an increase of vitamins in eggs; an increase of fatty acid concentration in the gastrointestinal tract; and increase in egg ; an improved efficiency in feed ation and digestibility; an increase in polysaccharide and lignin degradation; an increase in fat, starch; and protein digestion; an increase in vitamin availability, an increase in mineral availability, an increase in amino acid availability; improved gastrointestinal development; increasing villi length and e area; pH balance in the gastrointestinal tract; pH increase in the gastrointestinal tract, pH decrease in the gastrointestinal tract, a ion in methane and/or nitrous oxide emissions; a reduction in manure production; an improved efficiency of nitrogen utilization; an improved efficiency of phosphorous utilization; an increased resistance to colonization of pathogenic microbes that colonize chickens; an improvement in meat properties, reduced mortality, sed production of antimicrobials, sed clearance of pathogenic microbes, increased resistance to colonization of pathogenic microbes that infect chickens, increased resistance to colonization of enic microbes that infect humans improved gut health, etc; wherein said increase, decrease, or reduction is determined by ing against an animal not having been administered a composition of the present disclosure. {96100} A trait may be inherited in a dominant or recessive manner, or in a partial or incomplete—dominant manner. A trait may he monogenic (Le. determined by a single locus) or polygenic (Le. determined by more than one locus) or may ? lso result from the interaction of one or more genes with the nment. {@6101} in the context of this sure, traits may also result from the interaction of one or more avian genes and one or more microorganism genes, {@6102} As used herein, the term "homozygous" means a genetic condition existing when two identical alleles reside at a specific locus, but are positioned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism. Conversely, as used herein, the term "heterozygous" means a genetic condition existing when two ent alleles reside at a specific locus, but are oned individually on corresponding pairs of homologous chromosomes in the cell of a diploid organism. {00103} As used herein, the term "phenotype" refers to the observable teristics of an individual cell, cell culture, organism (erg, bird), or group of organisms which results from the interaction between that individual’s genetic makeup (126,, genotype) and the environment. {00104} As used herein, the term "chimeric" or "recombinant" when describing a nucleic acid sequence or a protein sequence refers to a nucleic acid, or a protein sequence, that links at least two heterologous polynucleotides, or two heterologous polypeptides, into a single macromolecule, or that renarranges one or more elements of at least one l nucleic acid or protein ce. For example, the term binant" can refer to an artificial combination of two otherwise separated segments of sequence, 6g, by chemical synthesis or by the manipulation of isolated segments of nucleic acids by c engineering techniques. {00105} As used herein, a "synthetic nucleotide sequence" or "synthetic polynucleotide sequence" is a nucleotide sequence that is not known to occur in nature or that is not lly occurring. Generally, such a synthetic nucleotide sequence will comprise at least one nucleotide difference when compared to any other naturally occurring nucleotide sequence. {00106} As used herein, the term "nucleic acid" refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides, or analogs f. This term refers to the primary structure of the molecule, and thus includes double and ~stranded DNA, as well as double— and —stranded RNA. It also includes ed c acids such as methylated and/or capped nucleic acids, nucleic acids containing modified bases, backbone cations, and the like. The terms ic acid" and "nucleotide sequence" are used interchangeably. {00107} As used herein, the term "gene" refers to any segment of DNA associated with a biological function. Thus, genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression. Genes can also include non—expressed DNA segments that, for example, form recognition sequences for other ns. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters {00108} As used herein, the term "homologous" or ogue" or "ortholog" is known in the art and refers to related sequences that share a common ancestor or family member and are determined based on the degree of sequence identity. The terms "homology," "homologous," "substantially similar" and, "corresponding substantially" are used hangeably . They refer to nucleic acid fragments wherein s in one or more nucleotide bases do not affect the ability of the nucleic acid fragment to mediate gene expression or produce a n phenotype.

These terms also refer to modifications of the nucleic acid fragments of the instant disclosure such as deletion or insertion of one or more nucleotides that do not substantially alter the functional properties of the resulting nucleic acid fragment relative to the initial, unmodified nt, It is therefore tood, as those skilled in the art will appreciate, that the disclosure encompasses more than the specific exemplary sequences. These terms describe the relationship between a gene found in one species, subspecies, variety, cultivar or strain and the corresponding or equivalent gene in another species, subspecies, variety, cultivar or strain, For purposes of this disclosure homologous sequences are compared. "Homologous sequences" or c‘honiologues" or "oithologs" are thought, believed, or known to be functionally related, A functional relationship may be indicated in any one of a number of ways, including, but not limited to: (a) degree of sequence identity and/or (b) the same or similar biological function. Preferably, both (a) and (b) are indicated. Homology can be determined using software programs readily available in the art, such as those sed in Current ols in Molecular Biology (FM. Ausubel er al, eds, 1987) ment 30, section 7,7l8, Table 7.7], Some alignment programs are MacVector (Oxford Molemilar Ltd, Oxford, UK) ALIGN Plus (Scientific and Educational Software, Pennsylvania) and Alian i Vector NTl, lnvitrogen, Carlsbad, CA). Another alignment program is Sequencher (Gene Codes, Ann Arbor, Michigan), using default parameters. {08109} As used herein, the term otide change" refers to, egx, nucleotide substitution, on, and/or insertion, as is well understood in the art. For example, ons contain alterations that produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the d protein or how the proteins are made. {@0110} As used herein, the term "protein modification" refers to, e.g., amino acid substitution, amino acid cation, deletion, and/or insertion, as is well understood in the art. {08111} As used herein, the term "at least a portion" or "fragment" of a nucleic acid or ptide means a portion having the minimal size characteristics of such ces, or any larger fragment of the full length molecule, up to and including the full length molecule. A fragment of a polynucleotide of the disclosure may encode a biologically active portion of a genetic regulatory element. A biologically active poition of a genetic regulatory element can be prepared by isolating a portion of one of the polynucleotides of the disclosure that comprises the genetic regulatory t and ing activity as described herein Similarly, a portion of a ptide may be 4 amino acids, 5 amino acids, 6 amino acids, 7 amino acids, and so on, going up to the full length polypeptide. The length of the poition to be used will depend on the particular application, A portion of a nucleic acid useful as a hybridization probe may be as short as 12 nucleotides; in some embodiments, it is 20 nucleotides. A portion of a polypeptide useful as an e may be as short as 4 amino acids. A portion of a polypeptide that ms the function of the full—length polypeptide would lly be longer than 4 amino acids. {@0112} Variant polynucleotides also encompass sequences derived from a mutagenic and recombinogenic procedure such as DNA shuffling Strategies for such DNA ing are known in the art. See, for example, Stemmer (1994) PNAS 91:10747-10751; Stemmer (1994) Nature 370389—391; i at al.( 1997) Nature Biotech. 15:436'438; Moore at ai.(1,997) J. Mol. Biol. 2723364347; Zhang at £110,997) PNAS 94:4504—4509; Craineri er ai.(l998) Nature 391:288~ 291; and US. Patent Nos, 5,605,793 and 5,837,458. For PCR amplifications of the polynucleotides disclosed herein, oligonucleotide primers can be designed for use in PCR reactions to amplify ponding DNA sequences from cDNA or genomic DNA extracted from any organism of interest. s for designing PCR primers and PCR g are generally known in the art and are disclosed in Sambrook 8! (11.0989) Molecular Cloning: A Laboratory Manual (2nd ed, Cold Spring Harbor Laboratory Press, Plainview, New York). See also lnnis e! al, eds. (1990) PCP; Protocols: A Guide to Methods and Applications (Academic Press, New York); Innis and Gelfand, eds. (1995) PCP; Strategies mic Press, New York); and Innis and Gelfand, eds. (1999) PCR Methods Manual (Academic Press, New York). Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene—specific primers, vectoruspecific primers, partiallyumismatched primers, and the like. {00113} The term "primer" as used herein refers to an oligonucleotide which is capable of annealing to the amplification target allowing a DNA polymerase to attach, thereby serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of primer extension product is d, 17.6., in the presence of nucleotides and an agent for polymerization such as DNA rase and at a suitable temperature and pH. The (amplification) primer is preferably single stranded for maximum efficiency in amplification. Preferably, the primer is an oligodeoxyribonucleotide. The primer must be iently long to prime the synthesis of ion products in the presence of the agent for polymerization. The exact lengths of the primers will depend, on many factors, including temperature and composition (A/"l‘ vs. G/C content) of primer A pair of bindirectional primers consists of one forward and one reverse primer as ly used in the art of DNA, amplification such as in PCR amplification. {00114} The terms "stringency" or gent hybridization conditions" refer to hybridization conditions that affect the stability of s, eg, temperature, salt concentration, pH, forinamide concentration and the like. These conditions are empirically optimized to maximize specific binding and minimize ecific binding of primer or probe to its target nucleic acid sequence, The terms as used include reference to conditions under which a probe or primer will hybridize to its target sequence, to a detectably greater degree than other sequences (eg. at least 2-fold over background). Stringent ions are sequence ent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5° C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH, The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe or primer Typically, stringent conditions will be those in which the salt tration is less than about 1.0 M Na-l- ion, lly about 0.01 to 1.0 M Na + ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 300 C for short probes or primers (erg. 10 to 50 nucleotides) and at least about 600 C for long probes or primers (tag. greater than 50 nucleotides). Stringent conditions may also be ed with the addition of destabilizing agents such as formamide. Exemplary low stringent conditions or tions of reduced stringency" include hybridization with a buffer solution of % ide, l M NaCl, 1% SDS at 370 C and a wash in 2> Accordingly, an "enhancer" is a DNA sequence that can ate promoter activity, and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA ts, It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions, It is r recognized that since in most cases the exact boundaries of regulatory sequences have not been completely d, DNA fragments of some variation may have identical promoter activity.

{M11161 As used herein, a "constitutive promoter" is a promoter which is active under most conditions and/or during most development stages. There are several advantages to using constitutive promoters in expression vectors used in biotechnology, such as: high level of production of proteins used to select enic cells or organisms; high level of expression of reporter proteins or le markers, allowing easy ion and quantification; high level of production of a transcription factor that is part of a regulatory transcription system; production of compounds that requires ubiquitous activity in the organism; and production of compounds that are required during all stages of development. Non—limiting exemplary constitutive promoters include, IaMV 35$ promoter, opine promoters, ubiquitin promoter, alcohol dehydrogenase promoter, etc. {661171 As used , a "non—constitutive promoter" is a promoter which is active under certain conditions, in certain types of cells, and/or during certain development stages. For example, tissue specific, tissue preferred, cell type specific, cell type preferred, inducible promoters, and promoters under development control are non—constitutive promoters. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues. {@9118} As used, herein, "inducible" 0r "repressible" promoter is a promoter which is under chemical or environmental factors control. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, n als, the presence of light, acidic or basic conditions, etc. {@9119} As used herein, a "tissue specific" promoter is a promoter that initiates transcription only in certain tissues. Unlike constitutive expression of genes, tissue—specific sion is the result of several interacting levels of gene regulation As such, in the art sometimes it is preferable to use promoters from homologous or closely related species to achieve efficient and, reliable expression of transgenes in particular s. This is one of the main reasons for the large amount of tissue~specific ers isolated from particular tissues found in both scientific and patent literature. {00120} As used herein, the term "operably linked" refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the on of one is regulated by the other, For example, a promoter is operably linked with a coding sequence when it is e of regulating the expression of that coding sequence (ie., that the coding sequence is under the transcriptional control of the promoter), Coding sequences can be operably linked to regulatory sequences in a sense or antisense orientation. In another example, the mentary RNA regions of the disclosure can be operably linked, either directly or indirectly, 5’ to the target mRNA, or 3’ to the target niRNA, or within the target niRNA, or a first con'ipleniei'itary region is ’ and its complement is 3’ to the target mRNA, {@6121} As used herein, the phrases binant construct", ssion construct", "chimeric construct", "construct", and "recombinant DNA uct" are used interchangeably herein, A recombinant construct comprises an artificial combination of nucleic acid nts, egx, tory and coding sequences that are not found together in nature, For example, a chimeric construct may comprise regulatory sequences and coding sequences that are derived from different s, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Such construct may be used by itself or may be used in conjunction with a vector. if a vector is used then the choice of vector is dependent upon the method that will be used to transform host cells as is well known to those skilled in the art. For example, a plasmid vector can be used. The skilled artisan is well aware of the genetic elements that must be present on the vector in order to successfully transform, select and propagate host cells comprising any of the isolated nucleic acid nts of the disclosure. The skilled artisan will also recognize that different independent transformation events will result in ent levels and patterns of expression (Jones er (1],, (1985) El‘leO J. 4:2411—2418; De Almeida er all, (1989) Mol. Gen. Genetics 218:78m86), and thus that multiple events must be ed in order to obtain lines displaying the desired expression level and pattern. Such ing. may be accomplished by Southern analysis of DNA, Northern analysis omeNA expression, immunoblotting analysis of protein expression, or phenotypic analysis, among others. Vectors can be plasmids, s, bacteriophages, pi‘o— viruses, ids, transposons, aitifieial chromosomes, and the like, that replicate autonomously or can ate into a chromosome of a host cell. A vector can also be a naked RNA polynucleotide, a naked DNA polynncleotide, a polynucleotide ed of both DNA and RNA within the same strand, a poly—lysine~conjugated DNA or RNA, a peptide—conjugated DNA or RNA, a liposome—conjugated DNA, or the like, that is not autonomously replicating As used herein, the term "expression" refers to the production of a fui'ictional oduct eg, an mRNA or a protein (precursor or n'iature). {@6122} ln some embodiments, the cell or organism has at least one heterologous trait. As used herein, the term rologous trait," refers to a phenotype imparted to a transformed host cell or transgenic organism by an exogenous DNA t, heterologous polynucleotide or heterologous nucleic acid. Various s in phenotype are of interest to the present disclosure, including but not limited to increasing a fowl’s yield of an economically ant trait (6.1g, eggs, egg volume, fowl weight, etc.) and the like. These results can be ed by providing expression of lieterologous products or increased expression of endogenous products in organisms using the methods and compositions of the present disclosure. In some embodiments, the isolated microbial strains of the present disclosure further ass mutants f. In some embodiments, the present disclosure further contemplates microbial strains having all or the identifying characteristics of the presently disclosed microbial strains. {00123} As used herein, the term "MIC" means maximal information coefficient. MIC is a type of nonparamentric analysis that identifies a score (MIC score) between active microbial strains of the present sure and at least one measured metadata (62g increase in weight).

Further, US. Application No. 15/217,57i filed on July 22, 2016 (issued as US. Patent No. 9,540,676 on January 10, 2017) is hereby incorporated by reference in its entirety. {00124} The maximal information coefficient (MIC) is then calculated between strains and ta and, between s as seen in 2009. s are pooled, to create a list of all relationships and their corresponding MIC scores. If the relationship scores below a given threshold, the onship is deemed/identified as irrelevant. If the relationship is above a given threshold the relationship deemed/identified as relevant, and is further subject to k analysis. The following code fragment shows an exemplary methodology for such analysis, according to one ment: Read total list of relationships file as links threshold = ()8 for i in range(len(links)): if links >-- threshold multiplierfi] 1 multiplierfi] 0 end if links___te1np multiplier‘*links final___links links___temp[links___temp 1:0] savetxt(output___file,final___links) output___file.closef) {00125} In some embodiments, the compositions of the present disclosure comprise one or more bacteria and/or one or more fungus that have a MIC score of at least about 0.1, 0. l 5, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.7, o. "J5, 0.8, 0.85, 0.9, or 0.95. {00126} With regard to MIC scores, and in view of and FIG 16. a cut—off based on this score is used to define useful and, non—useful microorganisms with respect to the improvement of specific traits. The point on FIG. IS and at which the data points on the cuive move transition from the log scale to the linear scale (with regard to the slope) is the inflection point. The organisms with MIC scores that fall below the inflection point are generally non—useful, while the organisms with MIC scores that are found above the inflection point are generally useful, as it peita ins to the specific characteristic being evaluated for the MIC score.

{W127} Based on the output of the k analysis, active strains are selected for ing products (e.g., ensembles, aggregates, and/or other synthetic groupings) containing the selected strains. The output of the network analysis can also be used to inform the selection of s for further product composition testing, as seen in 2010.

{W128} The use of thresholds is discussed above for analyses and inations, Thresholds can be, depending on the entation and application: (I) empirically determined (e. g., based on distribution levels, setting a cutoff at a number that removes a, specified or significant portion of low level reads); (2) any non—zero value; (3) percentag v’percentile based; (4) only strains whose normalized second marker (i,e., activity) reads is greater than normalized first marker (cell count) reads; (5) logZ fold change n activity and quantity or cell count; (6) normalized second marker (activity) reads is greater than mean second marker ity) reads for entire sample (and/or sample set); and/or any magnitude old described above in addition to a statistical threshold (ie, icance testing). The following e provides thresholding detail for distributions of RNA—based second marker measurements with respect to DNA—based first marker measurements, according to one embodiment.

} As used herein "shelfustable" refers to a functional attribute and new utility acquired by the microbes formulated according to the disclosure, which enable said microbes to exist in a useful/active state outside of their natural environment in the gastrointestinal tract (tie, a markedly different characteristic). Thus, shelf—stable is a functional ute created by the formulations/compositions of the disclosure and denoting that the microbe formulated into a shelf~stable composition can exist outside the gastrointestinal tract and under ambient conditions for a period of time that can be determined depending upon the particular formulation utilized, but in l means that the es can be formulated to exist in a composition that is stable under ambient conditions for at least a few days and generally at least one week. Accordingly, a —stable fowl supplement" is a composition comprising one or more microbes of the disclosure, said microbes ated in a composition, such that the composition is stable under ambient conditions for at least one week, meaning that the microbes sed in the composition (erg. whole cell, spore, or lysed cell) are able to impart one or more beneficial phenotypic properties to a fowl when administered (erg. increased weight gain, increased eggshell density, ed gastrointestinal health, and/or modulation of the gastrointestinal microbi orne), Isolated Microbes {00130} ln some aspects, the present disclosure provides isolated microbes, including novel strains of microbes, presented in Table 1 and Table 3. {00131} ln other aspects, the present disclosure es isolated whole microbial cultures of the microbes identified in Table 1 and Table 3. These cultures may comprise microbes at various concentrations. illlll32} In some aspects, the disclosure provides for utilizing one or more microbes selected from Table l and Table 3 to increase a phenotypic trait of interest in poultry. {@9133} To some embodiments, the disclosure provides ed microbial species belonging to taxonomic families of I.,actobacillaceae, Lachnospiraceae, Rummococcaceae, Peptostreptococcaceae, Streptosporangiaceae, I..euconostocaceae, Microbacteriaceae, Micrornonosporaceae, Clostridiaceae, Pseudomonadaceae, ococcaceae, Bacillaceae, Bacteroidaceae, Nectriaceae, Corynebacteriaceae, Rhodobacteraceae, and Hypocreaceae, {0133} In r embodiments, isolated microbial species may be selected from genera of family I_.actobacillaoeae, including Acetatifactor, Acetitornaculum, Anaerostipes, Butyrivibrio, iatonella, Cellulosilyticum, Coprococcus, Dorea, Hespellia, Johnsonella, Lachnoanaerobaoulum, I..achnobacterium, Lachnospira, lvlarvmbryantia, Moryella, ()ribacterium, Parasporobacterium, Pseudobutyrivibrio, oniella, Roseburia, Shuttleworthia, aoterium, Stomabacul urn, and Syntrophococous~ WO 81203 {8134} In further embodiments, isolated microbial species may be selected from genera of family Lachnespiraceae, including Bufyrivibrz‘o, Roseburia, Lacknaspira, Acetiromaculzmz, (Z'Oprocaccus, Jahnsonella, Catonella, Psezui’oburyrivz‘brio, Smtmpkacoccus, Sparobacterium, Paraspombacterium, Lachnabactermm, Shuttleworthia, Bored Anaerosl’zfpes, Hespeilia, Ilrfi'al/Vinbij/aillia, Oribacferium, i’l/Ioryelia, Blamm, Robinsonieila, osilyticum, Lachnoanaembacuhim, Stomatobaculum, Fusicarenibacz‘er, Acetanfizcmr, and Eisenbergieila. {8135} In further embodiments, isolated microbial species may be ed from genera 0f family Ruininoceccaceae, including coccus, Acezivibrio, Shorebacter, fiimm, Przpiliibacrer, Oscillospira, Gemmiger, Faecrzlz'bacterium, Pasfidiosipila, Anaerotmncus, lingenens, Aceranaembacierium, Subdoligrcmulum, Hydrogenoanaerabacterium, and Candidadus Saleaferrea. {0136} In further embodiments, ed microbial s may be selected from genera of family Peptcstreptococcaceae, including Anaerosphaera, Filijacmr, Ireptococcus, Sporaceligenium, and bacrer. {(3137} In, further embodiments, ed microbial species may be selected from genera of family Streptosporangiaceae, including Acrocarpospora, Herbidm‘pora, il/iz'cmbispom, Aficroierraspora, Nonamuraea, Planobispara, Pitmomonmpom, Planofetraspom, Sphaerisporangizmz, aspomngizmz, Therm(Jaclimivpam, ThermOC'aie/Iispora, and Thermopobzspam. [0138} In further embodiments, isolated ial species may be selected from genera of family Leuconostocaceae, including Fruciobacill’us, Leuconasmc, 081000000113, and Weissel/a. {8139} In further embodiments, isolated microbial species may be selected from genera of family Microbacteriaceae, including Agrez’a, Agrococcus, Agmmyces, Alpinomanas, Amnibacterizmz, Aureobactermm, Chijzseoglobus, Clavibacter, Compostimonas, Clyobactefium, Curtobacten’um, Diaminobm‘yricz’monas, Frigoribacteiium, Ii’mndihabil‘ans, Glacibactei", Gig/Ilatalpicola, Gulosibacren Herbiconmx, Homosermimanas, Humibacter, Kiugiella, Labecfl'ella, Legf'sonia, Leucabacter, Lysinimonas, iliarisedz’mmicola, Aficrobacferium‘ rl/Iz’crocella, il/ificroterricola, etocola, Olabacferium‘ Phycz’cola, Plantibacter’, f’om’imonas, Pseudociavibacfer, Rarhayibacz‘er, Rhodoglobus, Salinibactemgm, Schumaneila, cala, Yonghaparida, and Zimmermannella. {0140} In further embodiments, isolated microbial species may be selected from genera of family h/Iicrornonosporaceae, including Actinaurz’spom, Actinocatenispom, planes, Allocareliiglobosispom, Amorpkaspomngium, Ampul/ariellrt Asrmoa, ig/obosispom, Carenulophmeig Couchiaplanes, Daciy/aspomngmm, Hamadaea, Jr'shengella, Krasilnikovia, pora, Luea’emanne/la, ila’icromonospora, Phytohabitcms, Phyromonospom, Pilimelz'a, Pianopolyspora, Planosporcmgium, Plantactmospom, Polymorphospora, Psemimporcmgmm, Rugosimonospora, Salinispora, Spit/'z'i/iplanes, Verrucosz’spora, Virgisporangz’um, and l/a‘, {0141} In further embodiments, isolated microbial species may be selected from genera of family Clostridiaceae, including Aceranaerobacrcflum, Acelt'vibrio, Acidammobacrer, Alkaliphilus, bacrer, Anaerosztpes, Anoerotruncus, Anowi'zarmnum, Biyanrella, Bunificicoccus, Caldanaerocelia, Caloramaror, Caloranaerobactcr, Commicella, Candidatus Arrhromirus, Clostridmm, ocillus, Dorea, Erhcmologenbacterium, Faecalz'bacterium, Garciella, Guggenheimella, Hespellia, Linmingz’o, Ahtromncola, Oxobocter, Parasporobacterium, S'arcma, Saelmgenia, Sporobacter, Subdoltgramtlum, Tepidibactcr, Tepidimicrobium, Thermobrachtum, Thermohttlobacrer, and Tindallia, {0142} In further ments, ed microbial species may be selected from genera of family Pseudornonadaceae. [8143} In further ments, isolated microbial species may be selected from genera of family Nectriaceae. [8144} In some embodiments, the disclosure provides isolated microbial species belonging to genera of: I-Iypocreaceae. {8145} In some embodiments, one or more microbes from the taxa disclosed herein are utilized to impart one or more beneficial properties or improved traits to poultry production. {8146} Furthermore, the disclosure relates to microbes having characteristics substantially similar to that of a microbe identified in Table 1 and/or Table 3. {0147} The isolated microbial species, and novel strains of said species, fied in the present disclosure, are able to impart beneficial properties or traits to poultry production. [8148} For instance, the isolated microbes described in Table l and Table 3, or consortia of said es, are able to increase feed efficiency. The se can be quantitatively ed, for example, by measuring the ef"ect that said microbial ation has upon the modulation of feed efficiency. In some embodiments, feed efficiency is represented by the feed conversion ratio, which is calculated by measuring desirable animal output produced per pound of feed consumed.

With regard to fowl, the desirable output is typically pounds of meat produced per pound of feed consumed. {@149} In some embodiments, the isolated microbial strains are microbes of the present disclosure that have been genetically modified. In some embodiments, the genetically modified or recombinant microbes comprise polynucleotide sequences which do not naturally occur in said microbes. In some embodiments, the microbes may comprise heterologous cleotides.

In further embodiments, the heterologous polynucleotides may be operably linked to one or more polynucleotides native to the microbes. In some embodiments, the isolated ial strains of the present disclosure further encompass mutants thereof. In some embodiments, the present disclosure further contemplates microbial s having all of the fying characteristics of the presently disclosed microbial strains. 111 some embodiments, the heterologous polynucleotides may be reporter genes or selectable markers. In some embodiments, reporter genes may be selected from any of the family of fluorescence proteins (egg GFP, REP, YFP, and the like), fi—galactosidase, luciferase In some embodiments, selectable markers may be selected from cin phosphoti'ansferase, hygroinycin otransferase, aininoglycoside adenyltransferase, dihydrofolate reductase, acetolactase synthase, xynil nitrilase, B~glucuronidase dihydi‘ogolate i‘eductase, and chloramphenicol acetyltransferase, In some embodiments, the heterologous polynucleotide may be operably linked to one or more promoter.

} In some embodiments the isolated microbial strains express trai'isgenic or native enzymes selected from cellulases ellulases, exocellulases, glucosidases), pectinases, es, amylopectinases, ligninases, and phytases [6152} In some en'ibodiinents, the species of the taxa provided in Table 4 are not known to have been ed in compositions for administration to animals. . [6153} Table 4: Taxa ly Genera) of the present disclosure not known to have been utilized in animal agriculture, Corynebacterium Verrucosispora Hydrogenoanaerobacterium Subdoligranulum Paracoccus Leuconostoc Cellulosilyticum Laclmospiracea Ruminococcus Anaerofilum Roseburia Miciobacteiium idium XlV b Verrucosispora Bacteroides {9154} Microbial Consortia {0155} In some aspects, the disclosure provides microbial tia comprising a combination of at least any two microbes selected from amongst the microbes identified in Table 1 and Table 3. {0156} In n embodiments, the consortia of the present disclosure comprise two microbes, or three microbes, or four microbes, or five es, or six microbes, or seven microbes, or eight microbes, or nine microbes, or ten or more microbes. Said microbes of the consortia are different microbial species, or different strains of a microbial species. {0157} In some embodiments, the disclosure es consortia, comprising: at least one or at least two ed microbial species belonging to genera. of: Lacrobacz'ilus, Clostridz'um, Faecalz'bacter, Hydrogenoanaerobacterz'zmz, Acrocarpospom, Bacillus, Subdoiigrrmuium, Lezwonostoc, Laclmospimcea, Anaerqfiium, Microbactermm, Verrucosispora, Anaerofilum, ,Biaufla, Pseudomonas, acter, Corynebaclerium, Streptococcus, ocr: s Celluiosihw’cum, Rummococcus, Rosebum, oides, Filoirasidium, Gibberilia, Aialmpora, Pic-hid, and (l‘andida. Particular novel strains of species of these aforementioned genera can be found in Table l and Table 3. [0158} In some embodiments, the disclosure provides consortia, comprising: at least one or at least two isolated microbial species belonging to the family of: acillaceae, Lachnospiraceae, Rurninococcaceae, Peptostreptococcaceae, Streptosporangiaceae, Leuconostocaceae, Microbacteriaceae, Micromonosporaceae, Clostridiaceae, monadales, Nectriaceae, and Hypocreaceae; wherein Lachnospiraceae can be further specific to Clostridiurn clusters XlVa and XlVb; and wherein Peptostreptococcaceae can be further specific to Clostridium cluster XI. Particular novel strains of species of these aforementioned genera can be found in Table l and Table 3. {0159} In paiticular aspects, the disclosure provides microbial consortia, comprising species as grouped in Tables Smll. With respect to Tables 5—11, the letters A through I represent a non— limiting selection of microbes of the present disclosure, d as: {0160} A = Strain designation Ascusbbrw578 identified in Tabie l; {0161} B = Strain designation Ascusbbij___l436 identified in Table l; {0162} (I Strain designation Ascusbbi'___33 fied in Table l; {0163} l) Strain designation Ascusbbr___409 identified in Table l, {0164} E Strain designation Ascusbbr___l 85064 fied in Table 1; {0165} E Strain designation Ascusbbr___5796 identified in Table 1; {0166} G Strain designation Ascusbbr___10593 identified in Table l; {0167} H Strain designation Ascusbbr___4729 identified in Table 1; and {0168} 1 Strain designation Ascusbbr_7363 identified in Tabie 1.

Table 5: Eight and Nine Strain Consortia A,B,C,D,E,E,G,l ABCD..,FH AB,C,DE,G, H,l A,3,C,E,.E,G, H,l A, B,D,E,F— G, HE E,F,G,H,E B,,C,D E,F-,G, Hr A, B,,C,D E,F-,G, Hrm Table 6: Seven Strain Consortia A,B,C,D,E,E,G A,B,C,D,E,E,l—l AB,C, D, E,.",l AB,C, D, E, G, H A, B, C. D, E.G l A, B, C, D, E, '-l,l D,F,G,H }A,B,C,D,F,G,l A,,,,,BCDFHl A,B,CD,,GHl A,,,,BCE F,,G H E,F,,EG A,C,,DE.,G,H,E ACDECH‘ A,C,E,,FG,,EH A,D,E,F,G,,Hl BC,DEFGH B,,,,CDEE,G,| B,C,D,E,,,FHl BCD,._GHE B,,CD,,,,EFGH B,C,E,FG,,Hl B,,DE,E,G,,Hl C,D,E,,,FGH,l :Six Strain Consortia magu F AEQQEGE&&QQEH A,B,C,DiE,E A,B,C,D,F,G A,B,C,D,F,H EA,B,C,D,F,3 A,B,C,D,G,E A,B,C,D,H,i A,B,C,E,F,G A, B,C, E, F, H A,B,C,E,F,i EAagaaH Aacaa: F G : Aauafifl AflDfifJ Ekabffiki A,B,D,E,H,E A,B,D,F,G,H A,B,D,F,G,i QEEGHJ QEEQHEEAEDEHJ A,B,D,G,H,E A,B,E,F,G,H F,(3,i A,B,E,F,H,E A,B,E,G,H,i AflEQH'EAQQEEG AQQEEH AQDEEE AQQEQHEAQREQI A,C,D,E,H,i AQDEQHEAfiDffij Acmnfie Aflafifij AfififfifiiikflfiiGfi AQEGHJEAfiffiHJ iluiflifl' Alflfifliikflfiafll aaaqmaéaquaae RQQBQHEBfipffifi EQDffikiiachfiJ EQEEQHEB££I£J B,C,E,F,H,E RQEQHEERQEQHE EEQEQHE B,D,F;G,H,i REEGHJ EQQEEGH QQEQHJicpffifiu Table 8: Five Strain (Iansarfia B, I W: REGfitii aaekm ECJLEEG - 1' QD££J EQDEHJ EQDfikm c,E.F,G,: E,F,G,H,l AflgHiAfiCEEABD£ D,G,H,l AflflGiAflEHEAfifi H AQEHEAQH . iAEffi EAEEH AEGHEAfiGE 3a: AQQEEAQDFEAQQGEAQQH """"""""""""""""""?XEEG§AQH4§AQH BCFG l,,,BCFHi EQGfiiBfifid 3,QLH§BDEI ' l ' [0169} In some embodiments, the microbial consortia may be selected from any member group from S—l 1 Isolated Microbes — Source Material {@170} The microbes ot‘ the present disclosure were obtained, among other places, at various locales in the United States from the gastrointestinal tract of poultry Isolated es — Microbial Culture Techniques {(3171} The es of Table l and Table 3 were matched to their nearest taxonomic groups by utilizing classification tools of the Ribosomal Database Project (REP) for 165 rRNA sequences and the riendly Nordic ITS Ectomycorrhiza (UNITE) database for ITS rRNA sequences.

Examples of matching microbes to their nearest taxa may be found in Lan er al. (2012" PLUS one. 7(3):e3249l), Schloss and Westcott (ZOll. AMJZ. Environ. rlrfz'crobz’ol’, '7'7(l0):3219_3226) 7 and Koljalg e: a]. (2005. ./ 76w Phytoiogz‘sf. 166(3): l063—1068). {8172} The isolation, fication, and culturing of the microbes of the present sure can be effected using standard microbiological techniques. Examples of such techniques may be found, in dt, P. (ed) Methods for General and Molecular iology. American Society for Microbiology, Washington, DC. (1994) and Lennette, E H. (ed) Manual of Clinical Microbiology, Third, Edition. American Society for Microbiology, Washington, DC. (l980), each of which is incorporated by reference. {9173} Isolation can be effected by streaking the specimen on a solid medium (cg, nt agar plates) to obtain a single colony, which is terized by the phenotypic traits described hereinaboye (cg, Gram ve/negative, capable of forming spores aerobically/anaerobically, cellular morphology, carbon source metabolism, acid/base production, enzyme secretion, metabolic secretions, etc.) and to reduce the likelihood, of working with a culture which has become contaminated. {9174} For example, for es of the disclosure, biologically pure isolates can be obtained through repeated subculture of biological samples, each subculture followed by streaking onto solid media to obtain individual colonies or colony forming units. Methods of ing, thawing, and growing lized bacteria are commonly known, for example, Gherna, R. L. and C. A. Roddy. 2007, Culture Preservation, p 33 In C. A. Reddy, T. J. Beveridge, J, A, Breznak, G. A, Marzluf, T. M. Schmidt, and L. R. Snyder, eds. an Society for Microbiology, Washington, DC, 1033 pages; herein incorporated by reference. Thus freeze dried liquid formulations and cultures stored long term at "-700 C in solutions containing glycerol are contemplated for use in providing formulations of the present disclosure. [0175} The microbes of the disclosure can be propagated in a liquid medium under aerobic conditions, or alternatively anaerobic conditions. Medium for growing the bacterial s of the present disclosure includes a carbon source, a nitrogen source, and inorganic salts, as well as specially required substances such as vitamins, amino acids, nucleic acids and the like. Examples of le carbon sources which can be used for growing the es include, but are not limited to, starch, peptone, yeast extract, amino acids, sugars such as glucose, arabinose, e, glucosamine, maltose, and the like; salts of organic acids such as acetic acid, fumaric acid, adipic acid, propionic acid, citric acid, gluconic acid, malic acid, pyruvic acid, malonic acid and the like, alcohols such as ethanol and glycerol and the like, oil or fat such as soybean oil, rice bran oil, olive oil, corn oil, sesame oil. The amount of the carbon source added varies according to the kind of carbon source and is typically between 1 to 100 gramt’s) per liter of medium. Preferably, glucose, starch, and/or peptone is contained in the medium as a major carbon source, at a concentration of 0.16% (WW3. Examples of suitable nitrogen sources which can be used for growing the bacterial strains of the present disclosure include, but are not limited to, amino acids, yeast extract, tiyptone, beef t, peptone, potassium nitrate, um nitrate, ammonium chloride, ammonium sulfate, um phosphate, a or combinations thereof. The amount of nitrogen source varies according to the type of nitrogen source, typically between 0.1 to '30 grams per liter of media. The inorganic salts, potassium dihydrogen phosphate, dipotassium hydrogen phosphate, disodium hydrogen phosphate, magnesium e, magnesium de, ferric sulfate, ferrous sulfate, ferric chloride, ferrous chloride, manganous sulfate, manganous chloride, zinc e, zinc chloride, cupric e, calcium chloride, sodium chloride, calcium carbonate, sodium carbonate can be used alone or in combination The amount of inorganic acid varies according to the kind of the inorganic salt, typically between 0.001 to 10 grams per liter of medium. Examples of specially required substances include, but are not limited to, vitamins, nucleic acids, yeast t, peptone, meat extract, malt extract, dried yeast and combinations thereof Cultivation can be effected at a temperature, which allows the growth of the microbial strains, essentially, between 200C and 46°C. in some aspects, a temperature range is 30003990 For optimal growth, in some embodiments, the medium can be adjusted to pH 6.0—7.4. It will be appreciated that cially ble media may also be used to culture the microbial strains, such as Nutrient Broth or Nutrient Agar available from Difco, t, Mi. It will be appreciated that cultivation time may differ depending on the type of culture medium used and the concentration of sugar as a lTlEthl' carbon . {0176} In some aspects, cultivation lasts n 2496 hours. Microbial cells thus obtained are isolated using s, which are well known in the art. es include, but are not limited to, membrane filtration and centrifugal separation. The pH may be adjusted using sodium hydroxide and the like and the culture may be dried using a freeze dryer, until the water content becomes equal to '% or less. Microbial co—cultures may be obtained by propagating each strain as described hereinabove. In some aspects, microbial ustrain cultures may be obtained by propagating two or more of the strains described hereinabove. It will be appreciated that the ial strains may be cultured together when compatible culture conditions can be employed.

Isolated Microbes _ Microbial Strains {0177} es can be distinguished into a genus based on polyphasic taxonomy, which incorporates all available phenotypic and pic data into a consensus classification (Vandamme er a], 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics.

Microbial Rev 1996, 60407438). One accepted genotypic method for defining species is based on overall genomic relatedness, such that strains which share approximately 70% or more dness using DNAuDNA hybridization, with 5°C or less AT", (the difference in the melting temperature between homologous and heterologous hybrids), under standard conditions, are considered to be members of the same species. Thus, populations that share greater than the aforementioned 70% threshold, can be considered to be variants of the same species. Another accepted pic method for defining species is to isolate marker genes of the t disclosure, ce these genes, and align these sequenced genes from multiple isolates or variants. The microbes are reted as belonging to the same species if one or more of the sequenced genes share at least 97% sequence identity. {@178} The 163 or 188 rRNA sequences or ITS sequences are often used for making distinctions between species and strains, in that if one of the aforementioned sequences shares less than a specified % sequence identity from a nce sequence, then the two organisms from which the sequences were ed are said to he of different species or strains. {@179} Thus, one could consider microbes to be of the same species, if they share at least 80%, 85%, 90%, 95%, r.37%, 98%, or 99% sequence ty across the 168 or 188 rRNA sequence, or the lTSl or ITSZ ce, {0180} Further, one could define microbial strains of a species, as those that share at least 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity across the 168 or 188 rRNA sequence, or the US l or ITSZ sequence. {0181} Sequence identifiers of the present disclosure consist of SEQ ID 131031—385. SEQ ID NOszl~50 and 59—385 are bacterial polynucleotide sequences encoding 16S rRNA. SEQ ID NOs:51n58 are fungal polynucleotide sequences encoding ITS ces. {0182} In one embodiment, microbial strains of the present disclosure e those that comprise polynucleotide sequences that share at least 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 8676, 87%, 8876, 89%, 9076, 91%, 92%, 93%, 9476, 95%, 9676, 9"76, 9 °6,99% or 100% sequence identity with any one of SEQ 113 N05: 1, 2,,3 4,5, 6, ,8 9, 10, 11, 12, 13, 14,15,16, 17, 18, 19, 20,21 22, 23, 24, 25, 26, 27, 2s, 39, 3o, 31, :32, 33, 34, 35, 36, 37, 33,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,54, 55, 5, 5,7 58, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355,356, 357, 358, 359, :360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370,: 7,1 372,373, 374, 375, 376, 377, 78, 379,380, 381, 382, 383, 384, and 385 In a further embodiment, microhial strains of the present disclosure include those that comprise polynucleotide sequences that share at least 70%, 75%,80‘76, 81%, 82%, 83%, 84%, 85%, 86//6, 8796, 88%,89‘76, ‘7,6 9 76 93‘76, 94‘76, 95‘76,96%, 97%, 98%,J 99‘76 or 10076 sequence identity with any one of SEQ II) 19031—385, {0183} Comparisons may also be made with 23S rRNA sequences against reference sequences. {17184} Unculturable microbes often cannot be assigned to a definite species in the absence of a phenotype determination, the microbes can be given a candidarus designation within a genus provided their 168 or 18S rRNA sequences or ITS ces ibes to the principles of identity with known species.

} One approach is to observe the bution of a large number of strains of closely d species in sequence space and to identify clusters of strains that are well resolved from other clusters. This approach has been developed by using the concatenated ces of le core —keeping) genes to assess clustering patterns, and has been called rnultilocus sequence analysis (MLSA) or multilocus sequence phylogenetic analysis. MLSA has been used successfully to explore clustering patterns among large numbers of strains assigned to very closely related species by current taxonomic methods, to look at the relationships between small s of strains within a genus, or within a broader taxonomic grouping, and to address specific taxonomic questions. More generally, the method can be used to ask whether bacterial species exist that is, to observe whether large populations of similar strains invariably fall into well~resolved clusters, or whether in some cases there is a genetic uum in which clear separation into clusters is not observed. {@186} In order to more accurately make a determination of genera, a determination of phenotypic traits, such as morphological, biochemical, and physiological characteristics are made for comparison with a reference genus archetype. The colony morphology can include color, shape, pigmentation, production of slime, etc. Features of the cell are described as to shape, size, Gram reaction, extracellular material, presence of endospores, flagella presence and location, motility, and inclusion . Biochemical and physiological features describe growth of the organism at different ranges of temperature, pH, salinity and atmospheric conditions, growth in presence of ent sole carbon and nitrogen sources. One of ry skill in the art would be reasonably apprised as to the phenotypic traits that define the genera of the present disclosure. {9187} In one embodiment, the es taught herein were identified utilizing 168 rKNA gene sequences and ITS sequences It is known in the art that loS rRNA, contains hypervariable regions that can provide species/strain~specific signature sequences useful for bacterial identification, and that ITS sequences can also e species/strain—specific signature ces useful for fungal identification. {0188} Phylogenetic is using the rRNA genes and/or ITS sequences are used to define antially similar" species belonging to common genera. and also to define "substantially similar" strains of a given taxonomic species Furthermore, physiological and/or biochemical properties of the isolates can be utilized to highlight both minor and significant differences n strains that could lead to ad eous behavior in y. {(3189} Compositions of the present disclosure may include combinations of fungal spores and ial spores, fungal spores and bacterial vegetative cells, fungal vegetative cells and bacterial spores, fungal vegetative cells and bacterial vegetative cells. In some embodiments, compositions of the t disclosure comprise bacteria only in the form of spores. In some embodiments, compositions of the present disclosure comprise bacteria only in the form of vegetative cells. In some embodiments, compositions of the present disclosure comprise bacteria in the absence of fungi. In some embodiments, compositions of the present disclosure comprise fungi in the absence of bacteria. In some embodiments, compositions of the present disclosure comprise VBNC bacteria and/or fungi. In some embodiments, compositions of the present disclosure include dormant bacteria and/or fungi. {8190} Bacterial spores may include endospores and akinetes. Fungal spores may include statismospores, ballistospores, autospores, aplanospores, zoospores, mitospores, megaspores, microspores, meiospores, chlamydospores, urediniospores, teliospores, oospores, carpospores, poies, sporangiospores, zygospores, basidiospores, ascospores, and asciospores. {9191} In some embodiments, spores of the ition germinate upon administration to animals of the present disclosure. In some embodiments, spores of the composition germinate only upon administration to animals of the present disclosure.

Microbial Compositions {8192} In some embodiments, the es of the disclosure are combined into microbial compositions. {8193} In some embodiments, the microbial compositions include y feed, such as cereals (:barley, maize, oats, and the like), starches (tapioca and the like); oilseed cakes, and vegetable wastes. In some embodiments, the microbial compositions include Vitamins, minerals, trace elements, emulsifiers, aromatizing products, binders, colorants, odorants, ning agents, and the like. In some embodiments, the microbial compositions include one or more of an ionophore, vaccine; antibiotic; antihelmintic, de; cide; amino acids such as methionine, glycine, and arginine; fish oil; oregano; and biologically active molecules such as enzymes. {0194} In some embodiments, the microbial compositions of the present disclosure are solid.

Where solid compositions are used, it may be desired to include one or more carrier materials including, but not limited to: l earths such as silicas, talc, kaolin, limestone, chalk, clay, dolomite, diatomaceous earth; calcium sulfate; magnesium sulfate; magnesium oxide; zeolites, calcium carbonate; magnesium carbonate; ose; chitosan; c; ns; starch; skim" milk powder; sweetvwhey powder; maltodextrin; lactose; inulm; dextrose; products of vegetable origin such as cereal meals, tree bark meal, wood meal, and ll meal. {(3195} In some embodiments, the microbial compositions of the present disclosure are liquid. In r embodiments, the liquid ses a solvent that may include water or an alcohol or a saline or carbohydrate on, and other animal—safe solvents. In some embodiments, the microbial itions of the present disclosure include binders such as animal—safe polymers, carboxymethylcellulose, , nyl alcohol, and the like. {0196} In some embodiments, the microbial compositions of the present disclosure comprise thickening agents such as silica, clay, natural extracts of seeds or seaweed, synthetic derivatives of cellulose, guar gum, locust bean gum, alginates, and methylcelluloses. In some embodiments, the microbial itions comprise anti~settling agents such as modified starches, polyvinyl alcohol, xanthan gum, and the like. {@197} In some embodiments, the ial compositions of the present disclosure comprise colorants including organic chromophores classified as nitrosoj, nitro; azo, including monoazo, bisazo and, polyazo; acridine, anthraquinone, azine, diphenylmethane, intlamine, indophenol, methine, oxazine, phthalocyanine, thiazine, thiazole, triarylmethane, xanthene. In some embodiments, the microbial compositions of the present disclosure comprise trace nutrients such as salts of iron, ese, boron, copper, cobalt, molybdenum and zinc, In some embodiments, the microbial compositions comprise dyes, both natural and artificial. In some embodiments, the dye is green in color. {@198} In some embodiments, the microbial compositions of the present disclosure comprise an animal-safe de, bacteriocide, or nematicide, {@199} In some embodiments, ial compositions of the present disclosure comprise rides (e.g monosaccharides, disaccharides, trisaccharides, polysaccharides, oligosaccharides, and the like), polymeric saccharides, lipids, polymeric lipids, lipopolysaccharides, proteins, polymeric proteins, lipoproteins, nucleic acids, nucleic acid polymers, , inorganic salts and combinations thereof, In a r embodiment, microbial compositions se polymers of agar, agarose, gelrite, and gellan gum, and the like. In some embodiments, microbial compositions comprise plastic capsules, ons (e.g;, water and oil), membranes, and artificial membranes. In some embodiments, emulsions or linked r solutions may se microbial compositions of the present disclosure. See l-Iarel and Bennett (US Patent 8,460,72632). In one ment, the microbial composition comprises glucose. In one embodiment, formulations of the microbial composition comprise glucose. {8200} In some embodiments, microbial compositions of the present disclosure comprise one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal chelators, and/or dechlorinators, and combinations thereof. In one embodiment, the one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal chelators, and/or dechlorinators are not ally active once the microbial compositions are mixed with food and/or water to be administered, to the fowl. In one embodiment, the one or more oxygen scavengers, denitrifiers, nitrifiers, heavy metal clielators, and/or declilorinators are not chemically active when administered to the fowl. {0201} In some embodiments, microbial compositions of the present disclosure occur in a solid form (eg, dispersed lyophilized spores) or a liquid form (microbes interspersed in a storage medium), In some embodiments, microbial compositions of the present disclosure. are added in dry form to a liquid to form a suspension immediately prior to administration. {0202} In some ments, microbial compositions of the present sure comprise one or more preservatives. The preservatives may be in liquid or gas formulations. The preservatives may be selected from one or more of monosaccliaride, haride, trisaccliaride, polysaccharide, acetic acid, ascorbic acid, calcium ascorbate, erytliorbic acid, iso—ascorbic acid, erythrobic acid, potassium nitrate, sodium ascorbate, sodium rbate, sodium iso—ascoi‘laate, sodium nitrate, sodium nitrite, nitrogen, benzoic acid, calcium sorbate, ethyl lauroyl arginate, methyl—p—hydroxy benzoate, methyl paraben, ium acetate, potassium benzoiate, potassium bisulphite, potassium diacetate, ium lactate, potassium metabisulphite, potassium sorbate, propyl—p—hydroxy benzoate, propyl paraben, sodium acetate, sodium benzoate, sodium bisulphite, sodium nitrite, sodium diacetate, sodium lactate, sodium metabisulphite, sodium salt of methylw~hydroxy c acid, sodium salt of propylupuhydroxy benzoic acid, sodium sulphate, sodium sulfite, sodium dithionite, sulphurous acid, calcium propionate, dimethyl dicarbonate, natamycin, potassium sorbate, potassium bisulfite, potassium metabisulfite, propionic acid, sodium diacetate, sodium propionate, sodium e, sorbic acid, ic acid, ascorbyl palmitate, ascorbyl stearate, ted hydi'o—xyanisole, ted hydroxytoluene (BI-IT), butylated yl anisole (Bl-IA), citric acid, citric acid esters of mono~ and/or diglycerides, L—cysteine, L—cysteine hydrochloride, gum guaiacum, gum guaiac, lecithin, lecithin citrate, yceride e, monoisopropyl citrate, propyl gallate, sodium isulphite, tartaric acid, tertiary butyl hydroquinone, stannous chloride, thiodipropionic acid, dilauryl WO 81203 thiodipropionate, distearyl tliiodipropionate, etlioxyquin, sulfur e, formic acid, or tocopherol(s). {(1203} In some embodiments, microbial compositions of the present disclosure include bacterial and/or fungal cells in spore form, tive cell form, dormant cell form, and/or lysed form. In one embodiment, the lysed cell form acts as a mycotoxin binder, ag. mycotoxins binding to dead, cells. {0204} In some embodiments, the microbial compositions are shelf stable in a refrigerator (35" 40°F) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14,15,16,17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 5‘7, 58, 59, or 60 days. In some embodiments, the microbial itions are shelf stable in a refrigerator (355—4001?) for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21,22, 23,24, 25,26, 27, 28, 29, 3o, 31, 32, 33, 34, 35,36, 37, 38, 39, 40,41, 42, 43, 44, 45,46, 47, 48, 49, 5o, 51, 52, 53,54, 55, 56, 57, 58, 59, or 60 weeks. {(1205} In some embodiments, the microbial compositions are shelf stable at room temperature (68—72017) or between 504770117 for a period of at least 1, 2, 3, 4, .5, 6, 7, 8, 9, 10, ll, 12, 15, 14, , 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30,31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 4o, 47, 48, 49, 50, 51, 52, 53, 54, 55, 5o, 57, 58 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at room temperature (68-72017) or between 50—77? for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 3.3, 34, 35, 36, 37, 38, .39, 40,41, 42, 43, 44, 45 46, 4'7, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. {0206} In some embodiments, the microbial compositions are shelf stable at —23—35°’F for a period of at least 1, 2, 3, 4, 5 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1'7, 18, 19, 2o, 21, 22, 23, 2 , , 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45 46,47, 48, 49, 5o, 51, 52, 53, 54, 55, 56, 7, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stable at ~23—350F for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 21,22,23,24,25,26,27,28,29, 30, 31, 32,33, 34, 35, 36, 37,38, 39,40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 weeks. {(1207} In some embodiments, the microbial compositions are shelf stable at 77—10(‘PF for a period ofat least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2o, 21, 22, 2 ,24, WO 81203 , 26,27, 23, 29, 3o, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41,42, 43, 44, 45, 46,47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. In some embodiments, the microbial compositions are shelf stab1e at 77400013 for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 2o, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 32, 33, 34, 35, 36, 37, 38, 39, 4a, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 7, 58, 59, or 60 weeks, {02081 In some embodiments, the microbial compositions are shelf stable at 3OF for a period ofat least 1, 2, 3, 4, 5, 6, 7, 8, 9,10,11,12,13,14,15,l6,17,l8,l9, 20, 21, 22, 23, 24, , 26, 27, 28, 29, 3o, 31, 32, 33, 34, 35, 36, 37, 33, 39, 40, 41,42, 43, 44, 45, 46,47, 48, 49, 5o, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 days. in some embodiments, the microbial compositions are she1f stable at 101—21301? for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, l3, 14, 15, l6, 1'7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 36, 37, 38, 39, 40, 41, 42, 43, 44, 4:5, 46, 47, 48, 49, 50, 51, 52, 53, :54, 55, 56, 57, 5:3, 59, or 60 weeks, {(1209} In some embodiments, the microbial compositions of the present disclosure are shelf stable at refrigeration temperatures 017), at room temperature (68—72013), between 50—77017, between —23—35°F, between 7031000117, or between 101—21301? for a period of about 1 to 100, about 1 to 95, about 1 to 90, about 1 to 85, about 1 to 80, about 1 to 75, about 1 to 70, about 1 to 65, about 1 to 60, about 1 to 55, about 1 to 50, about 1 to 45, about 1 to 40, about 1 to 35, about 1 to 30, about 1 to 25, about 1 to 20, about 1 to 15, about 1 to 10, about 1 to 5, about 5 to 100, about 5 to 95, about 5 to 90, about 5 to 85, about 5 to 80, about 5 to 75, about 5 to 70, about 5 to 65, about 5 to 60, about 5 to 55, about 5 to 50, about 5 to 45, about 5 to 40, about 5 to 35, about 5 to 30, about 5 to 25, about 5 to 20, about 5 to 15, about 5 to 10, about 10 to 100, about 10 to 95, about 10 to 90, about 10 to 85, about 10 to 80, about 10 to 75, about 10 to 70, about 10 to 65, about 10 to 60, about 10 to 55, about 10 to 50, about 10 to 45, about 10 to 40, about 10 to 35, about 10 to 30, about 10 to 25, about 10 to 20, about 10 to 15, about 15 to 100, about 15 to 95, about 15 to 90, about 15 to 85, about 15 to 80, about 15 to 75, about 15 to 70, about 15 to 65, about 15 to 60, about 15 to 55, about 15 to 50, about 15 to 45, about 15 to 40, about 15 to 35, about 15 to 30, about 15 to 25, about 15 to 20, about 20 to 100, about 20 to 95, about 20 to 90, about 20 to 85, about 20 to 80, about 20 to 75, about 20 to 70, about 20 to 65, about 20 to 60, about 20 to 55, about 21.1 to 50, about 20 to 45, about 20 to 40, about 20 to 35, about 20 to 30, about 20 to 25, about 25 to 100, about 25 to 95, about 25 to 90, about 25 to 85, about 25 to 80, about 25 to 75, about 25 to 70, about 25 to 65, about 25 to 60, about 25 to 55, about 25 to 50, about 25 to 45, about 25 to 40, about 25 to 35, about 25 to 30, about 30 to 100, about 30 to 95, about 30 to 90, about 30 to 85, about 30 to 80, about 30 to 75, about 30 to 70, about 30 to 65, about 30 to 60, about 30 to 55, about 30 to 50, about 30 to 45, about 30 to 40, about 30 to 35, about 35 to 100, about 35 to 95, about 35 to 90, about 35 to 85, about 35 to 80, about 35 to 75, about 35 to '70, about 35 to 65, about 35 to 60, about 35 to 55, about 35 to 50, about 35 to 45, about 35 to 40, about 40 to 100, about 40 to 95, about 4(‘1 to 90, about 40 to 85, about 40 to 80, about 40 to '75, about 40 to 70, about 40 to 65, about 40 to 60, about 4(‘1 to 55, about 40 to 50, about 40 to 45, about 45 to 100, about 45 to 95, about 45 to 90, about 45 to 85, about 45 to 80, about 45 to '75, about 45 to 70, about 45 to 65, about 45 to 60, about 45 to 55, about 45 to 50, about 50 to 100, about 50 to 95, about 50 to 90, about 50 to 85, about 50 to 80, about 50 to 75, about 50 to 70, about 50 to 65, about 50 to 60, about 50 to 55, about 55 to 100, about 55 to 95, about 55 to 90, about 55 to 85, about 55 to 80, about 55 to 75, about 55 to 70, about 55 to 65, about 55 to 60, about 60 to 100, about 60 to 95, about 60 to 90, about 60 to 85, about 60 to 80, about 60 to 75, about 60 to 70, about 60 to 65, about 65 to 100, about 65 to 95, about 65 to 90, about 65 to 85, about 65 to 80, about 65 to 75, about 65 to 70, about 70 to 100, about 70 to 95, about 70 to 90, about 70 to 85, about 70 to 80, about 70 to 75, about 75 to 100, about 75 to 95, about 75 to 90, about 75 to 85, about 75 to 80, about 80 to 100, about 80 to 95, about 80 to 90, about 80 to 85, about 85 to 100, about 85 to 95, about 85 to 90, about 90 to 100, about 90 to 95, or 95 to 100 weeks {(1210} In some embodiments, the mierobia1 compositions of the present disclosure are shelf stable at refrigeration temperatures (35—40017), at room ature (68—72017), between 50—770F, between —23—35°F, between 704000197, or between 1O1~2130F for a period of 1 to 100, 1 to 95, 1 to 9D, 1 to 85, 1 to 80, 1 to 75, 1 to 70, 1 to 65, 1 to 60, 1 to 55, 1 to 50, 1 to 45, 1 to 40, 1 to 35, 1 to 30, 1 to 25, 1 to 20, 1 to 15, 1 to 10, 1 to 5, 5 to 100, 5 to 95, 5 to 90, 5 to 85, 5 to 80, 5 to 75, 5 to 70, 5 to 65, 5 to 60, 5 to 55, 5 to 50, 5 to 45, 5 to 40, 5 to 35, 5 to 30, 5 to 25, 5 to 20, 5 to 15, 5 to 10, 10 to 100, 10 to 95, 10 to 90, 10 to 85, 10 to 80,10'to 75, 10 to 70, 10 to 65, 10 to 60, 10 to 55, 10 to 50,10'to 45,10 to 40, 10 to 35, 10 to 30, 10 to 25, 10 to 20, 10 to 15, 15 to 100, 15 to 95, 15 to 90, 15 to 85, 15 to 80,15 to 75, 15 to 70,15to 65, 15 to 60, 15 to 55, 15 to 50, 15 to 45, 15 to 40, 15 to 35 15 to 30, 15 to 25, 15 to 20, 20 to 100, 20 to 95, 20 to 90, 20 to 85, 20 to 80, 20 to 75, 20 to 70, 20 to 65, 20 to 60, 20 to 55, 20 to 50, 20 to 45, 20 to 40, 20 to , 20 to 30, 20 to 25, 25 to 100, 25 to 95, 25 to 90, 25 to 85, 25 to 80, 25 to 75, 2510 70, 25 to WO 81203 65, 25 to 60, 25 to 55, 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 100, 30 to 95, 30 to 90, 3D to 85, 30 to 80, 30 to 75, 30 to 70, 30 to 65, 30 to 60, 30 to 55, 30 to 50, 3D to 45, 30 to 40, 30 U) 35, 35 to 100, 35 to 95,35 to 90, 35 to 85, 35 to 80, 35 to 75, 35 U) 70, 35 to 65, 35 to 60, 35 to 55, 35 to 50, 35 to 45, 35 to 46, 40 to 100, 40 to 95, 40 £0 90, 46 to 85, 40 to 80, 40 to 75, 40 U) 70, 40 to 65, 40 to 66, 40 to 55, 40 to 50, 40 to 45, 45 to 100, 45 10 95, 45 to 90, 45 to 85, 45 to 80, 45 to 75, 45 to 70, 45 to 65, 45 to 60, 45 to 55, 45 to 50, 50 to 100, 50 to 95, 50 to 90, 50 U) 85, 50 to 80, 50 to 75, 50 to 70, 50 to 65, 50 to 60, so to 55, 55 to 100, 55 to 95, 55 to 90, 55 to 85, 55 to 80, 55 to 75, 55 to 70, 55 to 65, 55 to 60, 60 to 100, 60 to 95, 60 to 90, 60 to 85, 60 U) 80, 60 to 75, 60 to 70, 60 to 65, 65 to 100, 65 to 95, 65 to 90, 65 U) 85, 65 to 80, 65 to 75, 65 to 70, 70 to 100, 701:0 95, ‘70 to 90, 70 to 85, 70 to 80, 70 to 75, 75 to 100, 75 to 95, 75 to 90, 75 to 85, 75 to 80, 80 to 100, 80 to 95, 80 to 90, 80 to 85, 85 to 100, 85 to 95, 85 to 90, 90 to 100, 90 to 95, or 95 to 100 weeks, {(1211} In, some embodiments, the microbial compositions of the t disclosure are shelf stable at refrigeration temperatures (35-40013), at room temperature (68—72013), between 50—77017, between —23—35°F, between 70400013, or between 101—2130]7 for a period of about 1 to 36, about 1 to 34, about 1 to 32, about 1 to 30, about 1 to 28, about 1 to 26, about 1 to 24, about 1 to 22, about 1 to 20, about 1 to 18, about 1 to 16, about 1 to 14, about 1 to 12, about 1 to 10, about 1 to 8, about 1 to 6, about 1 one 4, about 1 to 2, about 4 to 36, about 4 to 34, about 4 to 32, about 4 to , about 4 to 28, about 4 to 26, about 4 to 24, about 4 to 22, about 4 to 20, about 4 to 18, about 4 to 16, about 4 to 14, about 4 to 12, about 4 to 10, about 4 to 8, about 4 to 6, about 6 to 36, about 6 to 34, about 6 to 32, about 6 to 30, about 6 to 28, about 6 to 26, about 6 to 24, about 6 to 22, about 6 to 20, about 6 to 18, about 6 to 16, about 6 to 14, about 6 to 12, about 6 to 10, about 6 to 8, about 8 to 36, about 8 to 34, about 8 to 32, about 8 to 30, about 8 to 28, about 8 to 26, about 8 to 24, about 8 to 22, about 8 to 20, about 8 to 18, about 8 to 16, about 8 to 14, about 8 to 12, about 8 to 10, about 10 to 36, about 10 to 34, about 10 to 32, about 10 to 30, about 10 to 28, about 10 to 26, about 10 to 24, about 10 to 22, about 10 to 20, about 10 to 18, about 10 to 16, about 10 to 14, about 10 to 12, about 12 to 36, about 12 to 34, about 12 to 32, about 12 to 30, about 12 to 28, about 12 to 26, about 12 to 24, about 12 to 22, about 12 to 20, about 12 to 18, about 12 to 16, about 12 to 14, about 14 to 36, about 14 to 34, about 14 to 32, about 14 to 30, about 14 to 28, about 14 to 26, about 14 to 24, about 14 to 22, about 14 to 20, about 14 to 18, about 14 to 16, about 16 to 36, about 16 to 34, about 16 to 32, about 16 to 30, about 16 to 28, about 16 to 26, about 16 to 24, about 16 to 22, about 16 to 20, about 16 to 18, about 18 to 36, about 18 to 34, about 18 to 32, about 18 to 30, about 18 to 28, about 18 to 26, about 18 to 24, about 18 to 22, about 18 to 20, about 20 to 36, about 20 to 34, about 21.1 to 32, about 20 to 30, about 20 to 28, about 21.1 to 26, about 20 to 24, about 20 to 22, about 22 to 36, about 22 to 34, about 22 to 32, about 22 to 30, about 22 to 28, about 22 to 26, about 22 to 24, about 24 to 36 about 24 to 34, about 24 to 32, about 24 to 30, about 24 to 28, about 24 to 26, about 26 to 36, about 26 to 34, about 26 to 32, about 26 to 30, about 26 to 28, about 28 to 36, about 28 to 34, about 28 to 32, about 28 to 30, about 30 to 36, about 30 to 34, about 30 to 32, about 32 to 36, about 32 to 34, or about 34 to 36 months. {(1212} In some embodiments, the microbial compositions of the t sure are shelf stable at eration temperatures (3540017), at room temperature (6872017), between 50'77017, between "23435017, between 70—100013, or between 101—21301,T for a period of 1 to 36 1 to 34 1 to 321 to301to 281 to 26 1 to 24 1 to 22 1 to 20 1 to 18 1 to 16 1 to 14- 1 to 12 1 to 10 1 to 8 1 to 6 1 one 4- 1 to 2 4 to 36 4 to 34 4 to 32 4 to 30 4 to 28 4- to 26 4 to 24 4 to 22 4 to 20 4- to 18 4 to 16 4to 14 4 to 12 4 to 10 4 to 8 4 to 6 6 to 36 6 to 34 6 to 32 6to 30 6 to 28 6 to 26 6 to 24 6 to 226to206to186t0166t0146tolZ6t0106t08 8t0368to348to328to308t028 Ste 26 8 to 24 8 to 22 8 to 20 8 to 18 8 to 16 8 to 14 8 to 12 8 to 10 10 to 36 10 to 34 10 to 3210to 3010‘to2810t02610to 2410t02210to2010t01810t01610tol410t01212to36l2to 3412 to 32 12 to 30 12to 2812to 26 12 to 24 12 to 2212to 2012to1812to1612to1414to 3614to 3414to 3214to 3014to 28 14 to 26 14 to 2414to 22 l4to 2014t01814t01616to 3616 to 34 16 to 32 16 to 3G 16 to 28 16 to 26 16 to 2416 to 22 16 to 2016to1818 to 36 18 to 3418 to 32 18 to 30 18 to 2818 to 26 18 to 24 18 to o 20 20 to 36 20 to 34 2D to 32 20 to 20 to 28 2D to 26 20 to 24 20 to 22 22 to 36 22 to 34 22 to 32 22 to 30 22 to 28 22 to 26 22 to 24 24 to 36 24 to 34 24 to 32 24 to 30 24 to 28 24 to 26 26 to 36 26 to 34 26 to 32 26 to 3D 26 to 28 28 to 36 28 to 34 28 to 32 28 to 30 30 to 36 30 to 34 30 to 32 32 to 36 32 to 34, or about 34 to {02131 In some embodiments, the microbial compositions of the present disclosure are shelf stable at any of the disclosed temperatures and/or temperature ranges and spans of time at a nflauveluunkfiuiofatleast1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,2L 22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47, 48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73, 74, 75, '76, 77, 78, '79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 9i, 92, 93, 94, 95, 96, 97, or Encapsulation Compositions {0214} In some embodiments, the microbes or microbial compositions of the disclosure are encapsulated in an encapsulating composition. An encapsulating composition protects the microbes from external stressors prior to entering the gastrointestinal tract of poultry. In some embodiments, external stressors include thermal and physical ors associated with pelleting and extrusion. In some embodiments, external stressors include als t in the compositions to which Encapsulating itions further create an environment that may be cial to the microbes, such as minimizing the oxidative es of an aerobic environment on anaerobic microbes, preserving the viability of the microbes wherein vegetative cells or spores form during the pelleting extrusion process, etc. See Kalsta er a]. (US 662A), Ford (US 5,733,568A), and Mosbach and Nilsson (US 4,647,536A) for ulation itions of microbes, and methods of encapsulating microbes. {@215} In one embodiment, the compositions of the present disclosure exhibit a thermal tolerance, which is used interchangeably with heat tolerance and heat resistance. In one embodiment, thermal tolerant compositions of the present sure are tolerant of the high temperatures associated with feed manufacturing, mixing of feed and compositions of the present sure, storage in high heat environments, etc. In one embodiment, thermal tolerant compositions of the present disclosure are resistant to heat—killing and denaturation of the cell wall components and the intracellular environment. {021611n one embodiments, the encapsulation is a reservoir-type encapsulation. In one embodiment, the encapsulation is a matrix—type encapsulation In one embodiment, the encapsulation is a coated matrix—type encapsulation. Burgain er a]. (2011. J, Food Eng 1 04:11-67" 483) discloses numerous encapsulation embodiments and techniques, all of which are incorporated by reference. {@217} In some ments, the compositions of the present disclosure are encapsulated in one or more of the following: gellan gum, xanthan gum, K—Carrageenan, cellulose acetate phthalate, chitosan, , milk fat, whey protein, inate, raftilose, raftiline, pectin, saccharide, WO 81203 glucose, maltodextrin, gum arabic, guar, seed flour, alginate, dextrins, dextrans, celluloase, gelatin, gelatin, albumin, casein, gluten, acacia gum, tragacanth, wax, paraffin, stearic acid, glycerides, and erides. In some ments, the itions of the present disclosure are encapsulated by one or more of a polymer, carbohydrate, sugar, plastic, glass, polysaccharide, lipid, wax, oil, fatty acid, or glyceride. In one embodiment, the microbial composition is encapsulated by a glucose. In one embodiment, the microbial composition is encapsulated by a glucosencontaining composition. In one embodiment, formulations of the microbial ition comprise a glucose encapsulant, In one embodiment, formulations of the microbial composition comprise a glucosenencapsulated composition. {0218} In some embodiments, the encapsulation of the compositions of the present disclosure is carried out by an extrusion, emulsification, coating, agglomeration, lyophilization, " drying, or spray—drying. {0219} In one emhodiment, the encapsulating composition comprises inicrocapsules having a multiplicity of liquid cores encapsulated in a solid shell i‘llil'tfil‘lf l. For purposes of the disclosure, a "rmtltiplicity" of cores is define; as two or irmre. {0220} A first categoly of useful fusible shell materials is that of normally solid, fats, including fats which are already of suitable hardness and animal or vegetable fats and oils which are hydrogenated until their melting points are sufficiently high to serve the purposes of the present disclosure. Depending on the desired process and storage temperatures and the ic al selected, a particular fat can be either a normally solid or normally liquid material. The terms "normally solid" and lly liquid" as used herein refer to the state of a material at desired temperatures for storing the resulting apsules, Since fats and hydrogenated oils do not, strictly speaking, have melting points, the term "melting point" is used herein to be the minimum temperature at which the fusible material becomes sufficiently softened or liquid to he sfully emulsified and spray cooled, thus roughly corresponding to the maximum temperature at which the shell material has sufficient integrity to prevent release of" the choline cores. "Melting point" is similarly defined herein for other materials which do not have a sharp melting point. {0221} Specific examples of fats and oils useful herein i some of which require ing) are as follows: animal oils and fats, such as beef tallow, mutton tallow, lamb tallow, lard or pork fat, fish oil, and sperm oil, vegetable oils, such as canola oil, seed oil, peanut oil, corn oil, olive oil, soybean oil, sunflower oil, safflower oil, coconut oil, palm oil, linseed oil, tung oil, and castor oil; fatty acid nionoglycerides and diglycerides; free fatty acids, such as stearic acid, palmitic acid, and oleic acid; and mixtures thereof. The above listing of oils and fats is not meant to be exhaustive, but only exemplary. {0222} Specific examples of fatty acids include linoleic acid, oleic acid, dihomomy—linolenic acid, arachidonic acid, docosatetraenoic acid, vaccenic acid, ic acid, mead acid, erucic acid, gondoic acid, elaidic acid, oleic acid, palitoleic acid, stearidonic acid, eicosapentaenoic acid, valeric acid, caproic acid, enanthic acid, caprylic acid, pelargomc acid, capric acid, undecylic acid, laui'ic acid, tridecylic acid, myristic acid, pentadecylic acid, palmitic acid, margaric acid, stearic acid, nonadecyclic acid, arachidic acid, heneicosylic acid, behenic acid, tricosylic acid, lignoceric acid, pentacosylic acid, cerotic acid, osylic acid, montanic acid, nonacosylic acid, ic acid, henatriacontylic acid, lacceroic acid, psyllic acid, geddic acid, ceroplastic acid, hexatriacontylic acid, heptatriacontanoic acid, and octatriacontanoic acid. {0223} Another category of fusible materials useful as encapsulating shell materials is that of waxes. Representative waxes contemplated for use herein are as follows: animal waxes, such as beeswax, lanolin, shell wax, and Chinese insect wax; vegetable waxes, such as carnauba, candelilla, béyberry, and sugar cane; mineral waxes, such as paraffin, microcrystalline petroleum, ozocerite, n, and montan; tic waxes, such as low molecular weight polyolefin (eg, CARBOWAX), and polyol ether-esters (e.g sorbitol); Fiscl'ier—Tropsch process synthetic waxes; and mixtures f. Water—soluble waxes, such as CARBOWAX and ol, are not contemplated herein if the core is aqueous. {0224} Still other e compounds useful herein are fusible natural resins, such as rosin, balsam, shellac, and mixtures thereof. {0225} Various adjunct materials are contemplated for incorporation in fusible materials according to the present disclosure. For example, antioxidants, light stabilizers, dyes and lakes, flavors, essential oils, anti—calcing agents, fillers, pH izers, sugars (monosaccharides, disaccharides, ccharides, and polysaccharides) and the like can be incorporated in the fusible material in amounts which do not diminish its utility for the present disclosure. {0226} The core material contemplated herein constitutes from about 0.1% to about 50%, about 1% to about 35%. or about 5% to about 30% by weight of the microcapsules. In some embodiments, the core material contemplated herein constitutes no more than about 30% by weight of the microcapsules. In some embodiments, the core material plated herein constitutes about 5% by weight of the microcapsules. The core material is contemplated as either a liquid or solid at contemplated storage temperatures of the microcapsules. 311227} The cores may include other additives well—known in the pharmaceutical art, including edible sugars, such as sucrose, glucose, maltose, fructose, e, cellobiose, monosaccharides, disaccharides, charides, and polysaccharides, and es thereof; cial sweeteners, such as aspartame, saccharin, cyclamate salts, and mixtures thereof; edible acids, such as acetic acid ar), citric acid, ascorbic acid, tartaric acid, and mixtures thereof; edible starches, such as corn starch; hydrolyzed vegetable protein; water—soluble vitamins, such as Vitamin C; water~ soluble medicaments; water-soluble. ional materials, such as ferrous sulfate; flavors; salts; monosodium ate; antimicrobial agents, such as sorbic acid; antimycotic agents, such as potassium sorbate, sorbic acid, sodium benzoate, and benzoic acid; food grade pigments and dyes; and mixtures thereof, Other ially useful supplemental core materials will be apparent to those of ordinary skill in the art. {(1228} Emulsifying agents may be employed to assist in the formation of stable emulsions.

Representative emulsifying agents include glyceiyl monost aarate, polysorbate esters, ethoxylated mono— and diglycerides, and mixtures thereof {(1229} For ease of processing, and particularly to enable the successful formation of a reasonably stable emulsion, the ities of the core material and the shell material should be similar at the temperature at which the emulsion is formed In particular, the ratio of the viscosity of the shell to the Viscosity of the core, expressed in centipoise or comparable units, and both measured at the temperature of the emulsion, should be from about 22:1 to about 1:1, desirably from about 8:1 to about 1:1, and ably from about 3:1 to about 1:1. A ratio of 1:1 would be ideal, but a viscosity ratio within the recited ranges is useful. {(1230} Encapsulating itions are not d to apsule compositions as disclosed above. In some embodiments encapsulating compositions encapsulate the microbial compositions in an adhesive polymer that can be natural or synthetic without toxic ef"ect. in some embodiments, the encapsulating composition may be a matrix selected from sugar matrix, gelatin matrix, polymer matrix, silica matrix, starch matrix, foam matrix, etc. In some embodiments, the encapsulating composition may be selected from polyvinyl acetates; polyvinyl e copolymers; ethylene vinyl acetate (EVA) copolymers, nyl alcohols; polyvinyl alcohol ccpclyrners; celluloses, including ethylcelluloses, methylcelluloses, hydrcxymethylcelluloses, hydroxyprcpylcelluloses and carboxymethylcellulose, polyvinylpyrolidones, polysaccharides, ing starch, modified starch, dextrins, maltodextrins, alginate and chitosans; monosaccharides; fats; fatty acids, ing oils; ns, including gelatin and, zeins; gum arabics; shellacs; Vinylidene chloride and Vinylidene chloride copolymers, calcium lignosulfonates, acrylic copolymers; polyvinylacrylates; polyethylene oxide; acrylamide polymers and copolymers; polyhydroxyethyl acrylate, methylacrylamide monomers; and polychloroprene. {0231} In some embodiments, the encapsulating shell of the present disclosure can be up to 10mm 20am, 30pm, 40nm, 50nm, 60nm, 70_unr, 80pm, 90am, lt‘itium, llOum, lZGum, lSOum, 140nm, lSOum, l60um, l70nm, 180nm, 190nm, 200nm, 210nm, 220nm, 230nm, 240nm, 250nm, 260nm, 270nm, 280nm, 290nm, 300nm, 310nm, 320nm, 330nm, 34-0nm, 350nm, 360nm, 370nm, 380nm, 390nm, 400nm, 410nm, 420nm, 430nm, 440nm, 450nm, 460nm, 4’70nm, 480nm, 490nm, 500nm, 510nm, 520nm, 530nm, 540nm, 550nm, 560nm, 570nm, 580nm, 590nm, 600nm, 610nm, 620nm, 630nm, 640nm, 650nm, 660nm, 670nm, 680nm, 690nm, 700nm, 710nm, 720nm, 730nm, 740nm, 750nm, 760nm, 770nm, 780nm, 790nm, 800nm, 810nm, 820nm, 830nm, 840nm, 850nm, 860nm, 870nm, 880nm, 890nm, 900nm, 910nm, 920nm, 930mm, 940nm, 950nm, 960nm, 970nm, 980nm, 990nm, lOOOum, lOlOum, lOZOum, 1030mm, lO40gim, lOSOttm, 1060mm 1070mm, l080um, lOQOum, llOOum, , 1120mm, ll30um, ll40um, , lléOum, ll'70um, 1180mm, ll90gim, lZOOttm, lZlOttm, lZZOum, 1230mm, 1240gim, 1250mm, 1260mm 1270mm, l280um, 12.90pm, 1300mm, lLllOum, 1320mm, , l340um, 1350mm, , 1370un't, 1380mm, 1390gim, 1400mm, l4lOul’1’l, l420um, 1430mm, 1440gim, 1450mm, l460]..t1’1’1, , l480um, l490um, lSOOum, lSlOum, lSZGttm, 1530mm 1540uni, lfiSOuni, 1560un1, n, lSSOum, , 1600mm, lélOum, léZOurn, 1630um, 1640um, léSOum, 1660mm, 1670th, 1680mm 1690uni, l700un1, l7lOun1, l720tim, l730urn, l'740uni, l750uni, l760un1, n, l780um, l790um, lSOOum, 1810mm, lSZOurn, lSSOum, 1840mm lSSOum, 1860mm, 1870mm 1880mm 1890uni, lQOOuni, i, 1920tim, 1930mm 1940uni, lQSOum, 1960un1, l970urn, l980um, l990um, 2000mm, 2010mm, 2020urn, 2030mm, 2040tim, , 2060mm 2070tim, 2080mm 2090uni, ZlOOum, 21 lOuni, , 2130_unr, 2140un1, ZlSOuni, 2160um, 21’70urn, 2180mm, 2190um, 22(‘i0um, ZZlGum, 2220um, 2230um, 2240mm, 2250mm, , 2270um, 2280um, 2290um, 2300um, 2310um, 2320um, 2330um, 2340uni, 2350um, 2360um, , 2380um, 2390mm, 2400mm, 2410mm, 2420um, 2430um, 2440um, 245t‘ium, 246t‘ium, 2 70pm, 2480um, 2490um, , ZSIOum, 2520um, 2530um, 2540um, 2550um, 2560um, 2570um, 2580um, 2590um, 26(‘it‘ium, Zolt‘ium, 2620um, , 2640um, um, 266t‘ium, 2670um, 2680um, , 2700um, 2710um, 2720um, 2730um, 2740um, 2750um 2760um, 2770um, 2780um, 2790um, ‘ium, 281t‘ium, 2820um, 2830um, 2840um, 285t‘ium, 286t‘ium, 2870um, 2880um, , 2900um, 2910um, 2920um, 2930um, 2940um, 295t‘ium, 2960um, 2970um, 2980um, 2990um, or 3000um thiek.

Animal Feed {0232} In some embodiments, compositions of the present disclosure are mixed with animal feed. In some embodiments, animal feed may be t in various forms such as pellets, capsules, granulated, powdered, mash, liquid, or seminliquid. {@233} In some embodiments, compositions of the present disclosure are mixed, into the premix or mash at the feed mill, alone as a standalone premix, and/0r alongside other feed ves such as MONENSIN, vitamins, etc. In one embodiment, the compositions of the t disclosure are mixed into or onto the feed at the feed mill. In another embodiment, compositions of the present disclosure are mixed into the feed, itself. {0234} In some embodiments, feed of the present disclosure may be supplemented with water, premix or premixes, forage, fodder, beans (cg, whole, cracked, or ground), grains (eg, whole, cracked, or ground), bean— or based oils, beans or grain—based meals, bean~ 0r grain—based haylage or silage, bean— or grain—based syrups, fatty acids, sugar alcohols (eg, polyhydric alcohols), commercially available formula. feeds, oyster shells and those of other bivalves, and es thereof. {0235} In some embodiments, forage encompasses hay, haylage, and silage. In some embodiments, hays include. grass hays (rag, sudangrass, orehardgrass, or the like), alfalfa hay, and clover hay. In some embodiments, haylages include grass haylages, sorghum e, and a haylage In some embodiments, silages e maize, oat, wheat, alfalfa, clover, and the like. {0236} In some embodiments, premix or premises may be utilized in the feed. Premixes may comprise microuingredients such as vitamins, minerals, amino acids, chemical preservatives; pharmaceutical compositions such as otics and other medicaments; fermentation products, and other ingredients. in some embodiments, premixes are blended into the feed. {9237} In some embodiments, the feed, may include feed concentrates such as soybean hulls, soybean oils, sugar beet pulp, molasses, high protein soybean meal, ground, corn, shelled corn, wheat midds, distiller grain, seed hulls, and grease. See Anderson at al. (US, Patent 3,484,243), i er al. (US. Patent 6,090,416), Axelrod er a]. (US. Publication USZGJ6012’7530A1), and Katsumi er a]. (US. Patent 5,741,508) for animal feed and animal feed ments capable of use in the present compositions and methods. {9238} In some embodiments, feed occurs as a compound, which includes, in a mixed composition capable of meeting the basic dietary needs, the feed itself, vitamins, minerals, amino acids, and other necessary components. Compound feed may further comprise premixes. {0239} In some embodiments, microbial compositions of the present disclosure may be mixed with animal feed, premix, and/or compound feed. dual ents of the animal feed may be mixed with the microbial compositions prior to feeding to poultry. The microbial compositions of the present disclosure may be applied into or on a premix, into or on a feed, and/or into or on a compound feed.

Administration of Microbial Compositions {(3240} In some embodiments, the microbial itions of the present disclosure are administered to y Via the oral route. in some ments the microbial compositions are stered Via a direct injection route into the gastrointestinal tract. In further embodiments, the direct injection administration delivers the microbial compositions directly to one or more of the crop, gizzard, cecum, small intestine, and large ine. and provide a detailed anatomical View of the gastrointestinal tract of a chicken In some embodiments, the ial compositions of the present disclosure are administered to animals through the cloaca, In further embodiments, cloacal administration is in the form of an inserted suppository. {11241} In some embodiments, the microbial compositions are administered through drinking water, spraying on litter in which the animal is in contact with, mixing with medications or vaccines, and gavage. In some embodiments, the microbial compositions are sprayed directly on the animal, wherein the animal ingests the composition having been sprayed on the animal. In some embodiments, the microbial compositions are sprayed on and/or sprayed in feed, and the feed is administered to the animal. In further embodiments, the animal ingests the composition through the preening of feathers that have come into contact with the sprayed composition. {02421 In some embodiments, the microbial compositions of the t disclosure are administered to poultry on day 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 post—hatching. In some embodiments, the microbial compositions are administered to the exterior surface of an egg as a liquid, seminliquid, or solid on day 22, 21, 2(1, l9, 18, 17, 16, 15, 14-, 13, 12,. ,111, 9, 8, 7, 6,51-, 1-1, 3, 2, 1, or 0 pro—hatching In some embodiments, the ial compositions of the present disclosure are administered to poultry in multiple dosing sessions in week(s) 2, '3, 4, 56,7 8, 9, 10, 12, 1'3, 14, 15, 16, 17, 18, 19, 211, 21, 22, 23, 24, 25, 26, 27, 28, 29, and/or 311 week(s) postmhatching. In some embodiments, the microbial itions are administed immediately after hatching. In, some embodiments, the microbial compositions are administered into theeeg53, (e.3,5 tion) by itself or administered along with other products such as vaccines 1 In, some embodiments, the microbial composition is stered in a. dose comprise a total of, or at least, 11111, 21111, 3n11, 4inl, 37,1111 61ml, 7ml, 8ml, 9ml, 10ml, llinl, 121111, 131111, 14ml, 15ml, l6ml, 17ml, 18ml, 19ml, 20ml, 21ml, 22ml, 23ml, 24ml, 233,1111 26n11,27ml, 28ml, 29ml, 30ml, 31ml, 32ml, 33ml, 34ml, 35ml, , , 38ml, 39ml, 40ml, 41m, 42ml, 43ml, 44ml, 45ml, 46ml, 47ml, 48ml, 49ml, 50ml, 60ml, 70ml, 80ml, 90ml, 100ml, 200ml, 300ml, 400ml, 500ml, 600ml, 700ml, 800ml, 900ml, or l. {112441 In some ments the microbial composition is administered in a dose comprising a total of, or t 1018 1017,1016, 10", in", 10", 1012, 10", 1010, 109, 108, 107, 106, 105, 10", ", or 10‘ microbial cells. {112451 In some embodiments, the microbial compositions are mixed with feed, and the administration occurs through the ingestion of the microbial compositions along with the feed. In some embodiments, the dose of the microbial COFDpOSlthl’I is administered such that there exists 102 to 1012, 103 to 10", 104 to 10", 105 to 10", 106 to it)", 10" to in", 108 to 1012, 109 to 1012, ", 1011mm", 102w10",103mm",104t010",105to10", 106t010",107t010", 108 to 10", 10% 10", 1010 to 10", 102 to 10", 103 to 101", 1041:0109}, 105m 10"", 106 to 101", 107 to 101", 108m to", 109m 10"", 102 to 109, 103 to 109, 104 to 109, 105 to 109, 10" to 109, 107 to 109, 108 to 109, 102m 108, 10% 103, 104 to 103, 105 to 103, 10" to 10", 107 to 108, 102m 10", 103 to 107, 10% 10'", 105 to 107, 106 to 10"", 1021:0106, 103 to 106, 104 to 10", 105 to 106,102t0 105, 103 to 105, 104 to 105, 102 to 104, 103m 104, 102 to 103, 10", 10", 10"), 109, 10", 107, 10", 105, 104, 103, or 102 total microbial cells per gram or milliliter of the composition. {@246} In some embodiments, the administered dose of the microbial composition comprises 102 to 1013, 103 to 1018, 10% 1013, 105 to 1013, 106 to 1018, 10% 1018, 10% 1013, 109m 1013, 10mm ", IOHto 1013, 1012t01018, 10%) 1013, 1014:0103, 1015a) 1013, 101% 1013, 1017to 1018, 102 to 10", 103 to 10", 104m 10", 105 to to", 106 to 10", 107 to 10", 10% 10", to9 to to", 10mm ", 101% 10", 102 to to", 103 to 10", 104 to 10", 105 to 10", 106m 10", 107 to 10", 108 to ", 109 to 10", 1010 to 10", 103 to 101", 103 to 10", 104 to 101°, 105 to to", 106m 1010‘, 107 to ", 108w 1010‘, 109 to 101"), 102 to 109, 10-" to 109, to" to 109, 105 to 109, 106w 109, 107 to 109, 108w 109, 102 to 108, 103 to 103, 104 to 103, 105 to 103, 106 to 108, 10%» 108, 102 to 107, 103 to 107, 104 to 107, 105m 107, 106 to 107, 102 to 10", 103m 106, 10" to 10", 105 to 106,102 to 105, 103 to 105, 10% 105, 102 to 104, 103 to 104, 102 to 103, 1018, 10'", 1016, 1015, 10", 1013, to", 10", 1010 7 109, 108, 107, 106, 105, to", i03, or 102 total ial cells. [0247} In some embodiments, the composition is administered 1 or more times per day. In some aspects, the composition is administered with food each time the animal is feed, In some embodiments, the cen'ipesition is stered 1 to 10, l to 9, 1 to 8, l to 7, 1 to 6, l to 5, l to 4, l to 3, l to 2, 2to lO, 2to 9, 2to 8, 2to 7, 2to 6, 2to 5, Z to 4, Z to 3 3 to 10, 3 to 9, 3 to 8, 3 to 7,3t06,3to5,3to4,4to10,4to9,4to8,4to7,4tot3,4t05, Ste 10, 5to9, 5to 8,5to7, 5 to 6, 6t010, 6 t0 9, 6 to 8, 6 to 7, 7 to 10, '7 to 9, 7 to 8,8 to 10, 8 to 9, 9 to 10, l, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per day. [0248} In some ments, the microbial composition is administered 1 to 10, l to 9, l to 8, l to'7, 1 to 6, l to 5, l to4, 1 to3, l t02,2to 10,2to9,2to 8,2to 7,2t06,2to 5,2to4,2to3, 3to10,3t09,3to8,3to7,3t06,3t05,3to4,4to10,4to9,4to8,4t07,4t06,4t05,5t0 , 5 to9, 5 to 8, 5 to7, Ste 6, (Ste 10, 6to 9, 6to 8, 6to 7, 7to 10, 7to 9, 7to 8,8t010, Ste 9, 9 to 10, l, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per week. {11249} In some embodiments, the microbial composition is administered 1 to 10, l to 9, l to 8, 1 to7,1to6,1to§,1to4,1to3,ltoZ,2tolO,2to9, Zto ,2t06,2to ,2to3, 3t010,3t09,3t08,3to7,3to6,3t05,3to4,4to10,4to9,4t08,4t07,4t06,4to5,5to , 5to9, 5to 8, 5to7, 5t06, 6t0 10, 6to9, 6t0 8, 6to7, 7to 10, 7to9, 7w 8,8t0 10, 8to9, 9 to 10, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per month. {02501 In some embodiments, the microbial composition is administered 1 to 10, 1 to 9, l to 8, l to'7,1to6,1toS,lto4,1to3,1t02,2to10,2to9,2to8,2to7,2to6,2t05,2to4,2t03, 3to 10,3to9, 3to 8, to6,3toS,3to4,4to10,4to9,4t08,4to7,4to6,4t05,Sto , 5:09, 5t08, to6,6to10,6to9,6t08,6to7,7to10,7to9,7t08, Sto 10, 8to9, 9 to 10, l, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times per year. {(1251} In some embodiments, the feed can he uniformly coated with one or more layers of the microbes and/oi" microbial compositions disclosed herein, using tional methods of mixing, spraying, or a combination thereof through the use of treatment application equipment that is specifically designed and manufactured to accurately, safely, and efficiently apply gs. Such equipment uses various types of coating technology such as rotary coaters, drum coaters, fluidized bed ques, spouted beds, rotary mists, or a combination thereof. Liquid treatments such as those of the present disclosure can be applied via either a spinning "atomizer" disk or a spray nozzle, which evenly distributes the microbial composition onto the feed as it moves though the spray pattern. in some aspects, the feed is then mixed or tumbled for an additional period of time to achieve additional treatment distribution and drying.

} In some embodiments, the feed coats of the present disclosure can be up to Want, 20am, 30am, 40am, 50pm, 6Com, 70pm, 80pm, 90pm, 100nm, llOpm, 120um, l30um, 140nm, ISOum, l60um, l70um, 180nm, l90pm, 200nm, 210nm, 220nm, 230nm, 240nm, 250nm, 260nm, 27Dum, 280nm, 290nm, 300um, 310nm, 320nm, 330nm, 340nm, 350nm, 360nm, 370nm, 380nm, 390nm, 400nm, 410nm, 420nm, 430nm, 440nm, 450nm, 460nm, 470nm, 480nm, 490nm, 500nm, SlOpm, 520nm, 530nm, 540nm, 550nm, 560nm, 5'70um, 580nm, 590nm, 600um, 610nm, 620nm, 63Dum, 640nm, 650nm, 660nm, 670nm, 680nm, 690nm, 700nm, 710nm, 720nm, 730nm, '740um, 750nm, 76Dum, 770nm, 780nm, '790um, 800nm, 810nm, 820nm, 830nm, 840nm, 850nm, 860nm, 870nm, 880nm, 890nm, 900nm, 910nm, 920nm, 930nm, 94Dum, 950nm, 960nm, 970nm, 980nm, 990nm, lOOOum, lOlOum, lOZOum, 1030um, 1040_um, lOSOum, 1060um, 1070um, IOSOum, 1090um, llOOum, lllt‘ium, 112(‘ium, 1130um, 1140um, , 1160mm, 1170mm, 1180mm, , lZOOum, lZlOum, lZZOum, 1230tim, 1240um, lZSOum, 1260um, 1270um, 1280um, 1290um, , , 1320mm, 1330mm, 1340iim, 1350um, 1360um, 1370um, 1380mm, 1390um, l400um, , 1420um, 1430mm, 1440um, l450um, , , 1480mm, 1490iim, 1500th, 1510um, 1520um, 1530mm, 1540iim, 1550um, 1560um, 1570um, 1580mm, 1590um, 1600um, , 1620um, 1630mm, 1640um, 1650um, 1660um, 1670um, 1680mm, 1690iim, 1700um, 1710um, 720nm, 1730um, 1740ii1n, 1750um, 1760um, 1770um, 1780mm, 1790um, lSOOum, 1810um, 1820um, 1830mm, 1840um, lSSOum, , 1870um, 1880mm, 1890iim, 1900um, 1910um, 1920um, 1930mm, m, 1950um, 1960um, 1970um, 1980mm, 1990um, ZOOOum, 2010um, 2020um, :30pm, 204011111, 2050um, 206011111, 20’70um, 2080mm 2090iim, ZlOOum, 21 lOum, 2120um, 2130mm 2140iim, 2150um, 2160um, 2170um, 2180um, 2190mm, 2200um, 2210mm, 2220mm 22:30pm, 2240mm, 2250um, 226011111, 22’70um, 2280mm 2290iim, 2300um, 2310um, , 2330mm 2340iim, 2350um, 2360um, , 2380um, 2390mm, 24-00mm 2410mm, 2420mm 24:30pm, Z440um, 24-50mm 246011111, 21-170mm, , 2490iim, 2500um, ZSlOum, 2520um, 2530mm 2540iim, 2550um, 2560um, 2570um, 2580um, 2590mm, , 2610mm, 2620mm 2630um, Z640um, 2650um, 111, 26’70um, 2680mm 2690iim, 2700um, 2710um, 2720um, 2730mm 2740um, 2750um, 2760um, 2770an 2780um, Z790um, 2800mm, 2810ni'n, 2820mm 2830um, 2840um, 2850mm, 2860mm, 2870ni'n, 2880mm 2890um, 2900um, 2910uni, 2920uni, 2930mm 2940um, 2950um, 2960mm, 29370an m, 2990um, or 3000um thick.

} In some ments, the microbial cells can be coated freely onto any number of compositions or they can be formulated in a liquid or solid composition before 1oeing coated onto a composition. For e, a solid composition sing the rganisms can be prepared by mixing a solid carrier with a suspension of the spores until the solid carriers are impregnated with the spore or cell suspension. This e can then be dried to obtain the desired particles. {(1254} In some other embodiments, it is contemplated that the solid or liquid microbial compositions of the present disclosure further contain functional agents eg, activated carbon, minerals, vitamins, and other agents capable of improving the quality of the products or a combination thereof. {(1255} Methods of coating and compositions in use of said methods that are known in the art can be particularly useful when they are modified by the addition of one of the embodiments of the present disclosure. Such g methods and apparatus for their application are disclosed in, for example: US Pat. Nos. 245 and 7,998,502; and PCT Pat. App. Publication Nos. W0 2008/)76975, each of which is incorporated by reference herein. {@256} In some embodiments, the microbes or ial consoitia of the present disclosure exhibit a synergistic effect, on one or more of the traits bed herein, in the presence of one or more of the microbes or consortia coming into contact with one another. The synergistic effect obtained by the taught methods can be quantified, for example, according to Colby’s formula (77.6., (E) = X+Y — (X*Y/l00)). See Colby, RS, "Calculating Synergistic and Antagonistic Responses of Herbicide Combinations," 1967. Weeds. Vol. 15, pp. 20—22, incorporated herein by nce in its entirety. 'I'hus, "synergistic" is intended to reflect an outcome/parameter/effect that has been increased by more than an additive amount. {0257} In some embodiments, the microbes or microbial consortia of the present disclosure may be administered via drench. In one embodiment, the drencli is an oral drencli A drench administration comprises utilizing a drench kit/applicator/syringe tliat injects/releases a liquid comprising the microbes or ial consortia into the buccal cavity and/or esophagas of the animal. {@258} In some embodiments, the microbes or microbial consortia of the present disclosure may be administered in a time-released fashion, The composition may be coated in a chemical ition, or may be contained in a mechanical device or capsule that releases the microbes or ial consortia over a period of time instead all at once. In one embodiment, the es or microbial consortia are administered to an animal in a time—release capsule. In one embodiment, the composition may be coated in a chemical composition, or may be contained in a mechanical device or capsul that es the mcirobes or microbial consortia all at once a period of time hours post ingestion. {@259} In some embodiments, the microbes or microbial consortia are administered in a time released n between l to 5, l to 10, l to 15, l to 20, l to 24, l to 2.5, 1 to 30, l to 35, l to 40, l to 45, l to 50, l to 55, l to 60, l to 65, l to 70, l to 75, l to 80, l to 85, l to 90, l to 95, or i to 100 hours. 311260} In some embodiments, the microbes or microbial consortia are administered in a time— released fashion n 1 to 2, l to 3, l to 4, l to 5, l to 6, l to 7, l to 8, l to 9, l to 10, l to 11, l to 12, l to 13, 1 to 14, l to 15, l to 16, 1 to 17, l to 18, l to 19, 1 to 20, l to 21, l to 22,1t0 23, l to 24, l to 25, 1 to 26, 1 to 27, 1 to 28, l to 29, or 1 to 30 days.

Wilcroorganisms {(1261} As used herein the term "microorganism" should be taken y. It es, but is not limited to, the two prokaryotic domains, Bacteria and Archaea, as well as eukaryotic fungi, protists, and Viruses. {0262} By way of example, the microorganisms may include species of the genera of: Lactobacillus, Closffldium, floecalibacter', Hydrogcnoanaerobacterl‘zmi, Acrocarpospom, Bacillus, Subdoligranuhim, Leuconastoc, Lachnospim, Anacrqfihtm, ll/Ilcmbactermm, osz'spom, ‘a, Pseudomonas, Sporobacrer, Corynebacterium Streptococcus, Paracoccus, Celirlosibiricum, Ruminacocczrs, Bacteroidcs, Fiiobasidl'um, eiia, Alarospora, Pichz‘n, and Candida. in some embodiments, the microorganisms may include species of any general disclosed herein. {9263} In certain embodiments, the microorganism is unculturable. This should be taken to mean that the microorganism is not known to be culturable or is difficult to culture using methods known to one d in the art, {0264} 1n one embodiment, the microbes are obtained from s (erg, mammals, reptiles, birds, and the like), soil (cg, rhizosphere), air, water (eg, marine, freshwater, wastewater sludge), sediment, oil, plants (erg, roots, , stems), agricultural products, and extreme environments (cg, acid mine drainage or hydrothermal systems). In a further embodiment, microbes obtained from marine or freshwater environments such as an ocean, river, or lake. In a further embodiment, the microbes can be from the surface of the body of water, or any depth of the body of water (rag, a deep sea sample). {(3265} The microorganisms of the disclosure may be isolated in substantially pure or mixed es. They may be concentrated, diluted, or provided in the natural concentrations in which they are found in the source material. For e, microorganisms from saline sediments may be isolated for use in this disclosure by ding the sediment in fresh water and allowing the sediment to fall to the . The water ning the bulk of the microorganisms may be removed by decantation after a le period of settling and either administered to the GI tract of poultry, or concentrated by filtering or centrifugation, diluted to an appropriate concentration and administered to the GI tract of poultry with the hull: of the salt removed. By way of further example, microorganisms from mineralized or toxic sources may be similarly treated to recover the microbes for application to poultry to minimize the potential for damage to the animal. {0266} In another embodiment, the microorganisms are used in a crude form, in which they are not isolated from the source material in which they naturally reside. For example, the microorganisms are provided in combination with the source material in which they reside; for e, fecal matter or other composition found in the gastrointestinal tract. In this embodiment, the source material may include one or more species of microorganisms. {0267} In some embodiments, a mixed population of microorganisms is used in the s of the disclosure. {@268} In ments of the disclosure where the microorganisms are isolated from a source material (for example, the material in which they naturally reside), any one or a combination of a number of standard ques which will be readily known to skilled persons may be used, r, by way of example, these in general employ processes by which a solid or liquid e of a single microorganism can be obtained in a substantially pure form, usually by physical separation on the surface of a solid microbial growth medium or by tric dilutiye isolation into a liquid microbial growth medium, These processes may include isolation from dry material, liquid suspension, slurries or homogenates in which the material is spread in a thin layer over an appropriate solid gel growth medium, or serial dilutions of the material made into a sterile medium and inoculated into liquid or solid culture media {9269} Whilst not ial, in one embodiment, the material containing the microorganisms may be ated prior to the isolation process in order to either multiply all microorganisms in the material. h/licroorganisms can then be isolated from the enriched materials as disclosed above. {0270} In certain embodiments, as mentioned herein before, the microorganism(s) may be used in crude form and need not be isolated from an animal or a media. For e, feces, or growth media which includes the i'nici'oorganisms identified to be of benefit to increased feed efficiency may be obtained and used as a crude source of microorganisms for the next round of the method or as a crude source of microorganisms at the conclusion of the . For example, fresh feces could be obtained, and optionally processed.

Microbiome Shift and Abundance of Microbes {8271} In some embodiments, the microbiome of poultry, ing the gut iome (crop, gizzard, cecum, small intestine, and large intestine) comprises a diverse arrive of microbes with a wide variety of metabolic lities. The microbiome is influenced by a range of factors including diet, variations in animal metabolism, and breed, among others. Most poultry diets are plant—based and rich in complex polysaccharides that enrich the gastrointestinal microbial community for microbes e of breaking down specific polymeric components in the diet such as cellulose, hemicellulose, lignin, etc. The end ts of primary degradation sustain a chain of microbes that ultimately produce a range of organic acids together with hydrogen and carbon dioxide. Because of the complex and interlinked nature of the microbiome, changing the diet and thus substrates for primary degradation may have a cascading effect on gut microbial metabolism, with changes in both the organic acid es and the methane levels produced, thus impacting the quality and quantity of animal production and or the products produced, by the animal. See Menezes er a], (2011. FEWSA/ficrobioi, Ecol, ;256m265.) {0272} In some aspects, the present disclosure is drawn to administering microbial compositions described herein to modulate or shift the microbiome of poultry. {0273} In some embodiments, the microbiome is shifted through the administration of one or more microbes to the gastrointestinal tract. In further embodiments, the one or more microbes are those selected from Table 1 and/or Table 3. In some embodiments, the microbiome shift or modulation includes a decrease or loss of specific microbes that were present prior to the administration of one or more es of the t disclosure, ln some embodiments, the iome shift or modulation es an increase in microbes that were present prior to the administration of one or more microbes of the present disclosure, ln some embodiments, the mi crobiome shift or modulation includes a gain of one or more microbes that were not present prior to the administration of one or more microbes of the present disclosure. In a further embodiment, the gain of one or more microbes is a microbe that was not specifically included in the stered microbial consortium. {0274} In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the mierobiome such that the administered es are present in the iome for a period 0fat least 1 to 10,1 t0 9, 1 to 8,1 to 7,1 to 6,1 to 5,1 to 4 l to3,l to 0,2to9,2to8,2t07,2t06,2t05,2t04, 2t03, 3t0 10, 3to9,3t08,;to / 3to6, 3 to 5,3to4,4t0 10,4to9,4t08,4to 7,4to6,4to5, 5to 10, 5t09, 5to8, 5t07,5 to6, 6to ,6to 9, 6to 8, 6to/,7 to 10,7/to 9, 7 to 8,8 to IO, 8 t0 9, 9t0 IO, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days. {0275} In some embodiments, the stration of microbes 0f the present disclosure s in a sustained modulation of the microbiome such that the administered microbes are present in the microbiome for a period of at least 1 to 10,1 to 9,1 to 8, I t07,1 t0 6, l to 5,1 to 4,1 to 3, 1 t0 2,2t0 10,2to9,2t08,2to7,2to6,2to5,2to 3to 10, 3to9, 3to8, 3t07,3t06, 3 , 2to3, t0 .5, 3 to 4, 4 to 10, 4 t0 9, 4 to 8, 4 t0 7, 4 to 6, 4 to 5, ,5 to 10, 5 to 9, 5 t0 8, 5 to 7, 5 to 6, 6 to , 6 t0 9, 6t0 8, 6t0 7, 7 t0 l0, 7t0 9, 7 to 8,8 to 10, 8 to 9, 9 to 10, l, 2, 3, 4, ,5, 6, 7, 8 9, or 10 weeks. {(3276} In some embodiments, the administration of microbes of the present disclosure results in a sustained modulation of the mierobiome such that the administered es are t in the niicrobiome for a period of at least 1 to 10, l to 9, l to 8,1 to 7, l to 6, l to 5, l to 4, l to3,l to 2,22to 10, 2to9, 2t08, 2t07,2t06, 2t05, 2t0 4 2t03, 3t0 l03 to9,3 to8,3 to7,3to6,1 to 5, 3to4, 4t0 10,4to9, -4t0 8, 4to 7, 4to6, 4to5, 5to 10, 5t09,5 to8, 5t07, 5to6, 6to lO, 6to9, 6to8, 6to7,7tol0,7to9 7to8,8to lO, 8to9, 9t0 10, 1,2, 3,4, 5, 6,7,8 9, l0, l l, or 12 months {0277} In some embodiments, the presence of the stered microbes are detected by sampling the gastrointestinal tract and using primers to amplify the 168 or l8S rDNA sequences, or the ITS rDNA sequences of the administered microbes, In some embodiments, the administered microbes are one or more of those selected from Table 1 and/or Table 3, and the corresponding rDNA sequences are those selected from SEQ ID NOs1l ~385, {(3278} In some embodiments, the microbiome of a bird is measured by amplifying pol ynucleotides collected from gastrointestinal samples, wherein the poly/nucleotides may be 168 WO 81203 or 18S rDNA nts, or ITS rDNA fragments of microbial rDNA. In one embodiment, the microbiome is fingerprinted by a method of ring gradient gel electrophoresis (DGGE) wherein the amplified rDNA fragments are sorted by where they denature, and form a unique banding pattern in a gel that may be used for ing the iome of the same bird over time or the microbiomes of multiple birds. In another embodiment, the microbiome is fingerprinted by a method of terminal restriction fragment length polymorphism ('I‘URFLP), wherein labelled PCR fragments are digested using a restriction enzyme and then sorted by size.

In a further ment, the data collected from the 'I‘—RFLP method is evaluated by nonmetric multidimensional scaling (nl‘vaS) ordination and I’ERMANOVA statistics identify ences in microbiomes, thus allowing for the identification and ement of shifts in the niicrobiome. See also Shanks er a]. (2011. Appl. Environ. ,Mtcmbiol. 77(9):;9923001), Petri er a1. (2013. PLUS one. 8(12):e83424), and Menezes et a]. (2011. FER/L9 AJ’Z'CMMOZ. Ecol. 78(2):256—265.) {0279} In some embodiments, the administration of microbes of the present disclosure results in a modulation or shift of the microbiome which further results in a desired phenotype or improved trait. hIIC Scoring {0280} ing to the methods provided herein, a sample is processed to detect the presence of one or more microorganism types in the sample ( 1001; 2001). The absolute number of one or more microorganism organism type in the sample is determined (FIG. I, 1002; 2002), The determination of the presence of the one or more organism types and the absolute number of at least one sm type can be ted in parallel or serially, For example, in the case of a sample comprising a microbial community comprising bacteria (2.6., one i'nicroorganisi'n type) and fungi (126., a second microorganism type), the user in one embodiment detects the presence of one or both of the organism types in the sample (FIG. I, 1001; 2001). The user, in a furtl'ier embodiment, determines the absolute number of at least one organism type in the sample in the case of this example, the number of bacteria, fungi or combination thereof, in the sample ( 1002; , 2002). {0281} In one embodiment, the sample, or a portion thereof is subjected to flow cytometry (PC) analysis to detect the presence and/or number of one or more microorganism types (FIG. I, 1001, 1002, 2001, 2002). In one flow cytometer embodiment, individual microbial cells pass through an illumination zone, at a rate of at least about 300 *s‘l, or at least about 500 >"s4, or at least about 1000 *s‘l. However, one of ordinaiy skill in the art will recognize that this rate can vary depending on the type of instrument is employed. Detectors which are gated electronically measure the magnitude of a pulse representing the extent of light scattered. The magnitudes of these pulses are sorted electronically into "bins" or "channels," permitting the display of histograms of the number of cells sing a certain quantitative property (eg, cell staining property, diameter, cell membrane) versus the l number. Such analysis allows for the determination of the number of cells in each "bin" which in ments described herein is an "microorganism . type bin, e.g., a ia, fungi, de, protozoan, archaea, algae, dinoflagellate, virus, , etc. {0282} In one embodiment, a sample is stained with one or more fluorescent dyes wherein a fluorescent dye is specific to a particular microorganism type, to enable detection via a flow cytometer or some other detection and quantification method that harnesses cence, such as cence microscopy. The method can provide quantification of the number of cells and/or cell volume of a given organism type in a sample, In a further ment, as described herein, flow cytometry is harnessed to determine the presence and quantity of a unique first marker and/or unique second marker of the organism type, such as enzyme expression, cell surface protein sion, etc, Two or three—variable histograms or contour plots of, for example, light scattering versus fluorescence from a cell membrane stain (versus fluorescence from a protein stain or DNA stain) may also be generated, and thus an impression may be gained of the distribution of a variety of properties of interest among the cells in the population as a whole. A number of displays of such multiparameter flow cytometric data are in common use and are amenable for use with the methods described herein. {0283} In one embodiment of processing the sample to detect the presence and number of one or more microorganism types, a microscopy assay is employed ( 1001, 1002). In one embodiment, the microscopy is optical microscopy, where visible light and a system of lenses are used to magnify images of small samples. Digital images can be ed by a chargeucouple device (CCD) camera. Other microscopic techniques include, but are not limited to, scanning electron microscopy and transmission electron microscopy. rganism types are visualized and quantified according to the s provided herein.

WO 81203 {8284} In another embodiment of in order to detect the presence and number of one or more microorganism types, the sample, or a portion thereof is subjected to fluorescence microscopy.

Different fluorescent dyes can be used to directly stain cells in samples and to quantify total cell counts using an epifluorescence microscope as well as flow cytometry, described above. Useful dyes to quantify microorganisms e but are not limited to ne orange (A0), 4,6mdi— aminon2 phenylindole (DAPI) and Sncyanomlfi Dytolyl 'l‘etrazoliuin Chloride (CTC). Viable cells can be estimated by a Viability staining method such as the LlVE/DEAD® Bacterial Viability Kit (BaanightTM) which contains two nucleic acid stains: the greennfluorescent SYTO 9W dye penetrates all membranes and the red—fluorescent propidium iodide (PI) dye penetrates cells with damaged membranes. Therefore cells with compromised membranes will stain red, whereas cells with undamaged membranes will stain green. Fluorescent in situ hybridization (FISH) extends epifluorescence microscopy, allowing for the fast detection and enumeration of specific organisms. FISH uses cent labelled oligonucleotides probes (usually 15—25 basepairs) which bind specifically to organism DNA in the sample allowing the Visualization of the cells using an epifluorescence or confocal laser scanning microscope (CIASM). Catalyzed reporter deposition fluorescence in Sim hybridization (CARD—FISH) improves upon the FISH method by using oligonucleotide probes labelled with a horse radish peroxidase (HRP) to amplify the intensity of the signal obtained from the microorganisms being studied FlSl-I can be combined with other techniques to characterize microorganism communities. One combined technique is high affinity peptide c acid (PNA)—FlSl-L where the probe has an enhanced lity to penetrate through the Extracellular Polymeric nce (BPS) matrix. Another example is LIVE/DEADuEISl-l which combines the cell viability kit with FISH and has been used to assess the efficiency of disinfection in drinking water distribution s. {8285} In another embodiment, the sample, or a portion thereof is subjected to Raman micro— spectroscopy in order to determine the presence of a rganism type and the te number of at least one microorganism type ( 1001—1002; Fit}. 2;, 2001—2002). Raman spectroscopy is a non—destructive and labelufree technology e of detecting and measuring a single cell Raman spectrum (SCRS). A typical SCRS es an intrinsic biochemical "fingerprint" of a single cell. A SCRS contains rich information of the biomolecules within it, including nucleic acids, proteins, carbohydrates and lipids? which s characterization of different cell species, physiological changes and cell phenotypes. Raman microscopy examines the scattering of laser light by the chemical bonds of different cell biomarlrers. A SCRS is a sum of the spectra of all the biomolecules in one single cell, indicating a cell’s phenotypic e. Cellular phenotypes, as a consequence of gene expression, usually reflect pes. Thus, under identical growth conditions, different microorganism types give distinct SCRS corresponding to differences in their genotypes and can thus be identified by their Raman spectra {@286} In yet another embodiment, the sample, or a portion thereof is subjected to centrifugation in order to determine the presence of a microorganism type and, the number of at least one microorganism type ( 1001—1002; 02). This process sediments a geneous mixture by using the fugal force created by a centrifuge. More dense components of the mixture migrate away from the axis of the centrifuge, while less dense components of the e migrate s the axis. Centrifugation can allow fractionation of samples into cytoplasmic, membrane and extracellular portions. It can also be used to determine localization information for biological molecules of st Additionally, centrifugation can be used to fractionate total microbial community DNA. Different prokaryotic groups differ in their e—plus—cytosine (G+C) content of DNA, so density—gradient centrifugation based on G+C t is a method to differentiate organism types and the number of cells associated with each type. The technique generates a fractionated profile of the entire community DNA and indicates abundance of DNA as a function of G-l-C content. The total community DNA is physically separated into highly purified fractions, each representing a different G-t-C content that can be analyzed by additional molecular techniques such as denaturing gradient gel electrophoresis (DCKiE)/arnplified ribosomal DNA restriction is (ARDRA) (see discussion herein) to assess total microbial community ity and the presence/quantity of one or more microorganism types. {0287} In another embodiment, the sample, or a portion thereof is ted to staining in order to determine the presence of a microorganism type and the number of at least one microorganism type (EEG. 1, lOOlulOOZ, Fit}. 2, ZOOl—ZOOZ). Stains and dyes can be used to Visualize biological tissues, cells or organelles within cells. Staining can be used in conjunction with microscopy, flow cytometry or gel electrophoresis to Visualize or mark cells or ical molecules that are unique to different microorganism types. In vivo staining is the process of dyeing living tissues, whereas in vitro staining involves dyeing cells or structures that have been removed from their biological context. Examples of specific staining techniques for use with the methods described herein e, but are not limited to: gram staining to determine gram status of bacteria, endospore staining to identify the presence of endospores, Ziehl~Neelsen stamina, haematoxylin and eosin staining to examine thin sections of tissue, papanicolaou staining to examine cell samples from various bodily secretions, periodic acid—Schiff staining of carbohydrates, Masson’s trichome ing a three-color staining protocol to guish cells from the surrounding connective tissue, wsky stains (or common variants that include Wright‘s stain, lenner‘s stain, MaynGrunwald stain, Leishman stain and a stain) to examine blood or bone marrow samples, silver staining to reveal proteins and DNA, Sudan staining for lipids and Conklin’s staining to detect true endospores. Common biological stains include acridine orange for cell cycle determination; bismarck brown for acid mucins; carmine for glycogen; carmine alum for nuclei; Coomassie blue for proteins; Cresyl violet for the acidic components of the neuronal cytoplasm; l violet for cell walls; DAPI for nuclei; eosin for cytoplasmic material, cell membranes, some extracellular structures and red blood cells; ethidium bromide for DNA; acid fuchsine for collagen, smooth muscle or ondria; haematoxylin for nuclei; Hoechst stains for DNA; iodine for starch; ite green for bacteria in the Gimenez staining technique and for spores; methyl green for chromatin; n'iethylene blue for animal cells; l red for Nissl substance; Nile blue for nuclei; Nile red for lic entities; osmium tetroxide for lipids; rhodamine is used in fl ence i'nicroscopy; safranin for ~ Stains are also used in transmission electron copy to enhance contrast and include phosphotungstic acid, osmium tetroxide, ruthenium tetroxide, ammonium molyhdate, cadmium iodide, carbohydrazide, ferric chloride, ne, indium trichloride, lanthanum nitrate, lead acetate, lead citrate, lead(ll) nitrate, periodic acid, phosphomolybdic acid, potassium ferricyanide, potassium ferrocyanide, ruthenium red, silver nitrate, silver proteinate, sodium chloroaurate, thallium nitrate, thiosemicarbazide, uranyl e, uranyl nitrate, and vanadyl sulfate. {0288} In another embodiment, the sample, or a portion thereof is subjected to mass ometry (MS) in order to determine the presence of a microorganism type and the number of at least one microorganism type ( 1001—1002; FIG, 2, 2001—2002). MS, as discussed below, can also be used to detect the presence and, expression of one or more unique markers in a sample ( 10034004; 2003—2004). MS is used for example, to detect the presence and quantity of protein and/or e markers unique to rganism types and therefore to provide an assessment of the number of the respective microorganism type in the sample.

Quantification can be either with stable isotope labelling or labelmfree. De nova sequencing of peptides can also occur directly from MS/MS spectra or sequence tagging (produce a short tag that can be matched against a database). MS can also reveal post—translational modifications of proteins and identify metabolites. MS can be used in conjunction with chromatographic and other separation techniques (such as gas chromatography, liquid chromatography, capillary electrophoresis, ion mobility) to enhance mass resolution and determination. {@289} In another embodiment, the sample, or a portion thereof is subjected to lipid analysis in order to determine the presence of a microorganism type and the number of at least one microorganism type ( lOGIdOOZ; 20013002). Fatty acids are present in a relatively constant proportion of the cell biomass, and signature fatty acids exist in microbial cells that can differentiate microorganism types within a ity In one embodiment, fatty acids are extracted by saponification followed by derivatization to give the respective fatty acid methyl esters Es), which are then analyzed by gas chromatography. The FAIVIE e in one embodiment is then compared to a nce FA, (IE database to identify the fatty acids and their corresponding microbial signatures by multivariate statistical analyses. [0290} In the s of the methods ed , the number of unique first makers in the sample, or portion thereof (cg, sample aliquot) is ed, as well as the abundance of each of the unique first markers ( l003, 2003). A unique marker is a marker of a microorganism strain. It should be tood by one of ordinary skill in the art that depending on the unique marker being probed for and measured, the entire sample need not be analyzed.

For example, if the unique marker is unique to bacterial strains, then the fungal portion of the sample need not be analyzed. As described above, in some embodiments, measuring the absolute abundance of one or more organism types in a sample comprises separating the sample by organism type, cg, Via flow cytometry. [0291} Any marker that is unique to an organism strain can be employed herein. For example, markers can include, but are not limited to, small subunit ribosomal RNA genes (lbs/188 rDNA), large subunit ribosomal RNA genes (23 S/ZSS/ZSS rDNA), alary 5.88 gene, cytochrome c oxidase, beta—tubulin, elongation factor, RNA polymerase and internal transcribed spacer (ITS). {0292} Ribosomal RNA genes (rDNA), especially the small t ribosomal RNA genes, 216., 188 rRNA genes (lSS rDNA) in the case of eukaryotes and 168 rRNA (16$ rDNA) in the case of prokaiyotes, have been the predominant target for the assessment of organism types and strains in a ial community. However, the large subunit ribosomal RNA genes, 288 rDNAs, have been also targeted. rDNAs are suitable for taxonomic identification because: (i) they are tous in all known organisms; (ii) they possess both conserved and le regions; (iii) there is an exponentially expanding database of their ces available for comparison. In community analysis of samples, the conserved regions serve as annealing sites for the corresponding universal PCR and/or sequencing primers. whereas the variable regions can he used for phylogenetic differentiation, In addition, the high copy number of rDNA in the cells tates detection from environmental samples. {@293} The internal transcribed spacer (ITS), located n the l8S rDNA and 288 rDNA, has also been targeted. The ITS is transcribed but d away before assembly of the ribosomes The ITS region is composed of two highly le spacers, ITS l and ITSZ, and the intercalary .88 gene. This rDNA operon occurs in multiple copies in genomes. Because the ITS region does not code for rihosome components, it is highly variable. {9294} In one embodiment, the unique RNA marker can he an mRNA marker, an siRNA marker or a ribosomal RNA marker. {9295} Proteirncoding functional genes can also be used herein as a unique first marker Such markers include 1out are not limited to: the recombinase A gene family (bacterial RecA, a RadA and RadB, eukaryotic RadSl and Rad57, phage UvsX); RNA polymerase 6 subunit (RpoB) gene, which is sible for transcription initiation and elongation; chaperonins.

Candidate marker genes have also been identified for bacteria plus archaea: ribosomal protein 82 (rpsB), ribosomal protein SlO (rpsI), ribosomal protein Ll , translation elongation factor EF—Z, translation initiation factor IF—Z, metalloendopeptidase, ribosomal n L22, ffh signal recognition particle protein, ribosomal protein L4/Lle (rplD), ribosomal protein L2 {rplB), ribosomal protein S9 (rpsl), ribosomal protein L3 (rplC), phenylalanylutRNA synthetase beta subunit, ribosomal n Ll4b/L23e (i‘plN), ribosomal protein SS, ribosomal protein 819 (rpsS), ribosomal protein S7, ribosomal protein L16/LlOE (rplP), ribosomal protein 813 (rpsM), phenylalanylmtRNA synthetase 0!. subunit, ribosomal protein L15, mal protein L25/L23, ribosomal protein L6 (rplF), ribosomal protein Lll (rle), ribosomal protein L5 (rplE), ribosornal n SIZE/$23, ribosornal protein L29, ribosomal protein S3 {i‘psC), ribosomal protein 811 (rpsK), ribosomal protein LlO, ribosomal protein 88, tRNA pseudouridine synthase B, ribosomal protein Ll 8P/LSE, ribosomal protein SlSP/Sl3e, Porphobilinogen deaminase, mal protein 817, mal n L13 (rle), phosphoribosylformylglycinamidine cyelo—ligase (rpsE), ribonuclease H11 and ribosomal protein L24. Other ate marker genes for bacteria include: transcription elongation protein NusA (nusA), rpoB DNA—directed RNA polymerase subunit beta (rpoB), G'I'l)~binding n EngA, rpoC DNA~direeted RNA rase subunit beta', priA primosome assembly protein, transcription—repair coupling factor, CTP synthase (pyrG), secY preprotein translocase subunit SecY, nding protein Obg/CgtA, DNA polymerase I, i'psF 30$ ribosomal protein 86, poA DNAmdireeted RNA, polymerase t alpha, peptide chain release factor 1, rpll SOS ribosomal protein L9, polyribonucleotide nucleotidyltransferase, tsf elongation factor Ts (tsf), rplQ SOS ribosomal protein Ll‘7, tRNA (guanine—N(l)~)~methyltransfei‘ase (rplS), rplY probable SOS ribosomal protein LZS, DNA repair protein RadA, glucose—inhibited division protein A, ribosome—binding factor A, DNA mismatch repair n MutL, smpB inding protein (smpB), N— aoetylglucosarninyl transferase, S—adenosyLmethyltransferase MraW, UDP-N~ acetylmuramoylalanine--D—glutamate ligase, rplS SOS ribosornal protein Ll9, rplT SOS ribosornal protein L20 (rplT), ruvA Holliday junction DNA se, ruvB Holliday junction DNA helicase B, serS seryl—tRNA synthetase, rplU SOS ribosomal protein 12], rpsR 308 ribosornal protein S] 8, DNA mismatch repair protein MutS, rpsT 30$ mal protein 820, DNA repair protein ReoN, frr ribosorne recycling factor (frr), recombination protein RecR, protein of unknown function UPFOOS4, niiaA tRNA isopentenyltransferase, G’I‘P—binding protein YchF, chromosomal ation tor protein DnaA, dephosphouCoA kinase, 16$ rRNA processing protein RimM, A'I'Pmcone domain protein, l—deoxy—D—xylulose Suphospha’te reductoisomerase, 2C—rnethyl—D~erythritol 2,4—cyclodiphosphate synthase, fatty acid/phospholipid synthesis protein PlsX, tRNA(_'lle)_lysidine synthetase, dnaG DNA primase ((111216), ruVC ay junction resolvase, rpsP 30$ ribosomal protein 816, Recombinase A recA, riboflavin biosynthesis protein RibF, glycyl~tRNA synthetase beta subunit, trrnU tRNA (5" inethylaminomethylmlmthiouridylate)—inetliyltransferase, rpml SOS ribosomal protein L35, hemE uroporphyrinogen decarboxylase, Rod shapendetermining protein, rpmA SOS ribosomal protein L27 (rpmA), yl—tRNA hydrolase, translation tion factor lF~3 (infC), UDP—Nm acetylmuramyl~tripeptide synthetase, rme 50S ribosomal protein L32, rpIL SOS ribosomal protein L7/Ll2 (rpIL), leuS leucylutRNA synthetase, ligA NAB—dependent DNA ligase, cell division protein FtsA, G'I'P—binding protein 'I‘ypA, A'I'Pmdependent Clp protease, A'I'Pmbinding subunit Cle, DNA replication and repair protein RecF and UDP—N- acetylenolpyruvoylglucosamine reductase. {0296} Phospholipid fatty acids (PLFAs) may also be used as unique first markers according to the methods described herein. Because PLFAs are y sized during microbial growth, are not found in storage molecules and degrade rapidly during cell death, it es an accurate census of the current living community. All cells contain fatty acids (FAs) that can be extracted and esterified to form fatty acid methyl esters (FAMEs). When the FAMEs are analyzed using gas chromatography—mass spectrometry, the resulting profile tutes a rprint’ of the microorganisms in the sample, The chemical compositions of membranes for organisms in the domains Bacteria and Eukaiya are comprised of fatty acids linked to the glycerol by an ester— type bond (phospholipid fatty acids (PLFAs)). In contrast, the membrane lipids of a are composed of long and branched hydrocarbons that are joined to glycerol by an ether~type bond (phospholipid ether lipids (PLELs)). This is one of the most widely used nonegenetic ia to guish the three domains, In this context, the phospholipids derived from microbial cell membranes, characterized by different acyl , are excellent signature molecules, because such lipid structural diversity can be linked to specific ial taxa. [0297} As provided herein, in order to determine whether an organism strain is , the level of expression of one or more unique second markers, which can be the same or different as the first , is measured ( l004, 2004). Unique first unique markers are described above. The unique second marker is a marker of microorganism activity. For example, in one embodiment, the mRNA or protein expression of any of the first markers described above is considered a unique second marker for the purposes of this invention. {0298} In one embodiment, if the level of sion of the second marker is above a threshold level (eg, a control level) or at a threshold level, the microorganism is considered to be active (FIG. l, 1005; 2005). Activity is determined in one embodiment, if the level of expression of the second marker is altered by at least about 5%, at least about 10%, at least about %, at least about 20%, at least about 25%, or at least about 309/6, as compared to a threshold level, which in some embodiments, is a control level. {0299} Second unique markers are measured, in one embodiment, at the protein, RNA or metabolite level. A unique second marker is the same or different as the first unique marker {0300} As provided above, a number of unique first s and unique second markers can be detected according to the methods described herein. Moreover, the detection and quantification of a unique first marker is carried out according to methods known to those of ordinary skill in the art ( 004, FIG 2, 2003—20l4). {0301} Nucleic acid sequencing (Lag, gDNA, cDNA, rRNA, mRNA) in one embodiment is used to determine absolute abundance of a unique first marker and/or unique second, marker.

Sequencing rms include, but are not limited to, Sanger sequencing and highmthroughput sequencing methods available from Roche/454 Life Sciences, lllumina/Solexa, Pacific Biosciences, Ion Torrent and Nanopore The sequencing can be amplicon sequencing of particular DNA or RNA sequences or whole nietagenome/transcriptome n sequencing. {0302} Traditional Sanger sequencing (Sanger et al, (1977) DNA cing with chain— terminating inhibitors, Proc Natl. Acad. Sci. USA, ‘74, pp, 5463—5467, incorporated by reference herein in its entirety) relies on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication and is le for use with the methods described herein {0303} In another embodiment, the sample, or a portion thereof is subjected to extraction of nucleic acids, amplification of DNA of interest (such as the r'RNA gene) with suitable primers and the construction of clone libraries using sequencing vectors. Selected clones are then sequenced by Sanger sequencing and the nucleotide sequence of the DNA of interest is retrieved, allowing calculation of the number of unique rganism strains in a . {0304} 454 pyrosequencing from Roche/454 Life Sciences yields long reads and can be harnessed in the methods bed herein (Margulies er a]. (2005) , 437, pp. 376—380, US. Patents Nos. 6,274,320; 6,258,568; 6,210,891, each of which is herein incorporated in its entirety for all purposes). Nucleic acid to be sequenced (erg, ons or zed genomic/metagenomic DNA) have specific adapters affixed on either end by PCR or by ligation.

The DNA with adapters is fixed to tiny beads (ideally, one bead will have one DNA fragment) that are suspended in a water—inmoil emulsion. An emulsion PCR step is then performed to make multiple copies of each DNA fragment, resulting in a set of beads in which each bead contains many cloned copies of the same DNA fragment. Each bead is then placed into a well of a fiber— optic chip that also ns enzymes necessary for the sequencingubyusynthesis reactions. The addition of bases (such as A, C, G, or T) trigger osphate release, which produces flashes of light that are recorded to infer the sequence of the DNA fragments in each well. About 1 million reads per run with reads up to 1,000 bases in length can he achieved. Pairednend sequencing can be done, which produces pairs of reads. each of which begins at one end of a given DNA fragment. A molecular barcode can be d and placed between the adapter sequence and the sequence of st in multiplex reactions, allowing each sequence to be assigned to a sample bioinformatically. {0305} na/Solexa sequencing es average read lengths of about 25 basepairs (bp) to about 300 bp (Bennett et ai. (2005) Pharmacogenoniics, 6:373—3 82; Lange er al. (2014-). BMC Genomics 15, p. 63; Fadrosh er a1. (2014) Microbiome 2, p. 6; Caporaso at al. (2012) ISMCE l, 6, p. 1621—1624; Bentley et a1. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 45663—59). This sequencing technology is also sequencing—by— synthesis but employs reversible dye terininators and a flow cell with a field of oligos attached.

DNA fragments to be sequenced have specific adapters on either end and are washed over a flow cell filled with specific oligonucleotides that hybridize to the ends of the nts. Each fragment is then replicated to make a cluster of identical fragments. Reversible dye—tern'iinator nucleotides are then washed over the flow cell and given time to attach. The excess tides are washed away, the flow cell is , and the reversible ators can be removed so that the process can repeat and nucleotides can continue to he added in subsequent cycles. Paired— end reads that are 300 bases in length each can he achieved. An lllumina platform can produce 4 billion fragments in a paired—end fashion with 125 bases for each read in a single run. Barcodes can also be used for sample multiplexing, but indexing primers are used. {0306} The SOLiD (Sequencing by nucleotide Ligation and Detection, Life Technologies) process is a "sequencing—byaligation" approach, and can be used with the methods bed herein for detecting the presence and abundance of a first marker and/or a second marker (MG. 1, 1003—1004, 20032004) (Peckham er a1. SOLiDTM Sequencing and 2uBase Encoding.

San Diego, CA: American Society of Human Genetics, 2007, Mitra et al. (2013) Analysis of the inal microbiota using SOLil) 16$ rRNA gene sequencing and SOLiD shotgun sequencing.

BMC Genomics, 14(Suppl 5): $16; Mardis (2008) Next~generation DNA sequencing methods.

Annu Rev Genomics Hum Genet, 9387—402, each incorporated by reference herein in its entirety). A library of DNA fragments is prepared from the sample to be sequenced, and are used to prepare clonal bead populations, where only one species of fragment will be present on the surface of each ic bead. The nts attached to the magnetic beads will have a universal Pl r sequence so that the starting sequence of every fragment is both known and identical. Primers hybridize to the Pl adapter sequence within the y template A set of four fluorescently ed e probes compete for ligation to the sequencing primer. Specificity of the dimhase probe is achieved by interrogating every lst and 2nd base in each ligation reaction.

Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length. The SOLiD platform can produce up to 3 billion reads per run with reads that are ’75 bases long. Paired—end sequencing is available and can be used herein, but with the second read in the pair being only 35 bases long. Multiplexing of samples is possible h a system akin to the one used by Illumina, with a separate indexing run. {(3307} The lon Torrent system, like 454 sequencing, is amenable for use with the methods described herein for detecting the presence and abundance of a first marker and/or a second marker ( lOO3—l004; FIG, 2, 20034004), It uses a plate of microwells containing beads to which DNA, fragments are attached. It differs from all of the other systems, however, in the manner in which base incorporation is detected. When a base is added to a growing DNA strand, a proton is released, which slightly alters the surrounding pH. Mi ectors sensitive to pH are associated with the wells on the plate, and they record when these changes occur. The different bases (A, C, G, T) are washed sequentially through the wells, allowing the sequence from each well to be inferred. The Ion Proton platform can produce up to 50 million reads per run that have read lengths of 200 bases. The Personal Genome Machine platform has longer reads at 400 bases. Bidirectional cing is available. Multiplexing is le through the standard in— line molecular barcode sequencing. {0308} Pacific Biosciences o) SMRT sequencing uses a singleumolecule, real—time sequencing approach and in one embodiment, is used with the s described herein for detecting the presence and abundance of a first marker and/or a second marker ( 1003— 1004; 20033004). The PacBio sequencing system involves no amplification step, setting it apart from the other major next~generation sequencing systems. In one embodiment, the sequencing is performed on a chip ning many zeronmode waveguide (ZMW) detectors.

DNA polymerases are attached to the ZMW detectors and olinked beled nucleotide incorporation is imaged in real time as DNA strands are synthesized. The PacBio system yields very long read lengths (averaging around 4,600 bases) and a very high number of reads per run (about 47,000). The typical "pairednend" approach is not used with PacBio, since reads are typically long enough that fragments, through CCS, can be covered multiple times without having to sequence from each end independently. lexing with PacBio does not involve an independent read, but rather follows the standard "in-line" ing model. {0309} In one embodiment, where the first unique marker is the ITS genomic region, automated ribosomal enic spacer analysis (ARISA) is used in one embodiment to determine the number and ty of microorganism strains in a sample (FIG. I, 1003, 20 .13) (Ranjard et al. (2003). Environmental Microbiology 5, pp. 11114120, incorporated by reference in its entirety for all puposes). The ITS region has significant heterogeneity in both length and nucleotide sequence. The use of a fluorescence~labeled forward primer and an automatic DNA sequencer permits high resolution of separation and high hput The inclusion of an internal standard in each sample provides cy in sizing general fragments. {0310} In another embodiment, fragment length polymorphism (RFLP) of PCR—amplified i‘DNA nts, ise known as amplified ribosomal DNA restriction analysis (ARDRA), is used to characterize unique first markers and the abundance of the same in samples ( 1003, 2003) (Massol~Deya e! a]. (1995). Mol. Microb. Ecol. Manual. 3.3.2, pp. l~l 8, orated by nce in its entirety for all puposes). rDNA fragments are generated by PCR using general primers, digested with restriction enzymes, electrophoresed in agarose or acrylamide gels, and stained with ethidium bromide or silver nitrate. {0311} One fingerprinting technique used in ing the presence and abundance of a unique first marker is —strandeduconformation polymorphism (SSCP) (Lee et a]. (1996). Appl n Microbiol 62, pp. 31126120; Scheinert er al. (1996). J. Microbiol. Methods 26, pp. 103— 117; Schwieger and Tehbe (1998). Appl. Environ. Microbiol. 64, pp. 4870—4876, each of which is incorporated by nce herein in its entirety). In this technique, DNA fragments such as PCR products obtained with primers specific for the 168 rRNA gene, are denatured and directly electrophoresed on a non—denaturing gel. Separation is based on differences in size and in the folded conformation of single—stranded DNA, which nces the electrophoretic mobility.

Reannealing of DNA strands during electrophoresis can be prevented by a number of strategies, including the use of one pliosphorylated primer in the PCR followed by specific digestion of the phosphorylated strands with lambda exonuclease and the use of one biotinylated primer to perform magnetic separation of one single strand after denaturation. To assess the identity of the predominant populations in a given consortium, in one embodiment, bands are excised and sequenced, or SSCP—patterns can be hybridized with ic probes. Electrophoretic conditions, such as gel matrix, temperature, and addition of glycerol to the gel, can influence the separation. {0312} In addition to sequencing based methods, other methods for quantifying expression (cg, gene, protein expression) of a second marker are amenable for use with the methods provided herein for determining the level of expression of one or more second markers ( 1004; 2004). For e, quantitative R'I‘mPCR, microarray analysis, linear amplification techniques such as c acid sequence based amplification ) are all amenable for use with the methods described , and can be carried out according to s known to those of ordinary skill in the art. {0313} In another embodiment, the sample, or a n thereof is subjected to a tative polymerase chain reaction (PCR) for detecting the ce and abundance of a first marker and/or a second marker ( 1003—1004; 200‘3~2004). Specific microorganism strains activity is measured by reverse transcription of transcribed ribosomal and/or messenger RNA (rRNA and rnRNA) into complementary DNA (cDNA), followed by PCR (RT—PCR). {0314} In another embodiment, the sample, or a portion thereof is subjected to PCR—based fingerprinting ques to detect the presence and abundance of a first marker and/or a second marker (FIG. l, 10034004, 2003~2004), PCR products can be ted by electrophoresis based on the tide composition. Sequence variation among the different DNA molecules influences the melting behaviour, and therefore molecules with different sequences will stop migrating at different positions in the gel. 'I‘hus electrophoretic profiles can be defined by the position and the relative intensity of different bands or peaks and can be translated to numerical data for calculation of diversity indices. Bands can also be excised from the gel and subsequently sequenced to reveal the phylogenetic affiliation of the community members. ophoresis methods include, but are not limited to: denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single~stranded— conformation polymorphism (SSCP), restriction fragment length polymorphism analysis (REL?) or amplified ribosomal DNA restriction analysis (ARDRA), terminal ction nt length polymorphism analysis FLP), automated ribosornal intergenic spacer analysis (ARISA), randomly amplified polymorphic DNA (RAPID), DNA amplification printing (DAF) and Bh—PEG electrophoresis. {0315} In another embodiment, the , or a n thereof is subjected to a chip—based platform such as microarray or microfluidics to determine the abundance of a unique first marker and/or presence/abundance of a unique second marker ( 10034004, 2003—2004).

The PCR products are amplified from total DNA in the sample and directly hybridized to known molecular probes affixed to arrays. After the fluorescently labeled PCR amplicons are hybridized to the probes, positive signals are scored by the use of al laser scanning microscopy. The microarray technique allows samples to be rapidly evaluated with replication, which is a significant advantage in microbial community analyses. In general, the hybridization signal ity on rnicroarrays is directly proportional to the abundance of the target organism.

The universal hi sity 16$ microarray (PhyloChip) contains about 30,000 probes of 1,6SrRNA gene targeted to several cultured microbial species and "candidate divisions". These probes target all l2], demarcated prokaryotic orders and allow simultaneous detection of 8,741 bacterial and archaeal taxa. Another microarray in use for profiling microbial ities is the Functional Gene Array (FGA) Unlike PhyloChips, FGAs are designed primarily to detect specific metabolic groups of bacteria. Thus, FGA not only reveal the community structure, but they also shed light on the m Sim community metabolic potential. FGA contain probes from genes with known biological ons, so they are useful in linking ial ity composition to ecosystem functions. An FGA termed GeoChip contains >24,000 probes from all known metabolic genes involved in s biogeocheniical, ecological, and environmental processes such as ammonia oxidation, methane oxidation, and nitrogen fixation. {0316} A protein expression assay, in one embodiment, is used with the methods bed herein for determining the level of expression of one or more second markers {FlG l, 1004, MG. 2, 2004). For example, in one embodiment, mass spectrometry or an immunoassay such as an enzyme—linked immunosorbant assay (ELlSA) is utilized to quantify the level of expression of one or more unique second markers, wherein the one or more unique second markers is a protein. {@317} In one embodiment, the sample, or a portion thereof is subjected to Bromodeoxyuridine (BrdU) incorporation to determine the level of a second unique marker ( 1004; F16. 2, 2004). BrdU, a synthetic nucleoside analog of ine, can be incorporated, into newly synthesized DNA of replicating cells. Antibodies specific for BRdU can then be used for WO 81203 detection of the base analog. 'I'hus BrdU incorporation identifies cells that are actively replicating their DNA, a measure of activity of a rganism ing to one embodiment of the methods described herein. BrdU incorporation can be used in combination with FISH to provide the identity and activity of targeted cells. {0.318} In one embodiment, the sample, or a n thereof is subjected, to microautoradiography (BLAIR) combined with FISH to determine the level of a second unique marker ( 1004; 2004). MARnFISH is based on the incorporation of radioactive substrate into cells, detection of the active cells using autoradiography and fication of the cells using FISH.

The detection and, identification of active cells at singlencell resolution is performed with a microscope. IVIAR.~FISH provides information on total cells, probe ed cells and the percentage of cells that incorporate a given radiolabelled substance. The method provides an assessment of the in my function of targeted microorganisms and is an effective approach to study the in viva logy of microorganisms. A technique developed for quantification of cell~specific substrate uptake in combination with MAR—FISH is known as quantitative MAR (QMAR). {0319} In one embodiment, the sample, or a portion thereof is subjected to stable isotope Raman spectroscopy combined with FISH (Raman—FISI-I) to determine the level of a second unique marker ( l004; 2004). This technique combines stable isotope g, Raman spectroscopy and FISH to link metabolic processes with particular organisms. The proportion of stable e incorporation by cells affects the light scatter, ing in measurable peak shifts for labelled cellular components, including protein and mRNA components. Raman spectroscopy can be used to identify whether a cell synthesizes compounds including, but not limited to: oil (such as alkanes), lipids (such as triacylglycerols (TAGD, ic ns (such as heme proteins, metalloproteins), cytochrome (such as P450, cytochrome c), chlorophyll, chromophores (such as pigments for light harvesting carotenoids and rhodopsins), organic polymers (such as droxyalkanoates (PI-IA), polyhydroxybutyrate (PHBD, hopanoids, steroids, starch, sulfide, sulfate and secondary metabolites (such as vitamin B12). {0320} In one embodiment, the sample, or a portion thereof is subjected to DNA/RNA stable isotope probing (SIP) to determine the level of a second unique marker ( 1004; 2004). SIP s determination of the microbial diversity associated, with specific metabolic pathways and, has been generally applied to study microorganisms involved in the utilization of carbon and nitrogen compounds. The substrate of interest is ed with stable isotopes (such as 13C or 15N) and added to the sample. Only microorganisms able to metabolize the substrate will incorporate it into their cells. Subsequently, 13C,—I‘)ii"éIA and nlL‘tNA can be isolated by density gradient centr‘ifugation and used for metagenomic analysis. RNA—based SIP can be a responsive biomar‘ker for use in Sll’ studies, since RNA itself is a reflection of ar activity. {0321} In one embodiment, the sample, or a portion thereof is subjected to isotope array to determine the level of a second unique marker ( 1004; 2004). Isotope arrays allow for functional and phylogenetic screening of active microbial communities in a high— throughput fashion. The technique uses a combination of SIP for monitoring the substrate uptake profiles and microarray technology for determining the taxonomic identities of active microbial communities Samples are incubated with a J4C—labeled substrate, which during the course of growth becomes incorporated into microbial biomass. The MC—labeled rRNA is ted from unlabeled rRNA and then labeled with hi‘omes. Fluorescent labeled rRNA is hybridized to a enetic inici'oarray followed by scanning for radioactive and fluorescent signals, The technique thus allows simultaneous study of ial community composition and specific substrate consumption by metabolically active rganisms of complex microbial communities. [0322} In one embodiment, the sample, or a portion thereof is subjected to a metabolomics assay to determine the level of a second unique marker (FlG. l, 1004; FlG. 2, 2004). Metabolomics studies the metabolome which ents the collection of all metabolites, the end products of cellular processes, in a biological cell, , organ or organism. This methodology can be used to monitor the presence of rganisms and/or ial mediated processes since it allows associating specific metabolite profiles with different microorganisms. Profiles of ellular and extracellular metabolites associated with microbial activity can be obtained using techniques such as gas tographyumass spectrometry (GOD/18). The x mixture of a metabolomic sample can be separated by such techniques as gas chromatography, high performance liquid chromatography and capillary electrophoresis. Detection of metabolites can be by mass spectrometry, nuclear magnetic resonance (NB/ll?) spectroscopy, ion~rnobility ometry, electrochemical detection (coupled to HPLC) and radiolabel (when combined with tliinmlayer chromatography). {8323} According to the embodiments described herein, the presence and respective number of one or more active microorganism strains in a sample are determined (FIG. I, 1006; 2006). For example, strain identity ation obtained from assaying the number and presence of first markers is analyzed to determine how many occurrences of a unique first marker are present, thereby representing a unique microorganism strain (eg, by counting the number of sequence reads in a sequencing assay). This value can be represented in one embodiment as a pe'centage of total sequence reads of the first maker to give a percentage of unique microorganism strains of a particular microorganism type. In a further embodiment, this percentage is multiplied, by the number of microorganism types (obtained at step 1002 or 2002, see and to give the absolute abundance of the one or more microorganism strains in a sample and a given volume {0324} The one 0]" more microorganism strains are considered active, as described above, if the level of second unique marker sion at a threshold level, higher than a old value, eg, higher than at least about 5%, at least about l0%, at least about 20% or at least about 30% over a control level. {0325} In another aspect of the invention, a method for determining the absolute abundance of one or more microorganism strains is determined in a plurality of samples ( see in particular, 2007), For a microorganism strain to be fied as active, it need only be active in one of the samples, The samples can be taken over multiple time points from the same source, or can be from different environmental sources (e.g differei'it animals). {@326} The te abundance values over samples are used in one embodiment to relate the one or more active microorganism strains, with an environmental parameter (: 2008). In one embodiment, the nmental parameter is the presence of a second active rganism strain. ng the one or more active microorganism strains to the environmental parameter, in one embodiment, is carried out by determining the couoccurrence of the strain and parameter by ation or by network analysis. {9327} In one embodiment, determining the co—occurrence of one or more active microorganism s with an environmental parameter comprises a network and/or cluster analysis method to measure connectivity of strains or a strain with an environmental parameter within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In another embodiment, the network and/or cluster analysis method may be applied to determining the couoccurrence of two or more active microorganism strains in a sample ( 2008). In another embodiment, the network analysis comprises nonparametric approaches including mutual information to ish connectivity between variables. In another embodiment, the k analysis ses e analysis, modularity analysis, robustness measures, betweenness es, connectivity measures, transitivity measures, centrality measures or a combination thereof ( 2009). In another embodiment, the cluster analysis method, comprises building a tivity model, subspace model, distribution model, density model, or a centroid, model and/or using community detection algorithms such as the Louvain, Bron—Kerbosch, GiivanmNewman, ClausetnNewman—h/loore, Pons—Latapy, and Wakita-I'surumi algorithms ( 2010). {0328} In one embodiment, the cluster analysis method is a heuristic method based on rity optimization. In a further embodiment, the cluster analysis method is the Louvain method. See, e.g the method described by l et al. (2008). Fast unfolding of ities in large networks. Journal of Statistical ics: Theory and Experiment, Volume 2008, Octoher 2008, incorporated by reference herein in its entirety for all purposes. {0329} In another embodiment, the network analysis comprises predictive modeling of network through link mining and prediction, collective classification, link-based clustering, relational similarity, or a combination thereof. In another embodiment, the network analysis ses differential equation based modeling of populations. In another embodiment, the network analysis comprises Lotka~Volterra modeling. {(3330} In one embodiment, relating the one or more active microorganism strains to an environmental parameter (cg, determining the co—occurrence} in the sample comprises creating es populated with linkages denoting environmental parameter and microorganism strain ations. {0331} In one embodiment, the multiple sample data obtained at step 2007 (eg, over two or more samples which can be collected at two or more time points where each time point corresponds to an individual ), is compiled. In a further embodiment, the number of cells of each of the one or more microorganism strains in each sample is stored in an association matrix (which can be in some embodiments, an abundance matrix). In one embodiment, the association matrix is used to identify associations n active microorganism strains in a specific time point sample using rule mining approaches ed with ation (cg, abundance) data. s are applied in one embodiment to remove insignificant rules. {@332} In one embodiment, the absolute abundance of one or more, or two or more active microorganism strains is related to one or more environmental parameters ( 2008), eg, via co~occurrence determination. Environmental parameters are chosen by the user depending on the sample(s) to be analyzed and are not cted by the methods described herein. The environmental parameter can be a parameter of the sample itself, rag, pH, ature, amount of protein in the sample. Alternatively, the environmental ter is a parameter that affects a change in the identity of a microbial community (M2,, where the "identity" of a microbial ity is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is affected by a change in the identity of a ial community For example, an environmental parameter in one ment, is the food intake of an animal or the amount of eggs produced by poultry In one embodiment, the environmental ter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample. {@333} In some embodiments described herein, an environmental parameter is referred to as a metadata parameter. [0334} Other examples of metadata parameters include 1out are not limited to genetic information from the host from which the sample was obtained (eg, DNA mutation information), sample pH, sample temperature, expression of a particuiar protein or mRNA, nutrient conditions (e.g;, level and/or identity of one or more nutrients) of the nding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, tibility or ance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of natural products, or a combination thereof. [0335} For example, according to one embodiment, microorganism strain number changes are calculated over multiple samples according to the method of (119., at 2001—2007). Strain number changes of one or more active strains over time is compiled (eg, one or more strains that have initially been identified as active according to step 2006), and the directionality of change is noted (116., negative values ng decreases, positive values denoting increases).

The number of cells over time is represented as a network, with microorganism strains representing nodes and the abundance weighted rules representing edges. Markov chains and random walks are leveraged to determine connectivity between nodes and to define clusters.

Clusters in one embodiment are filtered using metadata in order to identify clusters associated with desirable inetadata ( 2008). {0336} In a further embodiment, microorganism strains are ranked according to importance by integrating cell number changes over time and strains present in target clusters, with the highest changes in cell number ranking the highest. {0337} Network and/or cluster is method in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, network analysis comprises linkage analysis, modularity analysis, ness es, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof. In r embodiment, network is comprises predictive modeling of network through link mining and prediction, social network theory, collective classification, link—hased clustering, relational similarity, or a combination thereof, ln r ment, network analysis ses differential equation based ng of populations ln yet another ment, network is comprises Lotka—Volterra modeling. {0338} Cluster analysis method comprises building a connectivity model, subspace model, distribution model, density model, or a centroid model. {0339} Network and r based analysis, for example, to carry out method step 2008 of can be carried out via a module. As used herein, a module can be, for example, any assembly, instructions and/or set of operatively—coupled electrical components, and can include, for example, a memory, a processor, ical traces, optical connectors, software (executing in hardware) and/or the like.

Network Analysis {0340} A network and/or cluster is method, in one embodiment, is used to measure connectivity of the one or more strains within a network, wherein the network is a collection of two or more samples that share a common or similar environmental parameter. In one embodiment, k analysis comprises linkage analysis, modularity analysis, robustness es, betweenness measures, connectivity measures, transitivity measures, centrality measures or a combination thereof, in another embodiment, network analysis comprises tive modeling of k through link mining and prediction, social network theory, tive classification, ased clustering, onal similarity, or a combination thereof. In another embodiment, network analysis comprises mutual information, maximal ation coefficient (MIC) calculations, or other nonparametric methods between variables to establish connectivity. In another embodiment, k analysis comprises differential equation based modeling of populations. In yet another embodiment, network analysis comprises Lotka— Volterra modeling. {0341} The environmental ter can be a parameter of the sample itself, cg, pH, temperature, amount of protein in the sample. Alternatively, the environmental parameter is a ter that affects a change in the identity of a microbial community (113., where the "identity" of a microbial community is characterized by the type of microorganism strains and/or number of particular microorganism strains in a community), or is ed by a change in the identity of a microbial community. For example, an environmental parameter in one embodiment, is the food intake of an animal or the amount of eggs produced. In one embodiment, the environmental parameter is the presence, activity and/or abundance of a second microorganism strain in the microbial community, present in the same sample, In some embodiments, an environmen tal parameter is referred to as a rnetadata parameter. [0342} Other examples of metadata parameters include 1out are not limited to genetic information from the host from which the sample was obtained (eg, DNA mutation n'iation), sample pI-I, sample temperature, expression of a particular protein or mRNA, nutrient conditions (cg, level and/or identity of one or more nutrients) of the surrounding environment/ecosystem), susceptibility or resistance to disease, onset or progression of disease, susceptibility or resistance of the sample to toxins, efficacy of xenobiotic compounds (pharmaceutical drugs), biosynthesis of l products, or a combination thereof.

Poultry Pathogen Resistance and Clearance [0343} In some aspects, the present disclosure is drawn to administering one or more microbial compositions described herein to poultry to clear the intestinal tract of patl'iogenic microbes. In some ments, the present disclosure is further drawn to administering microbial compositions described herein to prevent colonization of enic microbes in the gastrointestinal tract. In some embodiments, the administration of microbial compositions described herein further clear pathogens from the ment and the respiratory tract of fowl, and/or prevent colonization of pathogens on the ment and in the atory tract. In some embodiments, the administration of microbial compositions described herein reduce leaky gut/intestinal permeability, inflammation, and/or incidence of liver disease. {0344} In some embodiments, the microbial compositions of the present disclosure comprise one or more microbes that are t in the gastrointestinal tract of poultry at a relative abundance of less than 15%, 14%, l’ %, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, or 101%. {0345} In some embodiments, after administration of microbial compositions of the present disclosure the one or more microbes are present in the gastrointestinal tract of the poultry at a relative abundance of at least 0.5%, 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%. {0346} Pathogenic microbes of y include the following: M'ycoplasma galliseptieum, A/r’fieeoplasma meleagrirtlis, iMycoplasma synovz‘ae, Pasreurella mnlrocia’a, ia’z'um gens, Clostrirtlz'am colmum, Closrria’z'um botnlz’num, Salmonella nipz‘, Salmonella Iyplnnmrium, Salmonella enteriea, Salmonella pullomm, Salmonella gallinamm, Hemophilia? gallinamm, Eryszpelotlzrix insidiosa, Campylobaczer.jejznrn', Campylobacier (roll, Campylobaczer lari, Listeria monooi/togenes, Arcobacter blittzleri, ,Myeohacteriam avizmz, and pathogenic strains of Escherichia coli and Staphylocoecus aurius. In some embodiments, the pathogenic microbes e Viral pathogens In some embodiments, the pathogenic es are pathogenic to both poultry and humans. In some embodiments, the pathogenic es are pathogenic to either poultry or humans. {0347} In some embodiments, the administration of compositions of the present disclosure to poultry modulate the makeup of the gastrointestinal microbiome such that the administered microbes outcompete microbial pathogens present in the gastrointestinal tract~ In some embodiments, the administration of con'ipositions of the present disclosure to y harboring microbial pathogens outcompetes the pathogens and clears the poultry of the pathogens 1n some embodiments, the stration of compositions of the present disclosure stimulate host ty, and aids in clearance of the microbial pathogens 1n some embodiments, the administration of compositions of the t disclosure introduce microbes that produce bacteriostatic and/or bactericidal components that decrease or clear the poultry of the microbial pathogens. in some embodiments, the stration of compositions of the present disclosure introduces microbes that modulate the pH, nutrient availability, minteral compostion, and/or vitamin composition of the intestinal tract. In some embodiments, the stration of compositons of the present sure introduces microbes that se the gastrointestinal pH, resulting in the inhibition of pathogen growth. In some embodiments, the administration of compositons of the t disclosure introduces microbes that decrease the gastrointestinal pI-I, resulting in the inhibition of pathogen growth. {034811n some embodiments, challenging poultry with a microbial colonizer or microbial en after administering one or more compositions of the present disclosure prevents the microbial colonizer or microbial pathogen from growing to a relative abundance of greater than %, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, or 0.01%. In further embodiments, challenging poultry with a microbial colonizer or microbial pathogen after administering one or more compositions of the present sure prevents the microbial colonizer or microbial pathogen front colonizing poultry {0349} In some embodiments, clearance of the microbial zer or microbial pathogen occurs occurs in less than 25 days, less than 24 days, less than 23 days, less than 22 days, less than 21 days, less than 20 days, less than 19 days, less than 18 days, less than 17 days, less than 16 days, less than 15 days, less than 14 days, less than 13 days, less than 12 days, less than 11 days, less than 10 days, less than 9 days, less than 8 days, less than ’7 days, less than 6 days, less than 5 days, less than 4 days, less than 3 days, or less than 2 days post adn'iinistration of the one or more compositions of the present disclosure. {0350} In some embodiments, clearance of the microbial zer or microbial pathogen occurs within l~30 days, 1—25 days, l~20 day, 1-15 days, 1—10 days, l-S days, 5—30 days, 5~25 days, 5— days, 5—15 days, 5—10 days, 10-30 days, 10—25 days, 1020 days, 10-15 days, 15—30 days, l5~ days, 1520 days, 20-30 days, 20—25 days, or 25-30 days post administration of the one or more compositions of the present disclosure, Improved Traits 10351} In some aspects, the present disclosure is drawn to administering microbial compositions described herein to poultry to improve one or more traits h the tion of aspects of weight, musculature, meat characteristics, egg quantity, egg weight, egg volume, egg y, egg shell density, digestive chemistry, efficiency of feed utilization and digestibility, fecal output, methane production, overall bird health, prevention of colonization of pathogenic microbes, and clearance of pathogenic microbes. {0.3521 In some embodiments, the se in egg quantity is an increase of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 eggs relative to an animal not having been stered a composition of the present disclosure. In some embodiments, the se in egg quantity is an increase of less than 2, 3, 4, 5, 6, 7, 8, 9, or 10 eggs relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the increase in egg quantity is an increase of at least 10%, 2 %, 31%, 4(%, 50%, 60%, 70%, 80%, 90%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, or 200% relative to an animal not having been administered a composition of the present sure. {03531 In some embodiments, the increase in egg volume is an increase of at least 5%, 10%, %, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure. In some embodiments, the increase in egg volume is an increase of less than 5%, %, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been stered a composition of the present disclosure. {03541 In some embodiments, the fecal output is d by at least 1%, 2%, .96, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 1711/11, 18%, 19%, 20%, 21%, 22%, 23%, 24% 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure.

In some embodiments, the fecal output is reduced by less than 1%, 21? o, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 1511/12, 16%, 17% a 18%, 19%, 20%, 21%, 22%, 23%, 24%, %, 30%, 35%,406/21,45%, 500/ 70% 75% , 55%, 60%, 65%, 7 3 80%, 85%, 90%, 95%, or 100% relative to an animal not having been administered a composition of the present disclosure. 0355 In some embodiments the fowl havino been administered a com osition of the resent 3 C , , disclosure exhibit a wei‘Iht gain of at least 1% 2% 3% 4%E? 69/0 8'3/0.

L/ 3 7 3 7 5%, 7%, r 7 . 1 ‘%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 00%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% ve to a fowl not having been administered a composition of the present sure. {03561 In some embodiments, the fowl having been administered a ition of the present disclosure exhibit a weight gain of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 3.1%, %, 40%, 45%, 50%, , 5%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% relative to a fowl not having been administered a composition of the present disclosure, {0.3571 In some embodiments, the fowl having been administered a composition of the t disclosure exhibit a feed conversion ratio decrease of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 2 %, 23%, 24%, 25%, %, 35%, 40%, 45%, 50%, ,5%, 60%, 65%, 70%, 75%, 8(%, 85%, 90%, 95%, or 100% ve to a fowl not having been administered a composition of the present disclosure. {03581 In some embodiments, the fowl having been administered a ition of the present disclosure exhibit a feed conversion ratio decrease of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a fowl not having been administered a composition of the present disclosure, {03591 In some embodiments, the fowl having been administered a composition of the present disclosure exhibit a decrease in the number of necrotic enteritis~causing bacteria in the gastrointestinal tract of at least 1%, %, 3%, r- %, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 229/ , 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a fowl not having been administered a composition of the present disclosure. {03601 In some embodiments, the fowl having been administered a composition of the present disclosure t a decrease in the number of necrotic enteritis—causing bacteria in the gastrointestinal tract ofat least about 1%, 2%, 3%, 4/0, 5%, 65/0, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23 /0, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a fowl not having been stered a composition of the present disclosure. {0361} In some embodiments, the fowl having been administered a composition of the present disclosure exhibit a decrease in the number of pathogenic bacteria in the gastrointestinal tract of at least 1%, 2%, 3%, 49/0, 5%, 69/0, 7%, 89/0, 9%, 109/0, 11%, 129/0, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 3,.%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% relative to a fowl not having been administered a composition of the present disclosure. {0.362} In some embodiments, the fowl having been administered a composition of the t disclosure exhibit a decrease in the number of enic bacteria in the gastrointestinal tract of at least about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 1 %, 12%, 1’ %, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60% 65%, 70%, 75%, 80%, 85%, 90%, )5%, or 100% relative to a fowl not having been administered a composition of the t disclosure. {0.363} In some embodiments, improving the eggs produced by poultry is desirable, wherein the eggs include triglycerides, triacylglycerides, diacylglycerides, ylglycerides, phospholipids, cholesterol, glycolipids, and free fatty acids. In further embodiments, free fatty acids include short chain fatty acids (1.9., C40, C6:0, and (78:0), medium chain fatty acids (re, C100, C101, (712:0, :0, C141,, and C150), and long chain fatty acids (i.éf., C16:0, C16:1, 017:0, C1751, Ciao, Cisi, 018:2, (318:3, and C200). {0364} In some embodiments, improving the quantity of vitamins in eggs produced by poultry is desirable, Vitamins found in eggs include 131, B2, B3, B5, B6, 1312, choline, biotin, and folic acid. {0365} In some embodiments, improving the ty of ls in eggs produced by poultry is desirable Minerals found in eggs include phosphorous, iodine, selenium, and calcium. Trace amounts of the following may be found in eggs: barium, copper, iron, manganese, , lead, selenium, strontium, vanadium, selenium, um, and zinc. {0366} In some embodiments, increasing or decreasing chicken serum levels of calcium, phosphorous, magnesium, triglycerides, cholesterol, and saccharides is desirable. The modulation of these serum components impact egg traits such as thickness, porosity, density, ional content, desirable taste, fat content, terol t, and coloration. {0367} In some embodiments, improving the efficiency and digestibility of animal feed is desirable. In some embodiments, increasing the degradation of lignocellulosic components from animal feed is desirable. Lignocellulosic components include lignin, cellulose, and liemicellulose. {9368} In some embodiments, increasing the concentration of fatty acids in the gastrointestinal tract is desirable. Fatty acids include acetic acid, propionic acid, and c acid. In some embodiments, maintaining the pH balance in the gastrointestinal tract to prevent destruction of cial microbial consortia is desirable. In some embodiments, increasing the concentration of lactic acids in the gastrointestinal tract is desirable. Lactic acid is lowers the pH of the surrounding environment, including intracellular pH which can disrupt ial proton motive force. Lactic acid can also permeabilized the outer membrane of gram~negative bacteria such that they exhibit an increased susceptibility to antimicrobials. {9369} In some embodiments, decreasing the amount of methane and manure produced by poultry is desirable {9370} In some embodiments, a decrease in the amount of total manure ed is desirable. In further embodiments, a decrease in the total amount of phosphorous and/or nitrogen in the total manure produced is desirable. {0371} In some embodiments, improving the feed intake is desirable In some embodiments, improving the efficiency of nitrogen utilization of the feed and/or dry matter ingested by poultry is desirable. {(3372} In some embodiments, the improved traits of the present disclosure are the result of the administration of the presently described microbial compositions. It is thought that the ial compositions modulate the inicrobioine of poultry such that the biochemistry of one or more elements of the gastrointestinal tract is changed in such a way that the gastrointestinal liquid and solid substratum are more ently and more completely degraded into subcomponents and lites than the gastrointestinal tract of poultry not having been administered microbial compositions of the present disclosure, {0.37.3} In some embodiments, the increase in efficiency and the increase of degradation of the gastrointestinal substratum result in an increase in improved traits of the present sure. {0374} In some embodiments, the increase of any one or more of the traits of the present disclosure is an increase of about 01%, about 0.2%, about 0.3%, about 0.4%, about 05%, about 06%, about 07%, about 0. %, about 0.9%, about 1%, about 2%, about 3%, about 4%, about %, about 6%, about 7%, about 8%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 1 %, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 35%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, ' about 58%, about 59%, about 60%, about 61%, about 62%, about 63%, about 64%, about 66%, about 67%, about 68%, about 69%, about 70%, about 71%, about 72%, about 73%, about 74%, about 75%, about 76%, about 77%, about 78%, about 79%, about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% relative to the animal not having been administered one or more bia1 compositions of the present disclosure. [0375} In some embodiments, the increase of any one or more of the traits of the present disclosure is an increase of at 1east 0.1%, at least 0.2%, at least 03%, at least 0.4%, at least 0.5%, at least 0.6%, at least 0.7%, at least 0.8%, at least 0.9%, at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least %, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 141%), at least 15%, at least 16%, at least 17%, at least 181%), at least 19%, at least 2 %, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure. 103761 In some embodiments, the decrease of any one or more of the traits of the present disclosure is a decrease of about 0.1%, about 0.2%, about 03%, about 0.4%, about 05%, about 0.6%, about 07%, about 08%, about 0.9%, about 1%, about 2%, about 3%, about 4%, about %, about 6%, about 7%, about '%, about 9%, about 10%, about 11%, about 12%, about 13%, about 14%, about 15%, about 16%, about 17%, about 18%, about 19%, about 20%, about 21%, about 22%, about 23%, about 24%, about 25%, about 26%, about 27%, about 28%, about 29%, about 30%, about 31%, about 32%, about 33%, about 34%, about 3 5%, about 36%, about 37%, about 38%, about 39%, about 40%, about 41%, about 42%, about 43%, about 44%, about 45%, about 46%, about 47%, about 48%, about 49%, about 50%, about 51%, about 52%, about 53%, about 54%, about 55%, about 56%, ' about 58%, ' about 60%, about 61%, about 62%, about 63%, about 6' %, ' about 66%, about 67%, about 68%, about 69%, about 70%, about '71 %, about 72%, ' about 74%, about 75%, about 76%, ’ about 78%, about 79%, about 80%, about 81 %, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% relative to the animal not having been administered one or more microbial itions of the present disclosure. {0377} In some embodiments, the decrease of any one or more of the traits of the present disclosure is a decrease of at least 0.13/8, at least 0.2%, at least 0.3%, at least 0.4%, at least 0.5%, at least 0.6%, at least 0.7%, at least 0.8%, at least 0.9%, at least 1%, at least 2%, at least 3%, at least 4%, at least 5%, at least 6%, at least 7%, at least 8%, at least 9%, at least 10%, at least 11%, at least 12%, at least 13%, at least 143/8, at least 15%, at least 16%, at least 17%, at least 183/8, at least 19%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 3 %, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 4l%, at least 429/8, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 4 %, at least 49%, at least _,0%, at least 51%, at least 529/6, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 619/6, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 8 %, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 979/6, at least 98%, at least 99%, or at least 100% relative to the animal not having been administered one or more microbial compositions of the present disclosure.

Mode of Action: Gastrointestinal Health Improvement and Competitive Exclusion {0.378} The influence of the gastrointestinal microbiome on broiler health is well known (Roberts, 2015; , 2012, Lee (presentation); , 2014)—a healthy intestinal system will improve the overall welfare and performance of birds in a commercial farm g.

Although the exact roles and mechanisms of individual species within this intricate and complicated system are still largely unknown, the l beneficial effects of microorganisms on the host’s health and performance have been studied. The current dge of metabolism and mechanisms of action are summarized below. See . (Pourabedin and Zhao. 20l5, FEMS Microbiol. Lett. 362zfnv122), depicts a suite of interactions that are all modulated by the composition of the intestinal tract with a well—balanced population of commensal microbes with an adequate supply of prebiotic itions. For example, the cornrnensal bacteria are (1) ing antibacterial compounds to compete with other organisms, including pathogens, (2) producing simple fatty acids involved in lic regulation and energy use, (3) immunomodulating the localized immune responses in conjunction with lymphocytes and antigen presenting cells, etc. {0379} General Nutrition and Gut Health {0380} Increasin the concentration of beneficial molecules, includin short chain fattv acids and other or, anic acids in the tastrointestinal tract of the broiler im )roves bird erformance. {0381} Microbial short chain fatty acid production, in particular, are absorbed and metabolized by the bird and can provide 5% to 15% of the daily requirements for bird maintenance energy lowski, 2007; Annison, 1968, Gasaway, 1976ab). Previous studies have shown that supplementation of butyrate can improve both overall weight gain and feed—conversion when administered daily to the bird, and that supplementation of any organic acid (including funraric and lactic) can improve bird, weight gain (Levy, 2015; Gilliland, 1977; Afil, 2010). Levy, et al. (2015) showed that improvements in body weight gain and feed conversion sed linearly with increasing concentrations of encapsulated butyric acid levels. Butyrate also enhances vili development (Chamba, 2014) activates the immune response, and can also have a direct bactericidal effect (Gantois, 2006). {03821 1m rovinO‘ develo Jinent of the Iastrointestinal tract enhancing villi ‘rrowth and stimulating the immune . {0383} Supplementation of butyrate and other organic acids to the diets of birds have been shown to enhance vili development and stimulate the immune system (Chamba, 2014; Adil 2010; Adi12011). 103341 Internaliis.anagram.inatal).olizablannexasigfltliadiet {0385} Fermentation of various microbes can t carbohydrates to various end products Most shoit chain fatty acids produced by these microorganisms are absorbed and utilized by the bird (Rinttila, 2013; Annison, 1968; Gasaway, 1976ab). The synthesis of vitamins, including vitamins 13 and K, are also carried out by microorganisms (Cummings, 1997). {0386} Competitive ion {(3387} Bacteriocin production {(1388} Microorganisms within the gastrointestinal tract self—regulate through the production of various antimicrobial chemicals, Bacteriocins, for example, are commonly produced by lactic acid microorganisms and can prevent the colonization of pathogens 1:Chen, 2007; Juven 1990).

Short—chain fatty acids been shown to impact and inhibit enteric ia including Salmonella lyphz’murmm, but do not inhibit beneficial, native microorganisms (Van der Wielen et al., 2000).

Both propionic acid, butyr'ic acid, acetate has also been shown to inhibit pathogenic bacteria nek, 1999; Van der Wielen, 2000; Immerseei, 2003). [03891 Com )etitive use of nutrients bindin‘r sites {(1390} Birds are first inoculated with microorganisms shortly after birth. As the bird continues to develop, the microbiome colonizes and establishes , ultimately ng a stable ecosystems that houses organisms that occupy all niches and es all available nutrients (Callaway, 2008).

This ive, stable community can prevent ens from colonizing. {0391} Creatin environments that are not conducive to athooen, rowth {0392} Microorganisms residing within the gut reduce the redox potential within the gut, creating an environment suitable for obligate anaerobes to flourish (Cummings, 1997; Chicklowki, 20017; Juven 1990). Lactate and other short chain fatty acid production lowers the pH of the gastrointestinal environment, making it more difficult for pathogens to ze and grow (Pourabedin, 2015). Native microorganisms have also been shown to neutralize enterotoxins (M’Sadeq, 2015).

EXAl‘t/H’LES Example 1. Microbial Com osltions Associated with [m roved Feed nc ‘ rs ASE—154 Phase I and H" {0393} The objective of this study was to leverage the Ascus Biosciences technology to utilize mutual information to rank the impoitance of microbial strains residing in the gastrointestinal tract of broilers associated, with improved feed efficiency. For each sample, the presence and number (cell count) of each microorganism type was ined and integrated to yield the absolute cell count of each microorganism strain present in the samples. The active strains were identified, and all inactive strains were removed from uent analysis. The maximal information coefficient (MIC) was then determined for all active microorganisms as well as relevant performance metadata of each bird. s were pooled to create a list of all relationships and their corresponding MIC scores, 1f the relationship scored below a given threshold, the relationship was identified as irrelevant If the relationship was above a given threshold, the relationship was identified as relevant, and is further subjected to network analysis in order to identify the strains that best influenced desirable logical and performance characteristics. In this example, this approach was used to identify ganisms that improve feed efficiency / reduced feed conversion ratio. [0394} Phase 1 comprises the ation of 2.16 Cobb 500 broiler chickens over 21 study days, with actions/events performed on days 0, 14, 15, 16, 17, 18, 19, 20, and 21 (. Phase 11 comprises the utilization of 216 Ross 708 broiler chickens over 21 study days, with actions/events med on days 0, 14, 15, 16, 1'7, 18, 19, 20, and 21 (. The Cobb 500 and Ross 708 cial production broiler chickens were all male and were 1 day of age upon t (Day 0); Cobb 500 chickens were from Siloam Springs North and Ross 708 chickens were from Siloam Springs North. Chickens were separated into two main groups, l20 were utilized at day 0 and tagged and placed into floor pens, and 96 were ed at day l4 and were placed into individual cages. {0395} Phase I and H utilized Test Article I, Coccidiostat (Sacox 60); Lot Number/Expiration: 3/August 2017, which is manufactured, by arma Inc. Coccidiostat was commercially available at a concentration of 60g/lb with an inclusion level of SOg/ton, and was stored in a secured and temperaturemonitored dry area. The method of administration was via complete feed over a duration of El days (Starter). Coccidiostat was stered ad libirum in complete feed. {0396} Phase l utilized Feed Additive l, l’hytase 2500 from Nutra Blend, LLC; Lot Number: 06115AO7. Phytase 25:00 was commercially available at a concentration of 2,500 FTU/g with an inclusion level of 0.02%, and was stored in a secured and temperatureunionitored dry area. The method of administration is via complete feed over a duration of 21 days. Phytase 2500 was administered ad libitum in complete feed. {0397} The starter hasal diets were manufactured at Colorado y Research, lnc. (CQR) feed mill using a standard CQR formulated broiler diet representative of a commercial broiler diet (Industry Standard Average). Basal and treatment diet mixing, pelleting, and crumbling was conducted at CQR using a 500—lb ty vertical mixer, a 4,000~lb capacity vertical mixer, or a l4,000~lb horizontal mixer and California Pellet Mill system. Approximately 342 lbs of feed was mixed per treatment The feed was stored in 5011*) capacity feed sacks and/or bulk storage lains labelled with treatment identity and further identified with a color code~ {0398} The basal feed and treatment diets were sampled in ate (~300 g sample size). One sample of the basal and each treatment diet was submitted to the sponsor for assay and one sample was retained by CQR until study end. All samples were labelled with the CQR project , treatment , sample description, and date of collection.

Experimental Design Test Groups E0399} Upon placement, chicks were placed into pens based on breed and dietary treatment. The study was divided into two , the aforementioned Phase I and Phase II. The phases took place two weeks apart. The birds were placed in floor pens by treatment from 04141). For each phase, the test facility was divided into 1 block of 2 pens and 48 blocks of 2 individual cages each. Treatments were assigned to the pens/cages using a te randomized, block design; ages retained their ents throughout the study: The treatments were identified by numeric codes. Birds were assigned to the cages/pens randomly according to CQR standard operating procedure B 10. Specific treatment groups were designed as depictedin Iahle 12 {9400} Table 12: Experimental design ents of Phase I and II, treatment I and II.

Treatment Treatn'rent Strain No. 'ENo Floor No. of No. No.

Description BlI‘melOOI‘ Pens/ Birds/ Cages/ Birds," Pen Treatment Cage Treatment Treatment 0042% 48 (Dr 4) Salinomycin 7 ’ 60 (DO) No '7 ‘ 43 (D14) Salinomycin , 60 (DO) 0.042% . 48 (D14) Salinomycin . 60 (DO) 48 (D14) Salinomycin A 60 (DO) Housmg {G401} ment of treatments to cages/pens were conducted using a computer m. The computer~generated assignment was as follows: Birds housed in an environmentally control facility in large concrete floor pen (size 4’ X 8’) constructed of solid plastic (4’ tall) with clean litter (See . At day 14, 96 birds were moved into cages within the same environmentally controlled facility: Each cage was 24"X18"X24" (See Lighting was via incandescent lights and a cial lighting program was used. Hours of continuous light for eveiy 24 hour period was as s in Table 13. {0402} Table 13: Lighting programing for incandescent bird ng Approximate Bird Age (Days) Approximate Hours of Approximate Light Intensity Continuous Light per 24 Hour (Foot Candles) Period [8403} Environmental conditions tor the birds (1.6., 053 it in pen, temperature, lighting, feeder, and water space) was similar for all treatment groups. ln order to prevent hird migration, each pen was checked to assure no openings greater than 1 inch existed for approximately l4 inches in height between pens.

Vaccinations [6404} Birds were vaccinated for Mareks at the hatchery. Birds were vaccinated for Newcastle and infectious bronchitis by spray application on study day 0, No other vaccinations, except those in the experimental , were administered during the study. Records of the vaccinations (vaccine source, type, lot number, and expiration date) were i'naii'itained with the study records. No ations or medications other than those disclosed herein were utilized.

‘Water {@405} Water was provided at?! iihitum throughout the study. The floor pen water was via automatic bell rs. The battery cage water was via one nipple waterer. Drinkers were checked twice daily and cleaned as needed to assure a clean water supply to birds at all times. {8406} Feed was proved ad Iibitum throughout the study. The floor pen feed was via hanging, ~l7uinch diameter tube feeders. The cage feed was via one feeder , 9"x4". A chick feeder tray was placed in each floor pen for approximately the first 4 days.

Daily Observations {@407} The test facility, pens, and birds were observed at least twice daily for general flock ion, lighting, water, feed, ventilation, and unanticipated events. The miiiiinumuniaximum temperature of the test facility was recorded once daily. h/lortality and Cults- [9408} Starting on study day 0, any bird that was found dead was removed. Birds that were unable to reach feed or water were sacrificed and necropsiedi "identification of le cause of death and necropsy findings were recorded on the pen mortality record.

Body ‘Neight and Feed Intake {@409} ~96 birds were weighed ii'idividually each day (days l4—2'l). Feed remaining in each cage was weighed and recorded daily from days l4-21i The feed intake for each cage was determined for each day.

‘Neight Gain and Feed sion {@410} Body weight gain on a cage basis and an average body weight gain on a treatment basis was determined from days l4-21. Feed conversion was calculated for each day and overall for the period of days l4~2l using the total feed consumption for the cage divided by bird weight.

Average treatment feed conversion was determined for the period of days l4~2l by averaging the individual feed conversions from each cage within the ent.

Excreta and Digesta Collection {8411} At days 15, 18, and 21, excreta produced over a r period was collected by cage, pooled and dried to measure gross energy values with bomb calorimetry. Gross energy of the feed on day 14 was measured for gross energy to determine apparent metabolic energy (Al‘le).

On day 21, each bird was euthanized by cervical ation to collect the following using the described ures (gloves were d between each bird): Randomly select 25% of the birds: {@412} Make 2 aliquots into 1.5 ml tubes for each on: cecum, small intestine (anywhere), gizzard, and crop (including mucosal scrapings). ()ne t will n 150 pl of stop solution (5% phenol & 95% ethanol) to submerge the sample. The second aliquot did not contain stop solution and was stored at 4°C for shipping. {0413} Immediately placed the contents of one cecum in a 1.5mml tube prefilled with 150 pl stop {@414} Placed the contents of the second cecum into an empty 1.5mml tube. {0415} Immediately split the contents of the small intestine and placed half in 1.5—ml tube prefilled with 150 ul stop solution Placed the other half in an empty 1.5—ml tube. {0416} Dissected the gizzard out of the GI tract, removed the contents with forceps, split the contents and placed half in a 1.5uml tube prefilled with 150 til stop solution Placed the other half in an empty l.5~ml tube. {@417} Dissected the crop out of the GI tract, removed the contents with forceps/scraped out mucosal lining, and placed, half in a 1.5nml tube prefilled with 150 pl stop solution. Placed the other half in an empty 1.51111 tube.

For the Remaining Birds: {0418} Immediately placed the contents of one cecum in a 1.5mml tube prefilled with 150 pl stop solution. {@419} Immediately placed the contents of the small intestine into a 1.5—ml tube prefilled with 150 pl stop solution.

{G420} Dissected the gizzard out of the GI tract, removed the contents with forceps, and placed in a l.5—ml tube led with 150 pl stop solution. {@421} Dissected the crop out of the GI tract, removed the contents with forceps/scrape out l lining, and placed in a 1.5—ml tube prefilled with 150 pl stop solution. {@422} Store all s at 4°C until shipment.

Veterinary Care, Intervention, and Euthanasia {8423} Animals that developed significant concurrent disease, which were injured and/or whose condition may have affected the outcome of the study were removed from the study and euthanized at the time that the determination was made. Six days post challenge, all birds in cages were removed and lesion scored. {@424} Scales used in weighing of feed and feed additives were ed and/or certified by the State of Colorado. At each use the scales were checked using standard weights according to CQR rd operating procedures.

Dispositions {0425} An accounting was maintained of all diets. The amount mixed, used and discarded was documented. Unused feed was disposed of either by e sale and/or placing into a dumpster for commercial ort to a local landfill for . Disposition was documented in the study records.

Test Animals {8426} An accounting was maintained for birds received for the study. Disposal of mortalities and birds sacrificed during the study and at study end was discarded to the landfill at study end.

Documentation of disposition was provided with the study records. No food products derived from animals enrolled in this study entered the human food chain. {0427} Average Bird weights (Day l4~2l) (Table 14) {0428} Daily Bird Performance Summarized by Treatment (Day 14—21) ( Data ted (Phase ll {0429} Average Bird weights ( Day 1443]) (Table 15) {0430} Mortality and Removal Weights (Day 14u21) (Table 16) {0431} Daily Bird Performance Summarized by Treatment (Day 14-21) ( {8432} Table 14: Phase 1, Cobb 500 performance D14~21 ole-21 7 ,7 n21 Wt Feed a i Feed (kg) Consumed Conversion Treatment Group 1 (kg)_ I Averages Standard Deviations 0.096 0.090 . Dial-=2 1 n21 Wt Did Wt Feed (kg) (kg) Consumed l Conversion Treatment Group 2 (kg) Averages Standard Deviations 0.082 0.067 {0433} Table 15: Phase H, Ross 708 performances 708 Dbl—=21 : D14 ~ 21 1:32th n14 Wt Feed (kg) (kg) Gain (kg) edl a Conversion Treatment Group 1 (kg) Averages , ( 0.373 0.301 1503 WO 81203 Standard Deviations 0.058 0.034 0.042 0.063 0.117 0.143 0.078 E314 - 21 D14 — 21 D14 Wt Ffied (kg) Gain (kg) Consumed Conversiun 'l‘reatment Gmup 2— (kg) ' Averages .' 1.515 Standard Deviations g .C "' 0.244 CV‘s 0.123 0.086 0.234 0.168 0,161 Attumey Docks! N0: ASBE—()03/’03WO Table 16: Mmtzahty and Removal Weights for Phase [E (Day 14-21) Mortahty d No. Bards 3:; "T Cause Total M & R ‘~'= "-2: 3« Remammg » Wt Wt Cage SEX g . g E "It Gig) Days .1 4.; a a 14 — 21 (kg) Day 14 ' ' 12 M 9109 BAC- 2 1 1 0 0 DH 0304 0.000 0.304 0 7 V M 9105 BA( ; i ' 1 1 i 0 0 DH 0.262, 0.000 0.262, 0 . , , , , 0. ,,,,,, ,,,,,,,,,,, . _. , 460% 3A0 1 1 1 0 0 NA 0.360 0.000 0.360 0 5 g 1214062986 v8 {0435} GE Sample Preparation and Sequencing: After collection, the gastrointestinal (GI) samples were centrifuged at 4,000 rpm in a swing bucket centrifuge for 20 minutes at 4°C. The supernatant was decanted, and, an aliquot of each gastrointestinal content sample (biting) was added to a sterile l.7mL tube prefilled with 0.1 mm glass beads. A second aliquot was collected and stored in an empty, sterile 1.7 mL tube for cell counting. {0436} GI samples in empty tubes were stained and put through a flow cytometer to quantify the number of cells of each microorganism type in each sample. Gl samples with glass beads were homogenized with head beating to lyse microorganisms. DNA and RNA was extracted and purified from each sample and prepared for sequencing on an lllumina Miseq. Samples were sequenced using paired—end chemistry, with 300 base pairs sequenced on each end of the library. {(3437} Sequencing Read Processing and Data Analysis: Sequencing reads were quality trimmed and processed to fy bacterial species present in the GI tract based on a marker gene, 168 rDNA, or ITSl and/or ITSZ. Count data sets and activity datasets were integrated with the sequencing reads to determine the absolute cell s of active microbial species within the gastrointestinal microbial community. Production characteristics of the broiler over time, including feed conversion, weight, mortality, and lesion scores, were linked to the bution of active microorganisms within each sample over the course of the experiment using mutual information {(3438} Results One component of the Ascus Biosciences technology utilized in this application leverages mutual information to rank the importance of native ial s residing in the gastrointestinal tract of the animal to ic animal traits. The maximal information coefficient (MIC) scores are calculated for all microorganisms and the desired animal trait. Relationships were scored on a scale of 0 to l, with 1 representing a strong onship between the microbial strain and the animal trait, and 0 representing no relationship, A cut~off based on this score is used to define useful and non~useful microorganisms with respect to the improvement of specific traits. {(3439} The Mle were calculated between production characteristics, ing indicators for disease such as lesion scores, and the absolute dance of each active rganism. rganisms were ranked by MK: score, and microorganisms with the t MlC scores were selected as the most relevant target species. MIC scores of the microbes of the present disclosure are recited in Table l. The greater the MIC score, the greater the y of the microbe to confer an improvement in the performance and GI health of the bird.

Example ll. Microbial Com ositions of Broilers with Necr‘otic Enteritis Utilizin. a Closiridium mariner/rs Challene Model {0440} The ive of this study was to determine the difference in ial compositions during necrotic enteritis when challenged with various levels of Ciastridium peiffifingens. More specifically, the study sought to calculate MIC scores for microbes in the gastrointestinal tract of broilers challenged with the pathogen. In this instance, the MIC scores were calculated between production characteristics, including indicators for disease such as lesion scores and the absolute abundance of each active microorganism. Microbes with the highest h/IIC scores have the greatest ability to confer an improvement in the gut performance and gastrointestinal health of broilers. {0441} This study ed, 160 Cobb 500 broiler ns over 21 study days. The Cobb 500 cial production broiler chickens were all male and were 1 day of age upon receipt (Day 0); Cobb 500 chickens were from Siloam Springs North. Chickens were separated into four treatments with twenty birds per pen and two pens per treatment. {0442} The study utilized a feed additive, Phytase 2500 from Nutra Blend, LLC; Lot Number: 06115A07. Phytase 2500 occurred was commercially available at a concentration of 2,500 FTU/g with an inclusion level of 0.02%, and is stored in a d and temperature—morntored dry area. The method of administration was via feed over a duration of 21 days. {0443} The starter basal diets were manufactured at Colorado Quality Research, Inc. (CQR) feed mill using a standard CQR formulated broiler diet representative of a commercial broiler diet (Industry Standard Average) without tion. Basal and starter diet mixing, pelleting and ing was conducted at CQR using a SOO—lb capacity vertical mixer, a 4,000-lh capacity veitical mixer, or a l4,000~lh horizontal mixer and California Pellet Mill system. Approximately 540 lbs of feed was mixed per ent. The feed was stored in SOlb capacity feed sacks and/or bulk e bins labelled with treatment identity and further identified with a color code. {0444} The basal feed and treatment diets were sampled in ate (~300 g sample size). One sample of the basal and each treatment diet was submitted to the sponsor for assay and one sample was retained by CQR until study end. All samples were labelled with the CQR project number, treatment number, sample description, and date of collection.

Ex tal Desian Test Groups {(1445} The test facility was divided into 2 blocks of 4 pens. Treatments were assigned to the pens/cages using a completely ized block design. Birds were assigned to the pens randomly according to CQR rd operating procedure Bali). Specific treatment groups were designed as ed in Table 18. {0446} Table 18: Experimental design for treatments 1—4.

No.13irds/ No. of No. ofBirds/ Treatment Clgilligge ent Description Pens Treatment _—NonChatlenzedChallenged with l1alf typical dose (125 n1l/biid, 2.09.03:108 Cfu/ml Challenged with typical dose (2.5 ml/bird; 2.03.0)(103 cfu/ml) Cl’iallenged with twice the typical dose (5 nil/bird; 2.0— l l Housing {11447} Assignment of treatments to cages/pens were conducted using a computer program. The computer—generated assignment was as follows in Table 19 {11448} Table 19: Computer selection of treatments to pens. ent 4 {0449} Birds were housed in an environmentally control facility in wooden floor pens (N 4’ x 4’ minus 225 sq. ft for feeder space) providing floor space and bird density of ~06?) ftz/bird and temperature, lighting, feeder and water space was similar for all test groups 1: See Fit}. 9). Birds were placed in clean pens ning an appropriate depth of wood shavings to provide a comfortable environment for the chicks. Additional shavings were added to pens if they became too damp for comfortable conditions for the test birds during the study. Lighting was via incandescent lights and a commercial ng program was used as noted in the following table. {0450} Table 29: Lighting programing for incandescent bird lighting (Reproduced from Table 11 in previous example) Approximate Bird Age (Days) Approximate Hours of Approxii'nate Light Ii’itensity Continuous Light per 24 Hour (Foot Candles) Period {0451} In order to prevent bird migration and bacterial spread from pen to pen, each pen had a solid (plastic) divider for approximately 24 inches in height between pens. ations {G452} Birds were ated for Mareks at the hatchery. Birds were vaccinated at CQR for Newcastle and ious bronchitis by spray application on study day 0. No other vaccinations, except those in the experimental design, were administered during the study. s of the ations (vaccine source, type, lot number, and expiration date) were maintained with the study records. No vaccinations or medications other than those disclosed herein were utilized.

Water {0453} Water was provided ad Iibitum throughout the study via one Plasson drinker per pen.

Drinkers were checked twice daily and cleaned as needed to assure a clean water supply to birds at all times. {0454} Feed was proved ad libitum throughout the study via one hanging, NIT/"inch diameter tube feeder per pen. A chick feeder tray was placed in each floor pen for approximately the first 4 days. Birds were placed on their tive treatment diets upon receipt (day 0), according to the Experimental Design. Feed added and d from pens from day 0 to study end were weighed and recorded.

Daily Gbser’va’tions {8455} The test ty, pens, and birds were observed at least twice daily for general flock condition, lighting, water, feed, ation, and unanticipated events. If abnormal conditions or abnormal behavior was noted at any of the twiceudaily observations they were noted in the study records. The rninimurnumaximum ature of the test facility was recorded once daily.

Pen Cards [8456} There were 2 cards attached to each pen. One card identifies the pen number and the second will include the ent number.

Animal Handling [8457} Animals were kept under ideal conditions for livability, The animals were handled in such a manner as to reduce injuries and unnecessary stress. Humane measures were strictly enforced. nary Care, Intervention, and Euthanasia {G458} Birds that developed clinically significant concurrent disease unrelated to the test procedures were, at the discretion of the investigator or designee, removed from the study and euthanized in accordance with site standard ing procedures. In addition, moribund or injured birds may also be euthanized upon authority of a site veterinarian or a qualified technician. Any reasons for withdrawal were documented. In an animal died, or was removed and euthanized for humane reasons, it was recorded on the ity sheet for the pen and a necropsy performed, and was filed to document the reason for removal. If euthanasia was deemed necessary, animals were euthanized via cervical dislocation.

Mortality and Cults {9459} Starting on study day 0, any bird that was found dead was removed weighed and necropsied. Birds that are unable to reach feed or water were sacrificed and necropsied. The weight and probable cause of death and necropsy findings were recorded on the pen ity Body vlit/eight and Feed intake {0460} ~Birds were weighed by pen and dually on approximately days 14 and 21. The feed remaining in each pen was weighed and recorded on study days 14 and 21. The feed intake during days 14—21 were calculated.

Weight Gain and Feed Conversion {0461} Average bird weight, on a pen and individual basis, on each weigh day was summarized.

The average feed conversion was calculated on study day 21 using the total feed consumption for the pen divided by the total weight of ing birds. Adiusted feed conversion was ated using the total feed consumption in a pen d by the total weight of surviving birds and weight of birds that died or were removed from that pen.

Diesta Collection {0462} On day 21, each bird was euthanized by cervical dislocation to collect the following using the described procedures, gloves were changed between each bird. {0463} Immediately place the contents of one cecum in a 1.5—ml tube prefilled with 150 pl stop solution. {0464} Immediately place the contents of the small intestine into a 1.5uml tube prefilled with 150 pl stop solution. {0465} Dissect the gizzard out of the GI tract, remove the contents with forceps, and place in a 1.5—1nl tube prefilled with 150 pl stop on. {0466} Dissect the crop out of the GI tract, remove the contents with forceps/scrape out mucosal lining, and place in a 1.5nn1l tube led with 150 pl stop solution. {0467} Store all samples at 4"C until shipment.

Scales {(1468} Scales used in weighing of feed and feed additives were licensed and/or certified by the State of Colorado, At each use the scales were. checked using standard weights according to CQR standard operating procedures.

Closz‘ridium " er lens Challen e h’lethod of Administration {9469} The Cloistridtum gens culture was obtained from Microbial Research, Inc.

Administration of the C. peiffI/‘ingens :, Type A, o: and [32 toxins) cultures in this study were 'via the feed. Feed from each perfs feeder was used to mix with the culture. Prior to placing the cultures in the pens, the treatment feed was removed from the birds for approximately 4~8 hours. For each pen of birds, a fixed amount based on study design of the broth e at a concentration of imately 2.0 — 9.0 X 108 cfu/ml was mixed with a fixed amount of feed (~25g/bird) in the feeder tray and all challenged pens were treated the same. Most of the culture" feed was consumed within l~2 hours. So that birds in all treatments are treated similar, the groups that are not challenged also had the feed removed during the same time period as the challenged groups.

Clostridium Challenge {0470} The C. perfiirtgens culture ) was grown for «5 hours at ~37OC in fluid thioglycollate medium containing . CL—IS is a field strain of C. peifi‘mgens from a broiler outbreak in Colorado. A fresh broth culture was prepared and used each day. For each pen of birds, a fixed amount of the overnight broth culture was mixed with a fixed amount of treatment feed in the feeder tray (see administration). The amount of feed, volume, and quantitation of culture inoculum, and number of days dosed was documented in the final report, and all pens were treated the same. Birds received the C. perji‘z’ngens culture for one day (day l7).

Quantitation was ted by Microbial Research, Inc on the culture and s were documented in the final report. There was no target ity for this study.

Lesion Scoring {0471} Four days following the last C peifrmgens culture administration, five birds were randomly selected from each pen by first bird , sacrificed, and intestinal lesions scored for necrotic enteritis Lesions were scored as follows: {0472} l) = normal: No NE lesions, small intestine has normal elasticity (rolls back to normal position after being opened). {6473} l mild: Small intestinal wall is thin and flaccid (remains flat when opened and doesn’t roll back into normal position after being opened); excess mucus COVCI‘ll’Ig mucus ne. {@474} 2 moderate: Noticeable reddening and swelling of the inal wall; minor ulceration and necrosis of the intestinal membrane; excess mucus.

{B475} 3 severe: Extensive area(s) of necrosis and ulceration of the small intestinal ne; significant hemorrhage, layer of fibrin and necrotic debris on the mucus membrane (Turkish towel appearance). {(1476} 4 dead or moribund: Bird that would likely die within 24 hours and has NE lesion score of 2 or more.

Disgosltions Excess Test Articles {0477} An accounting was maintained of the test articles received and used for this study. Excess test articles were dispositioned or returned to the sponsor. Documentation was provided with the study s. {0478} An accounting was maintained of all diets. The amount mixed, used and discarded was documented. Unused feed was disposed of either by e sale and/or placing into a dumpster for commercial transport to a local landfill for burial. Disposition was documented in the study records.

Test s {0479} An accounting was maintained for birds received for the study. al of mortalities and birds iced during the study and at study end was discarded to the landfill at study end.

Documentation of disposition was provided with the study records. No food products derived from animals enrolled in this study entered the human food chain.

Data Collected {0480} Mortality and Removal s for Cobb 500 Males Spanning Days 0 to Study End (Table 21). {0481} Average Bird Weights and Performance at Day 14 Summarized by Treatment (Table 22). {0482} Average Bird Weights and Performance at Day 21 Summarized by ent (Table 23). {0483} Pen Weights and Feed Conversion for Cobb 500 Males Days 14—21 Summarized by Treatment (Table 24). {0484} Day 21 NE Lesion Scores for Cobb 50): Males Summarized by Treatment (Table 25).

Table 21: Martzahty and Removal Weights for Cobb 500sz165 Spanning Days 0 to S‘ dy End TotaEM Mnrtality Added Rammed Removal—i & RWt N0, Birds Cause of Death Wt (kg) Remaining Days: 0 — 0.000 0.000 0.000 0.000 0.000 0.000 Bloc Pen Removalr‘i N0. Birds Remaining Cause of Death Wt 3{ Nu. 1 2. 1 20 01000 20 1 4 2 20 1110130 20 ' ' 1 2 3 20 1 SDS 0225 0.235 19 , , , I ....i....§.....4..... W21)..." ‘WHHWHHWVWHHW""77"", HWHHWHH: 0.()0() 20 2 20 e = f g 0,000 20 2 4 6 20 é 110110 20 ' 7 7 2‘} 1 ; 0.900 2(3 3 8 20 0,0110% ' ' 2 4 6 20 3 3NE 1.904 1.904 17 2 1 7 20 . 0.000 20 2 § 8 20 1 ; g NE ; ; 0.672 0.672 19 No. S 14Avg Bi rd 0 Mortalitie Rename-(E Bird Wt Totals & Averages ’ . . 1.001 _ i (iV's " ; i 0.422% , 1.039% 8,047 Totals&Aver0ges ’ . 3 . 0.985 0.985 Standard Deviatiems : 0.010 0.001 0.000 0.000 CV’S 0.200% 0.200% 0.038% 0.038% 1 2 3 20 1 019 8.160 "0.42757 0.993 0.965 2 a 3 ""7210" 0 0 20 138060442 0993 0.993 Totals&Avemges ' , E . . 0.993 0.979 Standard Deviations : ' . . 0.000 0.020 CV’s g 3 "87.062112? 2.240% 0.006% 2.001% T011031 & Averages: 40 0 0 40 8.488 0.424 0.991 0.991 _ .

Standard Deviations ""70.070’i""" 0.005 0.003 g 0.003 CV’s i '"100307;"""’1?'.’1’)§0'355/i.""" 0.767% 0.767% Table 23: Average Bird Weights and mamzé at Day 21 Summarizéd by Treatment Day 21 Adjusted Bird Wt 061:) Totals &Averagcs / i / . .’ 1.007 Standard Deviatians 0.149 0.007 0.005 0.005 WO 81203 0.885% 0.448% 0.448% 1 i 2 Totals &Averziges , . g . . . "339 1 7 Standard Deviations . . . (3.044 CV’S ’ 3 . . ,. 4.214% 0.901 """ """ """" """" 2 ‘ ‘ 3 :t i : . i078 ’i‘otals8z-Average8 i 40 3 0 30 14.577 0.811 1.075 1020 ' ' Standard Deviations ""0033": 0.029 0.073 0.082 CV’s '"4.343%"""’3".’5éi%’"i"6.703% 8.086% Totziis &Averages 40 5 0 35 14.321 0 8218 i 120 1.010 L 7777 VVVVVVV '7 H Standard Deviations : 727 410M 0.085 0.039 W4.éiié%m§ 0.102% 7.535% 3.797% Table 24: Pen Weights and Feed Conversion for Cobb 500 Males Days 14-21 Summarized by Treatment [114—2 ‘1 Nu. Feed Avg Adj" Feed ity AH Birds Conversion Black Trt Bird Canversion Weighed D14—2 1 Rem Remm'éaiuz Gain Totals 8; Averages 16.862 : I r Standard Deviations : i : 0.149 0.007 0009 0.020 0.020 ' : : 7 CV’S 0,8855% €776.7885%§ 2,2110% 1.996% 1.996% 14.755 "715,102 Totalsé’z Averages Standard _ : _ 1 _ : 2 5 ; Deviatinns 0.245 0.012 0.042 0.097 ’ '- f ‘ "- 1.644011215449412 3 CV’S . 31035% 8.786% 1 ’3""3 10 1"" 0 0" 0 18 "14.120 0785 0.355 1.066 0.924 ’ ’ 2 8 10 0 0 0 0 20 "15024 0‘51 0.308 1.319 1.189 Totalsé’; Averages Standard : 7 . . .

Deviations i : 0.034 : i 0.187 _. _._, _ CV’S 1700700 0.992 1.490 g 1.099 T012658; . : Averages 40 0 0 0 0 40 14.321 0.710 0.292 1.332 1.04:3 7 7 7 ’ ’ Standard . .

Deviations 0.602 0.030 0.035 0.224 0.075 (W's ’ ’ g % 2";1.’202% ; 11.893% 10.80904, 7.199% WO 81203 {0489} Table 25: Day 21 NE Lesion Scores for Cobb 500 Maies Summarized by Treatment Average Totals 8; Avemges Standard Deviations CV’s 161.0% WO 81203 Totals & Averages Standard Deviations 1.2 C‘V’s 63.0% Averages Standard Deviation s apaplaha Totals & Averages Standard Deviations 0.8 CV’s 35.9% [0490} GE Sample ation and Sequencing: After collection, the intestinal (Gt) samples were centrifuged at 4,000 rpm in a swing bucket centrifuge for 20 minutes at 4°C. The supernatant was decanted, and an aliquot of each gastrointestinal content sample (l~2mg) was added to a sterile l.7mL tube prefilled with 0.1 mm glass beads. A second aliquot was ted and stored in an empty, sterile 1.7 mL tube for cell counting. [0491} G1 samples in empty tubes were stained and put through a flow cytometer to quantify the number of cells of each microorganism type in each sample. Gl samples with glass beads were homogenized with head beating to lyse microorganisms. DNA and RNA was extracted and ed from each sample and prepared for sequencing on an lllumina Miseq. Samples were sequenced using paired—end chemistry, with 300 base pairs ced on each end of the library. {0492} Sequencing Read Processing and Data Analysis: Sequencing reads were quality trimmed and processed to fy bacterial species present in the GI tract based on a marker gene, 16$ rDNA, or I'I‘Sl and/or ITSZ. Count data sets and activity datasets were ated with the sequencing reads to determine the absolute cell numbers of active microbial species within the gastrointestinal microbial community. Production characteristics of the broiler over time, including feed conversion, weight, mortality, and lesion scores, were linked to the distribution of active microorganisms within each sample over the course of the experiment using mutual information. {0493} s One component of the Ascus Biosciences technology utilized in this application leverages mutual information to rank the importance of native microbial strains residing in the intestinal tract of the animal to specific animal traits. The maximal information coefficient (MIC) scores are calculated for all microorganisms and the desired animal trait. Relationships WO 81203 were scored on a scale of 0 to l, with 1 representing a strong relationship between the microbial strain and the animal trait, and 0 representing no relationship. A cutuoff based on this score is used to define useful and nonnuseful microorganisms with respect to the improvement of specific traits. {@494} The MICs were calculated between production characteristics, ing indicators for disease such as lesion scores, and the absolute nce of each active microorganism.

Microorganisms were ranked by MIC score, and microorganisms with the highest MIC scores were selected as the most relevant target species. MIC scores of the microbes of the t disclosure are recited in Table l. The greater the MIC score, the greater the ability of the microbe to confer an improvement in the performance and GI health of the bird.

Example Ill. Media Recipes of the Present Disclosure {0495} Medium Preparation: {ll-496} Dry reagents for each medium (recipes below) were weighed out, and combined in a flask, Liquid reagents for each medium, if applicable, are then added to the flasks DI water was added to the flask to bring the medium to its final volume ally one liter). The medium was d, and then aliquoted into individual serum bottles or Hungate tubes. Serum bottles were filled with 2.5 rnL or 50 lTlL of medium, and Hungate were filled with 10 mL of medium. The serum s/hungate tube were bubbled with 20:80 COg/Ng for 45 minutes. The bottles were then stoppered, and autoclaved at l2l°C for IS minutes. After autoclaving, Cysteine—HCI was added to every bottle to e a final concentration of lmM CysteinemHCl. Any post autoclaving reagents were also added. All of the post autoclavmg reagents were sterile filtered using a 022 um filter prior to addition. {0497} Sample Preparation: 8} Samples from the gastrointestinal tract of broilers were mixed with 500 mL of IX RAB/[M and homogenized by ing in an anaerobic chamber. The samples were then serially diluted and added to the prepared serum bottle/hungate tube. The inoculated bottles were inclubated at 37°C for a minimum of 24 hours, Additional nds were added to the media after autoclaving when noted: (1) sterile butyric acid was added to achieve a final concentration of lOmN, (2) glycerol was added to achieve a final concentration of l0 mM, (3) acetic acid was added to achieve a final concentration of 10 mM, (4) amin acid D solution was added to achieve a final concentration of 10 rnM, and (5) arabinose and xylose solution was added to achieve a final concentration of 10 rniVl. {@499} For enrichments requiring diluted media, the final media preparation was diluted 1:10 with DI water prior to aving. The d media was aliquoted, into serum bottles or hungate tubes, and then bubbled, under 10:80 COg/i '2 for 45 minutes to an hour prior to aving. {@500} Media: {0501} Table 26: Spirillum Medium Component Bacto Peptone Succinate (NIH-)ZSO/Ll MOSOAlXT’HZO lOn1h Treatments were administered, to the pens at start of study day 0. The treatments will identified by numeric codes. Specific treatment groups are as follows. There were two ent groups, 1 and 2. Each group consisted of twenty birds per pen with a total of 20 pens. The total number of birds per treatment was 400. Treatment 1 consisted of nonnchallenged birds. Treatment 2 consisted of treatment with Ascusbbr___5796, Ascusbbr___3 8717,, and Ascusbbr____331885. The Ascus microbial consortia were administered to the birds in the treatment group Via drinking water daily. {(1516} Housing and Management {11517} Treatments were randomly assigned to each pen using Microsoft Excel random number generator by the Data r. Birds were assigned to the pens randomly.

} Birds were housed within an environmentally controlled in concrete floor pens providing floor space & bird density of {~0.55 ft2/bird (day 0); ~ 0.69 ft2/hird (day 21 after lesion scores)], temperature, humidity, lighting feeder and water space were similar for all test groups. Birds were placed in clean pens containing an appropriate depth of clean wood gs to provide a comfortable environment for the chicks. onal shavings were added to pens in order to maintain bird comfort. Ligl'iting was via incandescent lights and a commercial lighting program was used as follows. {@519} Table 34: Housing Description ''''''''''''''''''''''''''''''''''''l"Kfifiiiiiiiiiiaiéfilifiiém Approximate of Continuous ~Light ity Bird Age (days) Light (foot candles) per 24 hr period } Environmental conditions for the birds (ie. bird density, temperature, ng, feeder and water space) were similar for all treatment groups. In order to prevent bird migration and bacterial spread from pen to pen, each pen will have a solid wood or plastic divider for imately 24 inches in height between pens. {0521} Vaccinations and, Therapeutic Medication {0522} Birds were vaccinated for Mareks at the hatcheiy. Upon receipt (_study day 0), birds were vaccinated for Newcastle and Infectious Bronchitis and Coccivac by spray ation using a spray cabinet. Documentation of vaccine cturen lot number and expiration date was provided with the final . {0523} Water {@524} Water was provided ad Iz’bz‘rzim throughout the study via one automatic nipple drinker (4 nipples per drinker) per pen. Drinkers were checked twice daily and cleaned as needed to assure a clean and nt water supply to the birds. {"523 fiend {9526} Feed was provided ad Iibizum throughout the study via one hanging ~17~inch diameter tube feeder per pen. A chick feeder tray was placed in each pen for approximately the first 4 days. Birds were placed on their respective treatment diets upon receipt (day 0) according to the Experimental Design. Feed added and removed from pens from day 0 to study end was weighed and recorded. [0527} Dailv observations [6528} The test facility, pens and birds were observed at least twice daily for general flock condition, lighting, water, feed, ventilation and unanticipated events. If abnormal conditions or abnormal behavior is noted at any of the twice—daily observations they were documented and included with the study records. The niininiumuinaxiinum temperature of the test facility was recorded once daily. {@529} Pen Cards {@530} There were 2 cards attached to each pen. One card identifies the pen number and the second will e the ent number. [9531} Animal Handling {0532} The animals were kept under ideal conditions for livability. The animals were handled in such a manner as to reduce injuries and, ssary stress. Humane measures were strictly enforced. {0533} Veterinag Care: Intervention and Euthanasia {8534} Birds that develop clinically significant concurrent disease ted to the test procedures may, at the discretion of the Study igator, or a designee, be removed from the study and euthanized in accordance with site SOPs. In addition, moribund or. injured birds may also be euthanized upon authority of a Site Veterinarian or a qualified technician. The reason for withdrawal was documented. If an animal dies, or is removed, and euthanized for humane s, it was recorded on the mortality sheet for the pen and a necropsy med and was filed, to document the reason for removal. If euthanasia is deemed necessary animals were euthanized by cervical ation. {0535} Mortality and Culls {0536} From Day 0 to study end any bird that is found dead or is sacrificed was weighed and necropsied. The weight and prohable cause of death and necropsy findings were recorded on the mortality record, If sex~shps are noted at any time during the study they were removed, weighed, necropsied to confirm sex and recorded on the pen mortality record. i0537l Eilfeiahttandfieedlntahe {(3538} Birds were weighed by pen on approximately day 0, 17, 28 and 35. The feed remaining in each pen was weighed and recorded on study days 17, 28 and '35. The feed intake during days 0 l7, l7 28, and 0 35 was calculated, [0539} Weight Gains and Feed Conversion {(3540} Average bird weight, on a pen basis, on each weigh day was summarized Bird weight gain by pen days 17 28 was calculated. The average feed sion was calculated on the study days 17 and 28 (ie. days 0 l7, l7 35, and 0 35) using the total feed consumption for the pen divided by the total weight of surviving birds. Adjusted feed sion was calculated using the total feed consumption in a pen divided by the total weight of surviving birds and weight of birds that died or were removed from that pen. {(3541} Table 35: Results Treatment Description Non" Challenged with salinomycin Treated with salinomycin and Ascus Composition: Ascusbbr___5796, Ascus bbr___3 8'7l '7, Ascusbbr___3 3188 5 {0542} The birds were treated, with a composition of Ascus microorganisms to determine their effects on performance. Three microorganisms, Ascusbbr___5796, Ascusbbr___387l7, and Ascusbbr___331885 were stered daily to the experimental birds via their drinking water over the course of the entire experiment. All birds were on a commercially relevant pelleted feed that included salinoniycin.

} At the end of the ment, birds were sacrificed and weighed Feed conversion was calculated based on the total feed consumption for the pen divided by the total weight of the surviving birds. The treatment group was found to have a slight improvement in feed conversion (1%) and individual bird weight gain (4%) as compared to the control group.

Example V, TRTAL 2 — in viva evaluation of Ascus Nlicrobial ition vs. Clostridium perfringens Challenge {(3544} Basal and Experimental Diets {0545} The starter, grower and basal diets was manufactured using a feed mill and stored in bulk. {(3546} Final experimental diet mixing pelleting and crumbling was conducted using a 500~lb ty vertical mixer, a 4000~lb capacity vertical mixer and/or a 14,000—lb horizontal mixer and a California Pellet . Feed was stored in SO-lb capacity feed sacks and/or bulk storage bins labeled with treatment code. Phytase was included in all diets throughout the experiment. {ll-347} The g schedule utilized two feeds a starter feed in crumble form and a grower feed in pellet form. The starter feed was fed from days 0 to 1'7, and the grower feed was fed from days l7 to 35. The A scus microbial consortia were administered to the birds in the ent group via drinking water daily. {0548} Test System Species Broiler Chicken Strain Commercial production Breed/Cross Cobb 500 Supplier TBD Sex Males Age ~1 day of age upon receipt (day 0) ~35 days at final weights Identification Pen cards Number of birds: 900 (D0) Number of treatments: 3 Number of pens/treatment: '12 Number of birds/pen: 25 (DO) Number of birds/treatment: 300 (D0) Total number of pens: 36 {0549} Test Groups } Treatments were assigned to the pens using a complete randomized block design, Treatments were administered to the pens at start of study day 0, The treatments will identified by numeric codes Challenged control treatments comprise the administration of pathogens as the control Challenged Ascus itions comprise the administration of experimental mi crobes. Specific treatment groups are as follows: {@551} Table 36: Test Groups Challenged ,. t No. of No. of Number of Description Birds/Pen Pens Birds/TN Challenged Control (non—medicated) Challenged Control w / salinomycin Challenged, Ascus Composition stered: br_4729., Ascusbbr_331885, Ascusbbr_ 17021 1 (water application) [0552} Housing and Management [0553} Housing {0554} Treatments were randomly assigned to each pen using oft Excel random number tor by the Data Manager. Birds were ed to the pens randonily."Birds were housed within an environmentally controlled in concrete floor pens providing floor space & bird density of [~O.55 ft2/bird (day 0); ~ 0.69 fig/bird (day 21 after lesion scores)], temperature, humidity, lighting, feeder and water space were similar for all test groups. Birds were placed in clean pens containing an appropriate depth of clean wood shavings to provide a comfortable environment for the . Additional shavings were added to pens in order to maintain bird comfort.

Lighting was via incandescent lights and a commercial lighting program was used as follows. 30555} Table 37: Lighting imate Hours Approximate of Continuous ~Light Intensity Bird Age (days) Light (foot candles) per 24 hr period """"""""""""""""""""""""""" —13 1.0 l 3 Or 2 — 0.3 0.2 0.3 {@556} Environmental conditions for the birds (ie. bird density, temperature, lighting, feeder and water space) were r for all ent . In order to prevent bird migration and bacterial spread from pen to pen, each pen will have a solid wood or plastic divider for approximately 24 inches in height between pens. [0557} Vaccinations and Thera )eutic Medication [0558} Birds were vaccinated for Mareks at the hatchery. Upon receipt (study day 0), birds were vaccinated for Newcastle and Infectious Bronchitis and Coccivac by spray application using a spray cabinet. Documentation of vaccine manufacturer, lot number and expiration date was provided with the final report. [0559} Water Water was provided ad Itbz'r‘zmz throughout the study via one automatic nipple drinker (4 nipples per drinker) per pen. Drinkers were checked twice daily and cleaned as needed to assure a clean and nt water supply to the birds.

Feed was provided, ad m throughout the study via one hanging, ~l7—inch er tube feeder per pen. A chick feeder tray was placed, in each pen for approximately the first 4 days. Birds were placed on their respective treatment diets upon receipt (day 0) according to the Experimental Design. Feed added and, removed from pens from day 0 to study end, was weighed and recorded.

Daily observations The test facility, pens and birds were observed at least twice daily for l flock condition, lighting, water, feed, ventilation and unanticipated events If abnormal conditions or abnormal behavior is noted at any of the twice~daily observations they were documented and included with the study records. The minimum—maximum temperature of the test facility was ed once daily Pen Cards There were 2 cards attached to each pen. One card identifies the pen number and the second will include the treatment number Animal Handlino The s were kept under ideal conditions for livability The animals were handled in such a manner as to reduce injuries and ssary stress. Humane measures were strictly enforced.

Veterinarv Care ention and Euthanasia Birds that develop clinically significant concurrent disease unrelated to the test procedures may, at the discretion of the Study Investigator, or a designee, be removed from the study and euthanized in accordance with site SOPs. In addition, moribund or injured birds may also be euthanized upon authority of a Site narian or a qualified technician. The reason for withdrawal was documented. If an animal dies, or is removed and euthanized for humane reasons, it was recorded on the moitality sheet for the pen and a necropsy performed and was filed, to document the reason for l. If euthanasia is deemed necessaiy animals were euthanized by cervical dislocation.

WO 81203 {0571} Mortality and Culls {0572} From Day 0 to study end any bird that is found dead or is sacrificed was weighed and necropsied. The weight and le cause of death and necropsy findings were ed on the mortality record. If ips are noted at any time during the study they were removed weighed, necropsied to confirm sex and recorded on the pen mortality record. {0573} Bodv Weights and Feed, intake {0574} Birds were weighed by pen on approximately day 0, 17, 28 and 35. The feed remaining in each pen was weighed and ed on study days 17, 28 and 35. The feed intake during days 0 — 17, 1'7 — 28, and (‘i — 35 was calculated. {0575} Weight Gains and Feed Conversion {(3576} Average hird weigha on a pen basis, on each weigh day was summarized. Bird weight gain by pen days 17 — 28 was calculated. The average feed conversion was calculated on the study days 17 and 28 (ie days 0 — 1’7? 1‘7 — 35 and 0 — 35) using the total feed consumption for the pen d by the total weight of surviving birds. Adjusted feed conversion was calculated using the total feed consumption in a pen divided by the total weight of surviving birds and weight of birds that died or were removed from that pen. {(3577} Coeeldiosls Challenge {0578} All birds each received a lX dose of Coccivac by spray cabinet on approximately study day O~ {0579} Clastridium peijfiingem Challenge {ll-380} Clostridium Cl'iallenve: {0581} The Clasfridium perfi'mgeizs culture (CL—15) was grown ~5 hrs at N370 C in Fluid {0582} Thioglycollate medium containing starch, CL—l 5 is a field strain of Closzridmm perfrz’ngens from a broiler outbreak in Colorado. For each pen of birds, a fixed amount of the broth culture (NZ—3 inl/bii'd) was mixed with a fixed amount of treatment feed (~25g/bird) in the feeder tray. The amount of feed, volume and quantitation of culture inoculum, and number of days dosed were documented in the final report and all pens were treated the same, Birds will e the C. ‘z’ngens culture for one day (Study day W). The target is l O % mortality with a minimum 5% in the challenged, non~medicated group. {(3583} Method of Administration 30584} Administration of the (iosfridium pacrjringens (CL"15, Type A, 0t and B2 ) es in this study was Via the feed. Feed from each pen’s feeder was used to mix with the culture.

Prior to placing the cultures in the pens the treatment feed was removed from the birds for approximately 4 — 8 hours. For each pen of birds, a fixed amount («12.5 rd) of the broth e at a concentration of approximately 2.0 — 9.0 X108 cfu/ml was mixed with a fixed amount of feed (~25g/bird) in the feeder tray and all challenged pens were treated the same. Most of the enfeed was consumed within 1 — 2 hours. So that birds in all treatments are treated r, the groups that are not challenged will also have the feed removed during the same time period as the challenged groups. {0585} Lesion Scoring {0586} On study day 21., 5 birds were randomly selected from each pen (by first bird caught), sacrificed and evaluated for intestinal lesions scored for ic enteritis. Lesions were scored as follows: {0587} 0 = normal: no NE lesions, small intestine has normal elasticity (rolls back to normal position after being opened) {0588} l = mild: small intestinal wall was thin and flaccid (remains flat when opened and doesn’t roll back into normal position after being opened); excess mucus covering mucus membrane {0589} 2 moderate: able reddening and swelling of the intestinal wall; minor ulceration and necrosis of the intestine membrane; excess mucus {0590} 3 severe: extensive area(s) ot‘necrosis and ulceration of the small intestinal membrane; significant hemorrhage; layer of fibrin and necrotic debris on the mucus membrane (Turkish towel appearance) {0591} 4 dead or moribund: bird that would likely die within 24 hours and has NE. lesion score of 2 or more; or birds that died due to necrotic enteritis. 30592} Table 38: Results Avg Individual Adi. Feed NE— Lesion Mortality. Trt Gioup Bird Wt Gain (kg Conversion Score‘ {0593} The birds were treated with a composition of Ascus microorganisms to determine their s on performance and the prevention of Ciastr’idz‘zmr perfirigens infection. Three rganisms, Ascusbbr___4729, br___331885, and Ascusbbi'___ 170le were administered daily to the experimental birds via their ng water over the course of the entire experiment.

All birds were on a commercially relevant pelleted feed. {0594} Birds were challenged with C. perfi’ingens on day 17 of the study. On day 21, 5 birds were randomly selected, ied, and lesion scored. Mortality and feed, intake were measured throughout the ment. At the end of the experiment, birds were sacrificed, and weighed.

Feed conversion was calculated based on the total feed consumption for the pen divided by the total weight of the surviving birds. The treatment group receiving Ascus microorganisms was found to have improved feed, sion (10.4%) and pecent mortality (18.3%) when compared to the challenged control. However, lesion scores (8.6%) were higher in the Ascus microorganism group ed to to the nged control, The salinomycin control outperformed all groups.

Example V1. TRIAL 3 m in viva evaluation of Ascus h’lierobial Composition vs. Clustridium peifringens Challenge {0595} Basal and Ex aerimental Diets {(1596} The starter, grower and basal diets was manufactured using a feed mill and stored in bulk.

Final experimental diet mixing, pelleting, and crumbling was conducted using a SOO—lb capacity vertical mixer, a 4000~lb capacity vertical mixer and/or a 14,000—lb horizontal mixer and a California. Pellet Mill. Feed was stored in 50~lb capacity feed sacks and/or bulk storage bins labeled with treatment code. Phytase was included in all diets throughout the experiment, [0597} The feeding schedule utilized two feeds a starter feed in crumble form and a grower feed in pellet form. The starter feed was fed from days 0 to 17, and the grower feed was fed from days 17 to 35. The Ascus microbial consortia were administered to the birds in the ent group once prior to placement via spray application. [0598} Test Svstern WO 81203 Species Broiler Chicken Strain Commercial production Breed/Cross Cobb 500 Supplier TED Sex Males Age ~1 day of age upon receipt (day 0) 55 days at final weights fication Pen cards Number of birds: 1200 (DO) Number of treatments: 4 Number of pens/treatment: 12 Number of birds/pen: 25 (D0) Number of birds/treatment: 300 (DO) Total number of pens: 48 {0599} languages. {0600} Treatments were assigned to the pens using a complete randomized block design Treatments were administered to the pens at start of study day 0. The treatments will fied by c codes. Challenged eontrol treatments comprise the administration of pathogens as the control, Challenged Ascus compositions comprise the administration of experimental microbesSpecifie treatment groups are as follows {(3601} Table 39: Test Groups g) N0. of Number of . . 3 Treatment Description "1:5 Pen Birds/{rt Challenged Control (Non— medicated) Challenged Control wi th Salinomyein Challenged Ascus Composition administered: Ascusbbr_4729, Asc1.ts‘obr_3 3 l 885, Ascusbbr_l 7021 l (spray application) Challenged, Ascus ition administered: Yes Ascusbhi‘_4729, Ascusbbr_33, _ 200 Ascusbbr_l,27 (spray application) [0602} Housing and Management [9603} Housing {0604} Treatments were ly assigned to each pen using Microsoft Excel random number generator by the Data Manager. Birds were assigned to the pens randomly. {0605} Birds were housed within an environmentally controlled in concrete floor pens providing floor space & bird density of {4155 ftz/bird (day 0); ~ 0.69 ftZ/hird (day 21 after lesion scores)], temperature, humidity, lighting, feeder and water space were similar for all test groups. Birds were placed in clean pens containing an appropriate depth of clean wood shavings to provide a comfortable environment for the . Additional shavings were added to pens in order to maintain bird comfort. Lighting was via incandescent lights and a commercial lighting program was used as follows. [0606} Table 40: Lighting Approximate Hours Approximate of Continuous ~Light ity Bird Age (days) Light (foot candles) per 24 hr period (3.2 — 0.3 02 0.3 {(3607} Environmental conditions for the birds (ie. bird density, ature, lighting, feeder and water space) were similar for all treatment . In order to prevent bird migration and bacterial spread from pen to pen, each pen will have a solid wood or plastic divider for approximately 24 inches in height between pens. [(3608] Vaccinations and Theta )eutic Medication [(1609] Birds were vaccinated for Mareks at the hatchery. Upon receipt (study day 0), birds were vaccinated for Newcastle and Infectious Bronchitis and Coccivac by spray application using a spray cabinet. Documentation of vaccine manufacturer, lot number and expiration date was provided with the final report. [(3611] Water {(3612} Water was provided ad zmz throughout the study via one automatic nipple drinker (4 nipples per drinker) per pen. Drinkers were d twice daily and cleaned as needed to assure a clean and constant water supply to the birds. {(3613} Feed {(1614} Feed was provided ad libitum throughout the study via one hanging, ~l7—inch diameter tube feeder per pen. A chick feeder tray was placed in each pen for approximately the first 4 days. Birds were placed on their respective treatment diets upon receipt (day 0) according to the Experimental Design. Feed added and removed from pens from day 0 to study end was weighed and recorded.

} Daily observations {(3616} The test facility, pens and birds were observed at least twice daily for general flock condition, lighting, water, feed, ventilation and cipated events. If al conditions or abnormal behavior is noted at any of the twicedaily observations they were documented and included with the study records. The minimum—maximum ature of the test facility was recorded once daily [@617] Eetgards {0618} There were 2 cards attached to each pen. One card identifies the pen number and the second will include the treatment . {0619} Animal Handlino {0620} The animals were kept under ideal conditions for lity. The animals were handled, in such a manner as to reduce injuries and unnecessary stress. Humane measures were strictly enforced. {0621} Veterinary Care Intervention and Euthanasia {0622} Birds that develop clinically significant concurrent disease unrelated to the test procedures may. at the discretion of the Study Investigator, or a ee, be removed from the study and euthanized in ance with site SOPs. In addition, moribund or injured birds may also be euthanized upon ity of a Site Veterinarian or a qualified technician. The reason for awal was documented. If an animal dies, or is removed and euthanized for humane reasons it was recorded on the mortality sheet for the pen and a necropsy performed and was filed to document the reason for l. If euthanasia is deemed necessary s were euthanized by cervical dislocation {0623} Mortality and Culls {0624} From Day 0 to study end any bird that is found dead or is sacrificed was weighed and necropsied. The weight and probable cause of death and necropsy findings were recorded on the mortality record. If sex~slips are noted at any time during the study they were removed, d, necropsied to confirm sex and recorded on the pen mortality record. {0625} Body Wei, hts and Feed Intake {0626} Birds were weighed by pen on approximately day 0, 17, 28 and 35. The feed remaining in each pen was weighed and recorded on study days 17, 28 and 35. The feed intake during days 0 l7, l7 28, and 0 35 was calculated. {0627} Weight Gains and Feed Conversion {0628} Average bird weight, on a pen basis, on each weigh day was summarized. Bird weight gain by pen days 17 28 was calculated. The average feed conversion was calculated on the study days 17 and 28 (ie. days 0 1'7, 17 35, and 0 35) using the total feed ption for the pen divided by the total weight of surviving birds. Adjusted, feed conversion was calculated using the total feed consumption in a pen divided by the total weight of surviving birds and weight of birds that died or were removed from that pen. {8629} (Ioccidlosls Challenge {0630} All birds will each receive a 1x dose of Coccivac by spray cabinet on approximately study day 0. {0631} idium peijfi'ingens Challenge {9632} Clostridium Challenge {0633} The Closrrz'dz‘um peiffi/‘ingens culture (CL—15) was grown «5 hrs at ~37° C in Fluid {0634} Thioglycollate medium containing starch. CLuIS is a field strain of Clostridz’um perfrz’ngens from a r outbreak in Colorado. For each pen of birds, a fixed amount of the broth culture (~2—3 nil/bird) was mixed with a fixed amount of treatment feed bird) in the feeder tray. The amount of feed, volume and tation of culture inoculum, and number of days dosed were documented in the final report and all pens were treated the same. Birds will receive the C. peifi'z'ngem culture for one day (Study day 17). The target is 10 % mortality with a minimum 5% in the challenged, nonuniedicated group. {0635} Method of Administration {0636} Administration of the Closm‘dium penfringens (CLml 5, Type A, a. and [32 toxins) es in this study was via the feed. Feed from each pen’s feeder was used to mix with the culture.

Prior to placing the cultures in the pens the treatment feed was removed from the birds for approximately 4 — 8 hours. For each pen of birds, a fixed amount (~25 nil/bird) of the broth culture at a concentration of approximately 2.0 — 90 Kill8 cfu/nil was mixed with a fixed amount of feed (~25g/bird) in the feeder tray and all challenged pens were treated the same Most of the culture~feed was consumed within 1 — 2 hours. So that birds in all treatments are treated similar, the groups that are not challenged will also have the feed removed during the same time period as the challenged groups. {6637} Lesion Scoring {0638} On study day 21, 5 birds were ly selected from each pen (_by first bird caught), sacrificed and evaluated for intestinal lesions scored for necrotic enteritis. Lesions were scored as {(3639} O normal: no NE lesions, small intestine has normal city (rolls back to normal position after being opened) {8640} l mild: small inal wall was thin and flaccid (:remains flat when opened and doesn’t roll back; into normal position after being opened); excess mucus covering mucus membrane {0641} 2 = moderate: noticeable reddening and ng of the inal wall; minor ulceration and necrosis of the intestine membrane; excess mucus {0642} 3 = : extensive ) of necrosis and ulceration of the small intestinal membrane; significant hage; layer of fibrin and necrotic debris on the mucus membrane (Turkish towel appearance) {9643} 4 = dead or moribund: bird that would likely die within 24 hours and has NE lesion score of 2 or more; or birds that died d no to necrotic enteritis.

} Table 41: Results lndividual I ‘ NE- Lesion {8645} The birds were treated with a composition of Ascus microorganisms to determine their effects on performance and the prevention of Clostridium peijfigens infection. Two different microbial compositions were tested. The first composition consisted of ASCUSbbT_4-729, Ascusbbr_331885, Ascusbbr_ l70211, and the second ted of Ascusbbr_4729, Ascusbbr_33, Ascusbbr_l 27‘ Microorganisms were administered once to the experimental birds via spray application prior to pen placement. All birds were on a commercially relevant pelleted feed. {0646} Birds were challenged with C. perfringens on day 17 of the study. On day 21, 5 birds were randomly selected, sacrified, and lesion scored. Mortality and feed intake were measured throughout the experiment. At the end of the experiment, birds were sacrificed and weighed.

Feed conversion was calculated based on the total feed consumption for the pen divided by the total weight of the surviving birds. The treatment group receiving Ascus microorganism composition 1 (treatment 3) was found to have slightly improved feed sion (0.63%), slightly higher weight (2.93%), slightly lower lesion scores (4.23%), and lower pecent ity (30.37%) when compared to the challenged control. The treatment group receiving Ascus microorganism composition 2 ment 4) was found to have improved feed conversion (2.31%), higher weight (4.91%), lower lesion scores (18.31%), and lower pecent ity (37.22%) when compared to the challenged l. The salinomycin control outperformed all groups.

Example Vii. 'l‘RlAL 4 - in viva evaluation of Neerotic tis with liliultiple Aseus Niicrohial Compositions vs. Clostridium ingens {0647} Experimental Design {0648} Experimental Ration {@649} Rations consisted of non—medicated commercial-type broiler starter, grower, and finisher diets compounded ing to NRC guidelines and contained feedstuffs commonly used in the United States. Rations were fed ad libilum from date of chick arrival as s: Starter ~ DOT 0 until DOT 21, grower DOT 21 to DOT 35, and finisher DOT 35 to DOT 42 (study termination) Diets were fed as crumbles (starter feed) or pellets r and finisher feed). {0650} Animal lnformati on {9651} One thousand eight d (l,800) day—of—hatch Cobb male broiler chicks were obtained, The strain was Cobb X Cobb. Birds were sexed at the hatchery. All birds were vaccinated by spray cabinet with a commercial coccidia vaccine at ended dosage. Only healthy appearing chicks were used in this study. {9652} Housing [0653} Upon arrival chicks were raised in 5 x it) feet floor pens (stocking density of it) feet2 per bird) with approximately four (4) inches of fresh pine shavings (at placement), in a solid-sided barn, with concrete floors under ambient humidity. Litter was not replaced or amended during the course of this study. Feed and water were available ad libimm throughout the trial. Each pen contained 1 (one) tube feeder and 1 (one) hell drinker (50 bird to feeder/drinker ratio).

Thermostatically controlled gas heaters were the primary heat source for the barn (if needed).

One (1) heat lamp per pen provided supplemental heat during brooding. Fans were used to cool birds. Birds were provided a lighting program as per the primary breeder recommendations. The pen diagram was documented and included in final report with source data. {@654} Probrotie Administration {0655} After ia vaccine strations all chicks in ents 3 were coarse sprayed with 0.25 mil/chick of the Ascus probiotic and placed under bright light to allow preening. Once dry, chicks were placed in treatment appropriate pens. {@656} Table 42: Treatments TREATMENT COCCL CLOSTRIDTU BIRDS/P E EN DESCRWTIGN VACCWE 1W PERFRINGE CHALLENGE Nonmedicated DOT 19, 20, 63: Cocci Vaccine 21 (Challenge Control) icated Cocei Vaccine (Negative Control) Aseus Probietic: DOT 19, 20, & 1-\scusbbr_409, Aseusbbr_5796, Ascusbbr'___1686 Ascus Probiotic: DOT 19, 20, 63: Aseus’b’br___409fi 21 Ascusbbr___g5796, Aseus’b’br___185064 . HOT 19, 20, & 21: (Vastridium peifrmgens was added into: the water at a dose of approximately 1 X1 08 CFU/ml/bird.

DOT = Day of trial *Probiotics were sprayed on chicks at 0:25 nil/chick for Treatments 3 and 4 at 1 day of age prior to ent [0657} Bird Allocation and Pen Randomization [0658} One thousand eight hundred birds were assigned to three ent groups with twelve replicate pens per treatment and 50 birds per pen. Pen facility was divided into twelve blocks with each block containing each of the three treatment groups. Treatment groups were assigned to pens using randomized complete block. The study began when birds were placed (day—cl2 hatch; DOT 0), at which time birds were allocated to experimental pens. Only healthy birds were selected. On DOT 0, group body weights were ed by pen. No birds were replaced during the course of the study. [0659} Challenge Administration and Sample Collection and Analysis [0660} ic tis Challen e [0661} The challenge model consisted of coccidia from the DOT 0 vaccine, one coccidia seeding at DOT l4, and Clostridium [newer/[gens combination. [0662} Closrricfl'ium )eri'm ‘ensln Drinkino Water [0663} Treatment feed and water was awn for a few hours prior to administration of Clastridium IZJeljfiriI/zgens. A measured amount of Clostridium [neigfirz‘ngens was added to water that was consumed within 30 minutes was used for each pen. The Clostridz’um perffitngens culture was added to this water and thoroughly mixed and given to birds in each challenge pen.

Once the challenge water was consumed treatment feed and water were returned to pen.

Clostridium pendingens was added, to the water on DOT 19,, 20, and 21 to all bird except for Birds in Treatment Group 2. [0664} Coccidia Challenge [0665} Was from cycling of DOT O vaccination and E. maxima (20 ml per pen) spread around feeders and drinkers on DOT 14. (Except Treatment Group 2). [0666} Necrotic tis Lesion Scoring [0667} On DOT 21 three (3) birds per pen were humanely euthanized, necropsied and lesion scored [0668} Lesion score 0 = Normal [0669} Lesion score 1 = Slight mucus covering small intestine {8670} Lesion score 2 ic small intestine mucosa {0671} Lesion score 3 Sloughed and blood small intestine mucosa and contents {0672} Intestinal Content Sampling {0673} On DOT 21 and 42 collected samples of the small intestines of two (2) birds per pen. {8674} Feed Changes {0675} Birds received treatment appropriate feed from DOT O to DOT 42. On DOT 21 remaining starter feed was removed, weighed, and replaced with grower feed. On DOT 35: remaining grower feed was removed, weighed, and replaced with finisher feed. On DOT 42 remaining finisher feed was removed and weighed back. All unconsumed feed was weighed and disposed of in the SPRG onsite disposal pit. {9676} Body and Feed ‘Weight {0677} All, birds were weighed hy pen on DOT O, 21, 35, and 42, Feed added to each pen’s feeder was weighed at the beginning of each formulation period on DOT 0, 20, and 35 er, grower, and finisher respectively), Any additional bags of feed were weighed (and documented) for each pen (as required) during each ation period. Feed was buted as needed to feeders from ighed bags (assigned to each pen) throughout each period. Feed remaining in feeders (and feed bags if applicable) was weighed and disposed of on DOT 21, 3S, and 42.

Empty pen feeder weights were recorded prior to study initiation, The trial was ated on DOT 42, [0678} hianagement [0679} Disease Control {8680} No concomitant drug therapy was used during the study. Disposable plastic boot were worn by all study personnel required to enter pens (e.g collect birds for study procedures). The disposable plastic boots were removed as the person stepped out of pen to avoid tracking fecal material throughout the ty. Disposable plastic boots were ly disposed of after use. {0681} Monitoring {0682} All birds were red for general flock condition, temperature, lighting, water, feed, litter condition, and unanticipated house conditions/events. Findings were documented twice daily during the regular working hours (one observation recorded final study day). On ay, Sunday, and observed holidays, one (1) observation was ed. {0683} Mortality {8684} Pens were checked daily for mortality. Birds were only culled to relieve suffering. Date and rernovaal weight (kg) were recorded on all birds culled (or lound dead) IX gross necropsy was performed on all dead or culled birds to determine the bird sex and probable cause of death, Signs of Necrotic Enteritis or nonmspecific enteritis were noted. {9685} Bird and Feed Disposition {0686} All birds were disposed of by appropriate s. All ities and ing feeds (including mixer flushes) were buried in the Southern Poultry Research Group on site disposal l9637l mules. {0688} Scale maintenance and standardization procedures were followed prior to use {9689} Source Data Control and Handlinq {0690} Data. were recorded in ble ink. Entries were legible and source data sheet signed (or initialed), and dated by individual recording entry. All source data errors and/or changes were initialed, dated, and a brief explanation (or error code) written directly on form, l069ll EataManaasznr-srzt {0692} Data. management and statistical analysis of weight gain, feed consumption, and feed conversion, and lesion score results were med. {0693} Table 43: Results Avg Individual Adj. Feed Bird ‘Wt Gain Mortality NE» Lesion Score Conversion i {0694} The birds were treated with a composition of Ascus microorganisms to determine their effects on periormance and the prevention of Closrrid'ium rigefis infection Two diffeient microbial compositions were tested. The first composition consisted of Ascusbbrw409, Ascusbbr___5796, Ascusbbrul686, and the second ted of Ascusbbr___409, Ascushhr___5'796, and Ascusbbi'___185064. Microorganisms were administered once to the experimental birds via spray application prior to pen placement. All birds were on a commercially relevant ed feed. {9695} Birds were challenged with C, perfiz’ngens on day 17 of the study. On day 21, 5 birds were randomly selected, sacrified, and lesion scored. Mortality and feed, intake were measured throughout the experiment. At the end of the experiment, birds were sacrificed, and weighed.

Feed conversion was calculated based on the total feed consumption for the pen divided by the total weight of the surviving birds. The treatment group receiving Ascus microorganism composition 1 (treatment 3) was found to have slightly improved feed conversion (1.11%), lower lesion scores (70.0%), and lower pecent ity (36,7096) when compared to the challenged control. The treatment group receiving Ascus microorganism composition 2 (treatment 4) was found to have slightly improved feed sion (0,88%), lower lesion scores (20.0%), and lower pecent mortality (24-05%) when compared to the challenged control. Surprisingly, the challenged control exhibited the highest weight gain.

Example VIII. Comparative Analysis of hllC Scores from hed ‘Work of Other Groups {0696} Utilizing Ascus Biosciences’ technology, the performance of currently available microbial feed ve products was predicted. [0697} Direct~fed microbial ts that claim to enhance broiler performance are available on the market A few of these products contain microorganism strains that are native chicken gastrointestinal microorganisms or are within 97% sequence rity of native gastrointestinal microorganisms. Here, we’ve identified the strains that are used in these products, and calculated their platform score with respect to feed efficiency and body weight ( and ). As can be seen from the curves, many of the currently available s fall below the threshold used to define "useful" and "nonuuseful a) strains. The one strain above the cutoff, coccus m, has shown cial effects when fed to broiler chickens. {8698} Other common strains used in fowl/poultry direct fed ial products, were either not found in the gastrointestinal tract of any birds or were less than 97% similar to a strain found within the birds. Scores could not be generated for these microorganisms (Table 44). [0699} Table 44: Microbes not appearing on the curve in or .

Bacillus subfilis DSM 29870 Bacillus l‘s DSM 29871 Bacillus subtilis AJZ763 51 Bacillus valltmortz's AB021 198 Bacillus amylolz'quefitcz’ens USE/129869 Bacillus iqueflzciens DSM 29872 Bgfidobacrermm lz's [0700} Entemcnccusfaecium: 0.72083 [0701} Positive effects on overall weight gain, did not change FCR: Effects of y Enterococcus filecz’um on growth performance, carcass characteristics, faecal microbiota, and blood profile in rs. doi: 10.17221/8680—VETMED [0702} Positive effects of weight gain: Effects of Enterococcusflieciimt supplementation and floor type on performance, morphology of erythrocytes and intestinal microbiota in broiler chickens. doi: l0."DEED/000716682010.507241. [0703} ve effects on weight gain: Effects of Entemcoccusfaecium and dried whey on broiler performance, gut histomorphology and intestinal niicrobiota. D01; .1080/17450390601 106655 [0704} Positive effects on weight gain and intestinal development: intestinal Structure and Function of Broiler Chickens on Diets Supplemented with a Synbiotic Containing Enterococcus faecium and Oligosaccharides. doi:103 390/ijms9112205. [0705} Pediococcus acidilactici: 0.17931 [0706} Did not affect body weight: Effects of dietary probiotic (Pediococcus czcidilaczici) mentation on mance, nutrient digestibility, egg traits, egg yolk cholesterol, and fatty acid profile in laying hens. D01: doiorg/1033 82/ps2012—02370. [0707} Did not affect body weight: Efficacy of Bactocell® and rin® as Probiotics on Growth Performance, Blood ters and Intestinal Morphometry of Turkey Poults. {0708} No icant difference to performance; Growth performance and immune response of broiler chickens fed diets supplemented with probiotic and l:or) prebiotic preparations.

{G709} Prohiotic of l). acidilactici alone did not improve performance: Effect of Prohiotic, Prehiotic, and, Synbiotic on Broiler Performance. {0710} Lactobacillus salivarius DSM; 16351: 016462 (weight), 0.31742 (feed conversion) {0711} Does not improve body weight, slight effect on feed conversion ratio at times: Influence of prohiotic administration by feed or water on growth parameters of broilers reared on medicated and nonmedicated diets. DOI: doiorg/lO.3382/:iapr.2009—00084 {0712} Lactobacillus reuteri: 0.26096 {0713} Slight effect on feed conversion ratio at times: Influence of probiotic administration by feed or water on growth ters of broilers reared on medicated and nonmedicated diets, DOI: doi , org/l O. 33 BZ/japr,2009—00084. {(3714} Bacillus amyloliquefaciem AB255669: 0l8434 {0715} No effect on performance: Efficacy of protected sodium butyrate, a protected blend of essential oils, their combination, and Bacillus amyiolz’quejncz’ens spore suspension against artificially induced necrotic enteritis in broilers DOI: https://doiorg/l0.3382/ps201 1—01853, Example 1X. Volatile Fatty Acid and Carbon Source Assays Volatile Fatty Acid Assa , {0716} In order to assess the y of the strains to produce le fatty acids, HPLC was ed to measure the concentrations of acetic acid, hutyric acid, nic acid, and lactic acid in spent media {(3717} A single colony was picked from each of the desired strains (_from bic agar plates) and was inoculated into fresh media, At, the same time, a media blank was also prepared. The cultures and the media blank were incubated at 37°C until icant growth was visible (~S days). The ()D600 was determined for each culture, and the strain ID was med with Illurnina sequence. An aliquot of culture was filter sterilized into an acid washed and aved glass 15 ml, sample vial which was then ed by HPLC. {(3718} l-IPLC reactions were performed on a BioRad Aminex l-fPX—87l-I with the following conditions: 60°C, 0.5mL/rnin mobile phase 000325 N H2804, 500 psi, 35C RI detector, 45 min run time, injection volume of Stilt. Concentrations of acetic acid, butyric acid, propionic acid, and lactic acid were quantified for the medium blanks as well as the sterile filtered e samples. The strains were considered positive for volatile fatty acid production if the detected concentration of the individual fatty acids in the spent medium were higher than in the media blank. See Table 45. {@719} Table 45: VFA production from es of the present disclosure. lactic acetic . propionic butyric Strain ID l Condition / Media acid acid acid acid Ascusbbr 94 i O MRS i Ascusb br___94 l 0mi\/l___A cetic___Acid 4268C Salts Butyric Ascusbbr_9,l Acid br___9l BL Amino Acid D ............................................9.

Ascusbbr_9l CMC Amino Acid D Ascusbbr___84 Amino Acid D Ascusbbrm830 a BL Amino Acid D Ascusbbr 830 CMC Amino Acid D MZGSC_Arabin0se Ascusbbr_7779 Xylose lium Butyric MZGSC Salts Butyric Ascusbbr_7363 : Ascusbbr 72076 1:10MRS Ascusbbr 72076 BI...

Ascusbbr 72076 Ascusbbr___72076 Ascusbbr_6957 Ascusbbr___6957 a : ,IZGSC_Arabinose Ascusbbr6097 X 'lose Spirillium Butyric Ascusbbr 6097 Acid Ascusbbrm6097 BL Amino Acid D Ascusbbr___6097 CMC Amino Acid 1) Ascusbbrj796A l Ascusb’br___5796B Ascusbbr 5796C Ascusbbr 5796A Ascusbbr 5796B BL . BL Ascusbbrm ' A, 1:10MRS MZGSC_Arabinose Ascusbbr_ Xyiosc Ascusbbyfl ' . BL Amino Acid D Ascusbbr ' ., :MC Amino Acid D Ascusbbr ' m 1:10 MRS Ascusbbr___ br_4729 : br___42760A Ascusbbr_42‘760A a Acbb47€OB 1-\scusbbr_42760A Ascusb’br___42760A Ascusbbr_42760A Ascusbbr___409A br_4OQB Ascusbbr 409A Ascusbbr 409B Ascusbbr_409C BL i MZGSC___Arabinose fiéflfikfigfigflé________i Xflgfi______________________________________________________'_;_‘_________________________'_:;____________ _____________ Ascusbbr_409A BL Amino Acid D ' Ascusbbr___40913 L Amino Acid D AscusbbrAOQC a BL Amino Acid D Ascusbbr___409A CMC Amino Acid D Ascusbbr_4098 CMC Amino Acid D AscusbbrmAOQA 110 MRS Ascusbbr_387l7A Ascusbbr___38717B Ascusbbr 38717A i Ascusbbr 38717A Ascusbbr___359892 Ascusbbrj 5 Spiriilium Butyric Ascusbbr 33 Acid MZGSC Salts Butyric Ascusbbr_339 Acid Ascusbbr___339 CMC Amino Acid D 1-\scusbbr_33]885 Ascus’b’br___33 1 885 BL Amino Acid 1') Ascusbbr_33 Ascusbbr___33 _________________________________________________+_____________________________________________________________ Ascusbbr_32731A its Butyric Ascusbbr_32731A L Amino Acid D Ascusbbr 32731A CMC Amino Acid D Ascusbbr32’73 1A 1:10 MRS Ascusbbr__3273 lB 1; 10 MRS Ascusbbr_322104 1:10MRS B/IZGSCflAiElbiHOSG br___313454 Xyiose Ascusbbr_3] BI... Amino Acid D Spiiiliium c Ascusbbr 3089 Acid MZGSC_Arabinose Ascusbbr___285160 : yiose Ascusbbr_285160 BL Amino Acid D Acbb85160 1:10 MRS pirillium Butyiic Ascusbbr_28 Acid i MZGSC Salts Butyric br___ Acid Ascusbbrtl : BL Amino Acid D Ascusbbrm CMC Amino Acid D 1-\scusbbr_265z—\ 1:10 MRS Ascusbbrm26SB 110 MRS Ascusbbr_265A BL CflAiElbiHOSG Ascusbbr___265A Xyiose Ascusbbr 25200 BI...

Ascusbbr_25200 Ascusbbr___247 iZGSC___Arabinose MZGSC Salts Butyric Ascusbbr_247A Acid MZGSC Salts Butyric Ascusbbr___247B Acid 1-\scusbbr_247A BI... Amino Acid D Ascusbbrm247A CMC Amino Acid 1) Ascusbbr_247B i CMC Amino Acid Ascusbbr_215 8 CMC Amino Acid 1) Ascusbbr___21 1 69 Ascusbbr_21 169 Ascusb br___19 Ascusbbr_19 Ascusbbr___185064 1-\scusbbr_] 85064 Spiriiiium Butyric Ascusb’br___1789 Acid Ascusbbr_l 789 Ascusbbpfll 789 1-\scusbbr_] 789 piriiiium Butyric BL Amino Acid D Ascusbbr_l ‘73 C___Arabinose Ascusbbr___1 7 J'Eose br_1,686 Ascusbbr___1686 Ascusbbrl686 lOml‘vi Acetic Acid __Arabm3se Ascusbbr 1686 Xwiose Spirillium Butyric 1-\scusbbr_] 686 Acid Ascusbbgfll 686 BL Amino Acid D Ascusbbr_1686 CMC Amino Acid D Ascusbbpfll 686 1:10 MRS Ascusbbr 1 483 4 1:10 MRS Ascusbbr_14834 i Spiriilium ic Ascusbbr___14834 Aicid Ascusbbr_l4834 Ascusbbr_l4834 BL Amino Acid D Ascusbbrm14834 CMC Amino Acid D Ascusbbr_]4690A = ’br___1469OB = Ascusbbr_14690( dZGSCflArabinOse Ascusbbr 14690A leose Spirillium Butyric __A§_9_tj§l2lzg_._._.1_€}__€:;9__9A_l__§35~:_isi______________________________________________________________________________________________________ _____________ Arscusbbr_l,4690A BL Amino Acid D ' Ascusbbr___14690A 1:10 was Ascusbbr_l44 BL Amino Acid D Ascusbbr___1436 , Ascusbbr_]436A ]:lOMRS Ascusb’br___14363 1:10 MRS Ascusbbr_1436A BL B/IZGSCflAIElbiHOSG Asc1.isbbr___l436A Xylose Spirillium Butyric 1-\scusbbr_l 436A Acid RQGSC Salts c Ascusbbr 1436A Acid Ascusbbr l 1436A BL Amino Acid D br_l436A CMC Amino Acid 1) Spirillium Butyl‘ic Ascusbbr___136 Acid {ZGSC Salts Butyric Arscusbbr_136 Acid Ascusbbr___13398 CMC Amino Acid D l2GSC_Arabinose Ascusbbr128 leose Ascusbbrm127 Ascusbbi'_10593A AscusbbyfllOSQSB = lium Butyric Ascusbbr_lOS93A Acid MZGSC Salts Butyric Ascusbbr 10593A Acid BI... Amino Acid D Soluble Carbon Source Assay {8720} In order to assess the ability of the strains to degrade various soluble carbon sources, OD6OO was used to measure growth of strains on particular carbon sources over a period of time. {9721} A single colony from each of the desired strains (on anaerobic agar plates) was inoculated into fresh medium. Strains were inoculated into a carbon source assay anaerobically; the assay was set up in a 2m};- sterile 96well plate, with each well containing lVlZGSC salts, Vitamins, minerals, sodium sulfide, and a single carbon source. Carbon sources ed whole chicken feed, Soytone, Maltose, Raffinose, Starch, Arabinose, Sucrose, Xylose, Succinate, Cellobiose, Casamino acids, Glucose, Galactose, Manitol, Peptone, Gluconate, Malt Extract, Casein Digest, Beef Extract, and Chitosan. Cells were inoculated such that each well started at an OD600 of 0.01. The ODs were read at 600nm with the "Synergy H4 hybrid plate reader". Strain ll) was confirmed with na cing after all wells were in nary phase. {@722} XTT ion was simultaneously measured by adding lOOul of carbon source with strain culture to a ZOOul flat bottom plate. To this aliquot 50111 of the XTT mix (5ml of sterile XTT with l00ul of sterile N~methyl dibenzopyrazine methyl sulfate) was added, This culture was then ted for 1 hour at 3 70C anaerobically in the dark XTT reduction was determined by absorbance at 4’75nm cted for the non—specific absorbance at 660nm as well as the appropriate media and strain blanks. See Table 46.

WO 81203 {0723} Table 45: Carbon source growti‘1 assays with microbes 0 t1as present disc. £05111": r----------------------- ------------ T -------- --------—-------- -------- -------------- ------------ 01¢: g 5%:5 cmwm maoiom $33: wmofibmm ........................... :3me 3453 32.? @aflv—Ou ENE 53.5 "8&5 Em me WE m 3933mm 3:953 955w; 33:23 oEEefimu meUflmw Emmy 65th Hambxm :meEu Ascugbbr '91} ........................... ...........................

.............A:.......... n...... m m m m m+...+ + Ascusbbr 830 IIIITIIII Ascusbbr 7779 I... + -------- _____}_____________ _________ _______4________ + .________ ________ Ascushbr .u... 3 f: 3 I... + ________ __ ______________,___________ ___________.%_______ ________ Ascu hint 6957S In.

Ascusbbr_6097 .u...¢.... + ..................................... ................. .. ........+........ ..............+2-........... ............

Ascusbbr 4-729 + .............+.......... .. mm .......+........+....... .........+........ .. ................. .......................... .....

Ascusbhr 499 Ascusbbr 38717 Ascusbbr 36257 +------- ++ .._...._...._...._...

Ascusbbr 359892 Ascugbbr 35 A5911shbr .339 Ascusbbr 331385 Ascusbbr ’ % Ascusbbr 3273,! Ascusbbr322104- ...

Ascusbbr 3134-54 .u.. ________ ________ ______________.___________ ____________}_______ ________ Ascusbbr 31 I...

Ascusbbi' 3039 + + ++ .--------.-------- Ascushbl‘ .u.......

Ascugbbr 28 I...

Asmshbr 'PfiS L +m I... + 4.......... ........ m m .AL.......AL.........L....... ........L........ ........ ........... .............. .L....... ........

Ascushbrji'flflfi i Ascushbr 2158 Ascushbr} 11 69 ____________________________________,_____________ ---------- --------v--------v_________ ________ -------i-------- ________ ________ ______________,___________ ___________.%_______ ________ Ascusbbr19 Ascusbbr 185064 Ascusbbr 1789 _______+_____________._________ +_______+_________.________ __n____.............................

Ascugbbr 17 br 1686 + ________ ________ ______________.___________ ____________}_______ ________ Ascusbbr 1483!} Ascushbr 14690 ________ ________ _____________{____________ ___________,________ ________ Ascusbhr__ 44 Ascusbbr_143 6 .............+.......... .....................+........ ........+2- Ascusbbr 128 ________ ________ _____________4____________ ___________.________ ________ lnsoluble Carbon Source Assav {8724} In order to assess the ability of the s to degrade ble carbon sources, visual inspection was leveraged to qualitatively determine a strain’s degradation capabilities. {8725} For pure cultures, a single colony from each of the desired strains (from anaerobic agar plates) was inoculated into anaerobic Hungate tubes containing Lowe’s semi defined media with ose paper, starch, or grass as the sole carbon source. {Lowe er a]. 1985. J. Gen. Microbiol. l3l:2225~2229). A medium blank was also prepared. Cultures were d visually for degradation of insoluble carbon sources. See . ments {0726} The same protocols as described above for the VFA assay and the soluble carbon source assay were used for enrichment assays, but instead of inoculating with a single colony, fresh gastrointestinal sample was used. Gastrointestinal sample inocula and enrichments were na ced to determine presence or absence of target strains. cing datasets were ated with cell count data to determine if target strains grew in ViiFO. e X. Competitive exclusion assays (in vitro) {0727} in order to assess the ability of the strains to compete against pathogens in the intestinal tract of the fowl, competitive exclusion against Closrrz‘dz’um perfringens or salmonella enterica was measured, by co—culturmg strains together in a medium representative of the broiler GI tract as well as in a minimal salts medium. After ntial cell growth, each co— culutre was sequenced. The relative abundance of each strain was then used to determine the efficacy of the strains at competing with or inhibiting the pathogen. {0728} Single colonies of the strains and pathogens were inoculated into 500 pl, of MRS and TSB anaerobically. The OD readings were ed the following day, and fresh MRS and TSB co~cultures were inoculated such that each strain was at a starting OD of 0.01, 300 uL of the staiting inoculum was collected and sequenced to provide a relative abundance at T0, and the starting abundance of each strain was confirmed {(3729} Strains were considered successful at competing against the pathogenic strains if the pathogen experienced a theoretical percent decrease (relative abundance as determined by sequencing * coculture OD) of at least 50% when compared to the starting inoculum, Strains were considered to have a weak competitive exc1usion effect if the final OD of the co—cuEture was lower than the OD of the pure pathogen e. Strains were considered negative if they were overgrown by the en. See Table 47 for results. When cocultured with Closirz‘dium 'ngens 15 of the 24 strains (62. 5%) exhibited an inhibitorv effect against C perfi’igens Of the strains cocultured with 13’a1n101lzelia enterica, 4 of the 7 strains (57.14%) tested exhibited an exhibitory effect against S enferz’ca Strains that shared similar 16S sequences (97% sequence similarity) tended to exhibit similar effects on the pathogens—this includes Ascusbbr____33A and B; Ascusbbr___409A and B; Ascusbbr___.5796A, B, and, C; Ascusbbr___14690A, B, and C; and Aseusb’br___38717A and B. s related to Asusbbr 10593 however did show have a few differing. results Ascusbb1_10593A and B both inhibited 13 3111611511 but Ascus13131_10593A seemed to have a 51113,111:11y stronge1 inh1131tory .

Table 47: Strain ition data for C. perji‘ii'zgens and S. enterica.

(Hostridium Salmonella perfringens 1211 terica Ascusbbr__19 NT Ascusbbr_33A br_3315 Ascusbbrfl1436 Ascusbh1‘___1686 bbrj796A Ascushbrfi79613 Ascusbbr_5796C Ascusbbr_21169 15115111— 105931-— Ascusbm 1059313 AscusbandfiQOA AscusbbrfilatégflB Ascusbbr_14690(3 Ascushln‘wi‘}2 731 Ascusbbr_42760 AscusbbrASSSIL Ascusbbi‘_185064 Ascushhr__331885 - : Strain was outcompeted by the +2 Strain weakly inhibited the pathogen ++ : Strain inhibited the pathogen NT 2 Condition not tested Numbered Embodiments of the sure l. A microbial composition comprising at least one microbial strain selected from Table l and/or Table 2. 2. A microbial composition comprising at least one microbial strain, wherein the at least one microbial strain comprises a 168 rRNA sequence selected from SEQ ID l\05:1—507 or SEQ Nosz338—364; or an lTS sequence selected from SEQ ID NOs: 5168. 3. The microbial ition of claim 2‘" wherein the at least one ial strain comprises Ascusb_4729. 4. The ial composition of claim 2, wherein the at least one microbial strain comprises Ascusb_l 7021 l . The microbial composition of claim 2‘" wherein the at least one microbial strain comprises Ascusb_1686. 6. The microbial composition of claim 2, wherein the at least one microbial strain comprises Ascusb_33.

/. The microbial composition of claim 2, wherein the at least one microbial strain ses Ascusb___1 28. 8. The microbial composition of claim 2, n the at least one microbial strain comprises b___4729 and Ascusb___l 7021 1. 9. The microbial composition of claim 2, wherein the at least one microbial strain comprises Ascusb___4729, Ascusb___33, and Aswsb___3 l 3454.

. The microbial composition of any one of claims 1—9, wherein said microbial ition is encapsulated 11. A composition comprising: (a) a microbial, composition of any one of claims 1—10, and (b) an acceptable carrier. 12. The composition of claim ll, n the microbial ition is encapsulated. 13. The composition of claim ll, wherein the ulated microbial composition comprises a polymer selected from a saccharide polymer, agar polymer, agarose polymer, protein polymer, and lipid polymer, 14. The composition of claim 11, wherein the acceptable carrier is selected from the group consisting of: edible feed grade material, mineral e, water, glycol, molasses, and corn oil.

. The composition of claim 1 1, wherein the at least two microbial strains forming the microbial consortium are present in the composition at 101‘ to 10" cells per gram of said composition. 16. The composition of claim ll, wherein said composition is mixed, with animal feed.

WO 81203 17. A method of imparting at least one improved trait upon an animal, said method comprising administering the composition of claim 1 l to said animal. 18. The method of claim 17, wherein said animal is a fowl. 19. The method of claim 18, wherein said fowl is a broiler chicken.

. The method of claim 18, n the stration comprises inj ecting the composition into one or more of the crop, gizzard, cecum, small intestine, or large intestine of the animal. 21. The method of claim 17, wherein said composition is administered at least once per month. 22. The method of claim 21, wherein said composition is administered at least once per week. 23, The method of claim 22, wherein said composition is administered at least once per day. 24. The method of claim 17, wherein the administration occurs each time the animal is fed.

. The method of claim 17, wherein the administration is a cloacal administration. 26. The method of claim 25, wherein the cloacal administration comprises inserting a suppository comprising the composition into the rectum of the animal. 27. The method of claim 17, wherein the stration is an oral administration. 28. The method of claim 27, wherein the oral administration comprises administering the composition in combination with the animal‘s feed, water, litter, medicine, or vaccination. 29. The method of claim 27; wherein the oral administration comprises applying the composition in a gel or viscous solution to a body part of the animal, wherein the animal ingests the composition.

. The method of claim 17; wherein the administration ses spraying the composition onto the animal; and wherein the animal ingests the composition. 31. The method of claim 17; wherein said at least one improved trait is selected from the group consisting of: an increase in weight; an increase in egg production; an increase of musculature; an increase of vitamins in eggs; an increase of fatty acid tration, in the gastrointestinal tract; and increase in egg volume; an improved efficiency in feed utilization and ibility; an se in polysaccharide and lignin degradation; an increase in fat, starch; and/or protein digestion; an increase in vitamin availability; an se in mineral availability; an increase in amino acid availability; pH balance in the gastrointestinal tract; a reduction in methane and/or nitrous oxide ons; a reduction in manure production; an improved efficiency of nitrogen utilization; an improved efficiency of phosphorous utilization; an increased resistance to colonization of pathogenic microbes that colonize chickens; reduced mortality, increased production of antii'nicrobials; increased clearance of enic es; increased resistance to colonization of pathogenic es that infect chickens; increased resistance to colonization of pathogenic microbes that infect humans; wherein said increase or reduction is determined by comparing against an animal not having been stered said composition. 32. The method of claim 31; wherein said increase in weight is an increase by at least 1%. 33. The method of claim 31; wherein said reduction in manure production is a reduction by at least 1%. 34. The method of claim 31; wherein said increase in polysaccharide degradation is an increase in the degradation of lignin, cellulose and/or hemicellulose.

. The method of claim 31, wherein said increase in fatty acid concentration is an increase in acetic acid, propionic acid, and/or butyric acid. 36. The composition of claim 11, wherein the at least one microbial strain exhibit an increased utility that is not ted when said at least one microbial strain occurs alone, or when said at least one microbial strain is present at naturally occurring concentrations. 37. The composition of claim 11, wherein the at ne microbial strain exhibits a synergistic effect on imparting at least one improved trait in an animal. 38. A poultry feed supplement capable of increasing a desirable phenotypic trait in a bird, the feed supplement comprising: (a) a microbial consortium of any one of claims l~9 present at a concentration that does not occur naturally in said bird, and (b) an acceptable carrier. 39. The poultry feed n'ient of claim 38 wherein the microbial consortium is ulated. 40. An isolated microbial strain selected from any one of the microbial strains in Table 1 and/or Table 2. 41. An isolated microbial strain selected from the group consisting of: (a) ___4729 deposited as PATEN’l7201703004 (b) Ascusb___l70211 deposited as PATENI‘201703002 (c) Ascusb___l 686 deposited as 4016; (d) Ascusb___33 deposited as 367266; (e) Ascusb___l 28 deposited as PATENTZOl703004; (f) Ascusb___127 ted as Bn67265; (g) Ascusb___l4834 deposited as PTAn124016; (h) Ascusb____3 13454 deposited as PATENT201703003; (i) Ascusb___28 deposited as PTA" l 2403 9; (i) ___l 44 deposited as l?'l'A~l 24039; (k) Ascusb___3 '12 deposited as PA’I‘ENTZO l 703 002; and (l) Ascusb____21 5 8 deposited as PTAm124039 42. An isolated microbial strain comprising a polynucleotide sequence sharing at least 90% sequence identity with any one of SEQ ID NOS: 1—58 and 4. 43. A substantially pure e of an isolated microbial strain according to any one of claims 40 to 42. 44. A method of modulating the microbiome of a fowl; the method comprising administering the composition of claim 12. 45. The method of claim 44, wherein the administration of the ition imparts at least one improved trait upon the fowl. 46. The method of claim 45, wherein the at least one improved trait is selected from the group consisting of: an increase in weight; an increase in egg production; an increase of musculature; an increase of vitamins in eggs; an increase of fatty acid concentration in the gastrointestinal tract; and increase in egg volume; an ed efficiency in feed utilization and digestibility; an increase in polysaccharide and lignin degradation; an increase in fat; starch; and/or n digestion; an increase in vitamin availability; an increase in l availability; an increase in amino acid availability; pl-l balance in the gastrointestinal tract; a reduction in methane and/or nitrous oxide emissions; a reduction in manure production; an improved efficiency of nitrogen utilization; an improved efficiency of phosphorous utilization; an increased resistance to colonization of pathogenic microbes that ze chickens; reduced mortality; increased tion of antimicrobials; sed clearance of pathogenic microbes; increased resistance to colonization of pathogenic microbes that infect chickens, increased ance to colonization of pathogenic microbes that infect humans; wherein said increase or reduction is determined by comparing against an animal not having been administered said composition. 47. The method of claim 46, wherein said increase in weight is an increase by at least 1%. 48. The method of claim 46, wherein said reduction in manure production is a reduction by at least 1%. 49. The method of claim 46, wherein said increase in polysaccharide ation is an increase in the degradation of lignin, cellulose, and/or hernicellulose. 50. The method of claim 46, wherein said increase in fat digestion, starch digestion, and/or protein digestion is an se lay at least 1%. 51. The method of claim 46, wherein said increase in fatty acid concentration is an increase in acetic acid, propionic acid, and/or butyric acid, 52. The method of claim 45, wherein the tion of the microbiome is an increase in the proportion of the at least one microbial strain of the iorne, wherein the increase is measured relative to a fowl that did not have the at least one microbial strain administered, 53. The method of claim 45 wherein the modulation of the iome is a se in the proportion of the microbial strains present in the microbiome prior to the administration of the composition, wherein the decrease is measured relative to the niicrobionie of the fowl prior to the administration of the composition. 54. A method of increasing resistance of poultry to the colonization of pathogenic microbes, the method comprising the administration of the composition of claim 11, wherein the pathogen is unable to ze the intestinal tract of the poultry.

WO 81203 55. The method of treating poultry for the presence of at least one pathogenic microbe, the method comprising the administration of the composition of claim 1 l. 56. The method of claim 55;. wherein after administration of the ition the ve abundance of the at least one pathogenic microbe decreases to less than 5% relative nce in the gastrointestinal tract. 57. The method of claim 56. wherein the relative abundance of the at least one pathogenic microbe decreases to least than 1% relative abundance in the gastrointestinal tract. 58. The method of claim 56, wherein the at least one enic mi crohe is undetectable in the gastrointestinal tract 59. The method of claim 58, wherein less than 10 days post administration of the composition the at least one pathogenic microbe is undetectable in the gastrointestinal tract. 60‘ The method of claim 58, wherein within 5~l 5 days post stration of the composition the at least one pathogenic microbe is undetectable in the gastrointestinal tract. 61. The method of claim 56, wherein the at least one pathogenic microbe is also undetectable in or on eggs laid by the poultry. 62. The method of any one of claims 54—61, wherein the at least one pathogenic microbe is selected from: Mycoplasma galliseplicnm, Alycoplasma meleagridis, vacoplasma synoviae, Pasteurella multocida, Clostria’iam perf’ingens, (Z'lostridizim colinzim, (l’lostridium borzilinum, Salmonella typi, ella Iypliimarium, ella enter’ica, Salmonella pulloram, Salmonella gallinarum, Hemophilas gallinarum, Einipelotnrix insidiosa, Campylobacterjejzn/zi, Campylobacfer coli, Campyloliacrer lai'i, Listeria monocytogenes, Arcobacler' blileeri, il/i’fiicolwacterium avizmz. and pathogenic strains of Escherichia coli and Staphylococcus aureas. 63. The method of claim 62, wherein the at least one pathogenic microbe is selected from salmonella or C'Zoslridium.w 64. The composition of claim ll, wherein the microbial ition comprises bacteria and/or fungi in spore form. 65. The composition of claim ll, wherein the microbial ition comprises a dechlorinator and/or an oxygen scavenger. {@730} In aspects, the aforementioned microbial species—that is, a ed microbial population that comprises a bacteria with a 168 nucleic acid sequence, and/or a fungi with an ITS nucleic acid, ce. which is at least about 97% identical to a nucleic acid sequence ed from the group consisting of: SEQ ll) NOs: l—SSS—are members of a Markush group, as the present disclosure. rates that the members belong to a class of microbes terized by various physical and functional attributes which can include any of the following: a) the ability to convert a carbon source into a volatile fatty acid such as acetates butyrate, propionate, or combinations thereof; b) the ability to degrade a soluble or insoluble carbon source; c) the ability to impart an increase in weight gain to fowl administered the microhe(s); d) the ability to modulate the microbiome of the gastrointestinal tract of fowl administered the microbe; e) the ability to be formulated into a shelf-stable composition; f) the ability to t a decrease in feed conversion ratio in fowl having been administered the niicrolJe(s); g) the ability to impart a se in pathogen~associated lesion formation in the gastrointestinal tract; h) the ability to impart a decrease in pathogenic microbes in the gastrointestinal tract; and/or i) possessing a MlC score of at least about 0.2. if a bacteria and possessing a MIC score of at least about 02 if a fungi. Thus, the members of the h/larkush group possess at least one property in , which can be responsible for their function in the claimed relationship. {8731} As used herein "shelfustable" refers to a functional attribute and new utility acquired by the es formulated according to the disclosure, which enable said microbes to exist in a useful/active state outside of their natural environment in the gastrointestinal tract (Le, a markedly different characteristic). Thus, shelf—stable is a functional attribute created by the formulations/compositions of the disclosure and denoting that the microbe formulated into a shelfustable composition can exist outside the gastrointestinal tract and under ambient conditions for a period of time that can be determined depending upon the particular formulation utilized, but in general means that the microbes can be formulated to exist in a composition that is stable under ambient conditions for at least a few days and generally at least one week. ingly, a "shelf—stable fowl supplement" is a composition comprising one or more microbes of the sure, said, microbes formulated in a composition, such that the composition is stable under ambient conditions for at least one week, meaning that the microbes comprised, in the composition (rag, whole cell, spore, or lysed cell) are able to impart one or more beneficial phenotypic properties to a fowl when administered (eg increased weight gain, increased ll y, improved gastrointestinal health, and/or modulation of the gastrointestinal niicrobiome), {0732} In some embodiments, the ed microbial strains of the present disclosure further encompass s thereof. In some embodiments, the present disclosure further contemplates microbial strains having all of the identifying teristics of the presently disclosed microbial strains, Table 45: Budaggest Treaty Deposits of the sure Depository Accession Number Date of Deposit ATCC PTA~124016 March 2, 2017 ATCC PTAu124039 March 10, 2017 Bigelow PATENTZOl 703001 March 1 7, 2017 PATENTZOI 703002 March 24, 2017 Bigelow PATENT201703003 March 24, 2017 w PA'I‘ENT201703004 May 16, 2016 13—67269 iii/lay 16, 2016 3—67270 Nlay 16, 2016 INCORPQRAT]()N BY REFERENCE {0733}A1l, references, afiicles, publications, patents, patent publications, and patent applications cited herein are incorporated by reference in their entireties for all purposes. {0734} However, mention of any reference, article, publication, patent, patent ation, and patent application cited herein is not, and should not be taken as, an acknowledgment or any form of suggestion that they constitute valid prior art or form part of the common l knowledge in any country in the world, l‘x) >-- HR) CLAIR/{S A method for decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) stering to a fowl an effective amount of a shelfnstable fowl ment comprising: i) a purified microbial population that comprises a bacterium with a 168 nucleic acid sequence, and/or a fungus with an ITS c acid sequence, which is at least about 97% identical to a nucleic acid sequence ed from the group consisting of SEQ ll) NOS: 143385, and, said bacterium and/or fungus have a MIC score of at least about 0.2; and ii) a shelfvstable r suitable for fowl administration, wherein the fowl administered the effective amount of the shelfvstable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and ./' 0]" a decrease in pathogenmassooiated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement, The method of claim 1, wherein the fowl is a broiler.

The method according to claim 1, wherein the fowl supplement is stable under ambient conditions for at least one week, The method according to claim 1, wherein the fowl supplement is formulated as an: encapsulation, tablet, e, pill, feed additive, food ingredient, food additive, food preparation, food supplement, water additive, water-n'iixed additive, heat-stabilized additive, moisterure-stabilized ve, consumable solution, consumable spray ve, consumable solid, consumable gel, injection, itory, drench, or combinations thereof.

The method ing to claim 1, wherein the fowl supplement is encapsulated in a polymer or carbohydrate The method according to claim l, wherein administering comprises: feeding the fowl supplement to a fowl.

The method according to claim 1, wherein administering comprises: spraying the fowl supplement onto a fowl.

The method according to claim 1, wherein the purified microbial population is present in the fowl supplement at a concentration of at least 102 cells.

The method according to claim 1, wherein the purified microbial population comprises a bacterium with a 16S c acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:1—50 and 59" . The method according to claim 1, wherein the ed microbial population comprises a fungus with an 1TS nucleic acid sequence that is at least about 97% cal to a nucleic acid sequence selected from the group consisting of: SEQ TD NOs:51n58. 11. The method according to claim 1, wherein the purified microbial population comprises a ium with a 16S nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOszl—SO and 59, The method ing to claim 1, wherein the purified microbial population comprises a fungus with an HS nucleic acid ce that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID 1403:5168.

The method according to claim 1, wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence selected from the group consisting of: SEQ ID NOS: 1-50 and 59-385. 14. The method ing to claim 1, wherein the purified microbial population comprises a fungus with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID l—SS.

The method according to claim 1, wherein the purified microbial population comprises a bacterium with a. 168 nucleic acid sequence and a fungus with an ITS c acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1—385. 16. The method according to claim 1, wherein the purified microbial population comprises a bacteria with a 163 nucleic acid sequence that is at least about 97% identical to SEQ 11) 17. The method according to claim 1, wherein the purified ial population comprises a bacterium with a 168 c acid sequence comprising SEQ 11) NO: 1, and wherein the bacterium is as deposited as 201703004. 18. The method according to claim 1, wherein the purified ial population only contains organisms that are members of a group selected from: Lactobacz’llus, Clostrz'dz‘um, Faccalz‘bacrer, HydrogenOrtnaerobacrerium, Acrocarpwpom, Bacillus, Subdoltgramu’um, Leuconostoc, Lachnospimcea, Anczerqfiium, Microbacrerium, Verrucosz'spora, filum, Biaurz'a, Pseudomonas, Sporobacter, bacrerz’um, Streptococcus, Paraceccus, (jelfllIOiEil17Ifcuifi, Ruminococcus, Roscbura, Bacieroz’des, sidz’um, Gibberella, Afatospora, Pichz'a, and Candida. 19. The method according to claim 1, wherein the fowl stered the effective amount of the fowl supplement exhibits at least a 1% decrease in feed conversion ratio, at least a 1% increase in weight, and or at least a 1% decrease in pathogen~associated lesion ion in the intestinal tract, The method according to claim 1, wherein the fowl administered the effective amount of the fowl supplement exhibits at least a 10% decrease in feed conversion ratio, at least a % increase in weight, and or at least a 10% decrease in pathogen-associated lesion formation in the gastrointestinal tract, A shelf~stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population that comprises a bacterium with a 168 nucleic acid sequence and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% cal to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1—385; and b) a shelf-stable carrier le for fowl administration, wherein the purified population of bacteria and/or fungi of a) is present in the supplement in an amount effective to decrease feed sion ratio, increase fowl weight, and / or decrease pathogenuassociated lesion formation in the intestinal tract of fowl, as compared to a fowl not having been administered the suppiement. 22. The shelf—stable fowl supplement according to claim 21, wherein the purified population of bacteria and/or fungi comprises bacteria with a 168 nucleic acid sequence that is at least about 9 % identical to SEQ ID 1\O: 1.

The shelf—stable fowl ment according to claim 21, wherein the purified population of bacteria and/or fungi comprises bacteria with a 16S nucleic acid sequence that is at least about 99% identical to SEQ ID NO: 1. 24. The shelf—stable fowl supplement according to claim 21, n the purified population of bacteria and/or fungi ses bacteria with a 16S nucleic acid sequence comprising SEQ ID NO: 1.

The shelf—stable fowl ment according to claim 21,, wherein the purified population of bacteria and/or fungi comprises bacteria with a 16S c acid sequence comprising SEQ ID NO: 1,, and wherein the bacteria are as deposited as PATENTS-101703004. 26. The shelf—stable fowl supplement according to claim 21 further sing: (i) a purified population of bacteria comprising a 168 nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ 11') N0: 160 and 593%, and/or (ii) a purified population of fungi that comprise fungi with an1'1‘S nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected, from the group consisting of: SEQ ID N’Ozfil—SS.

The shelf—stable fowl supplement according to claim 26,, wherein the purified population of ia comprises bacteria with a 168 nucleic acid, sequence that is at least about 99% cal to a nucleic acid sequence selected from the group consisting of: SEQ ID N01— 50 and 59—385.

The stable fowl ment according to claim 26,, wherein the purified tion of fungi comprises fungi with an ITS nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOSE—58 WO 81203 29. The shelf—stable fowl supplement ing to claim 26, wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid ce selected from the group consisting of SEQ TD N0: L50 and 59-385.

. The shelf—stable fowl supplement according to claim 26, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence selected from the group consisting of: SEQ TD NO:51—58. 31. The stable fowl supplement according to claim 26, wherein the purified population of bacteria ses bacteria with a 168 c acid sequence that is at least about 97% identical to SEQ ll) N03. 32. The shelf—stable fowl ment according to claim 26, wherein the purified tion of bacteria comprises bacteria with a 168 nucleic acid sequence that is at least about 99% identical to SEQ ID N03 33 The shelf—stable fowl supplement according to claim 26, wherein the purified tion of bacteria comprises bacteria with a 168 nucleic acid ce comprising SEQ ll) 34. The shelf—stable fowl supplement according to claim 26, wherein the purified population of bacteria comprises SEQ ID NO: 1, and wherein the ia are as deposited as PATENT201703001i . The shelf-stable fowl supplement according to claim 26, wherein both a purified population of bacteria (i) and a purified population of fungi (_ ii) are present in the supplement. 36. The shelfmstable fowl supplement according to claim 2],, formulated for administration to a broiler. 37. The shelfvstable fowl supplement according to claim 2], wherein the supplement is stable under ambient conditions for at lea st one week. 38. The shelfvstable fowl supplement according to claim 2], formulated as an: encapsulation, encapsulation, tablet, capsule, pill, feed additive, food ingredient, food additive, food preparation, food supplement, water additive, water~mixed additive, heat—stabilized additive, moisterure—stabilized additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, itory, drench, or combinations thereof. m 5-0 The shelf—stable fowl supplement according to claim 21, wherein the ed population of bacteria and/or fungi is present in the fowl supplement at a concentration of at least 102 cells. 40. The shelf—stable fowl supplement according to claim 21, wherein the fowl administered the supplement ts an increase in weight as compared to fowl not having been administered the ment. 41. The shelf—stable fowl supplement according to claim 21, wherein the fowl administered the supplement exhibits a decrease in pathogen—associated, lesion formation in the gastrointestinal tract as compared to fowl not having been stered the ment.

The shelf—stable fowl supplement ing to claim 21, wherein the fowl administered the supplement exhibits a sed incidence of Ciostridz'um perfimgens—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 43. The shelf—stable fowl supplement according to claim 21, wherein the fowl administered the supplement ts a 1% decreased incidence of Ciosmdmm perfringensnassociated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 44. The shelfvstable fowl supplement according to claim 21, wherein the fowl administered the supplement exhibits a 10% decreased incidence of Closrrz’dirmz pa:(fringing—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 45. The shelfvstable fowl supplement according to claim 21, n the fowl administered the ment exhibits a 20% decreased incidence of Closrrz’dirmz pa:(fringing—associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 46. A method for decreasing feed conversion ratio, increasing fowl weight, and / or decreasing pathogen-associated lesion formation in the gastroii'itestinal tract of fowl, the method con'iprising: a) administering to a fowl an effective amount of a shelfustable fowl ment comprising; i) a purified microbial population of Lacrobaciiius bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ll) N01, and said bacterium has a MlC score of at least about 0.2; ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an se in feed conversion ratio, an increase in weight, or a decrease in pathogen-associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. 47. The method of claim 46, wherein the fowl is a broiler.

The method according to claim 46, wherein the fowl supplement is stable under ambient conditions for at least one week.

The method according to claim 46, wherein the fowl supplement is formulated as an: ulation, tablet, capsule, pill, feed additive, food ingredient, food ve, food preparation, food supplement, water additive, watervmixed additive, heat—stabilized additive, moisteruremstabilized additive, able solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, or ations thereof.

The method ing to claim 46, wherein the fowl supplement is encapsulated in a polymer or carbohydrate.

The method according to claim 46, wherein administering comprises: feeding the fowl supplement to a fowl.

The method according to claim 46, wherein administering comprises: spraying the fowl supplement onto a fowl.

The method according to claim 46, wherein the purified ial tion is present in the fowl supplement at a concentra‘ti on of at least l0 cells.

The method ing to claim 46, further comprising: l‘x) >-- \O (i) a purified population of bacteria comprising a 168 nucleic acid ce that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1—50 and 59—385, and/or (ii) a purified population of fungi comprising an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOsz5l—58.

L11 L!) The method according to claim 54, wherein the purified population of bacteria ses bacteria with a 168 nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID N05: 1—50 and 59—385.. 56. The method according to claim 54, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOsz51—58.

L11 \1 The method according to claim 54, wherein the purified population of ia comprises bacteria with a. 168 nucleic acid sequence selected from the group consisting of SEQ ll) NO: 1—50 and 59—385 58. The method according to claim 54, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence selected from the group ting of SEQ ll) N015'l—58, U1 L0 The method ing to claim 54, wherein the purified population of bacteria comprises bacteria with a. 168 nucleic acid sequence that is at least about 97% identical to SEQ ll) 60. The method according to claim 5-4, wherein the purified population of bacteria. comprises ia with a 168 nucleic acid sequence that is at least about 99% cal to SEQ ID N011. 61. The method according to claim 54, wherein the ed population of bacteria ses bacteria with a 168 nucleic acid sequence comprising SEQ ll) N01. 62. The method according to claim 54, wherein the purified population of bacteria comprises SEQ ID NO: 1. and wherein the ia are as deposited as PATENT20,170300l. h) R)O The method according to claim 54, wherein the purified population of bacteria and/or fungi only contain organisms that are members of a group selected from: aniobacillus, Closl'ridium, fl’aecalibacter, Hydrogenoanaerobacferium‘ Acrocarpospom, us, SubdoIigmmu’um, ostoa Lachnospimcea, Anaerqfilum, mbacrermm, osispora, Anaerofilum, Biaurz'a, Pseudomomts, Sporobacrei", Corynebacrerz’um, Streptococcus, Paracoccus, Cellulosilyrz’cum, Ruminococcus, Rosebura, Bacremides, Filobasidium, Gibberella, Alarospora, Pichia, and Candida.

The method according to claim 46, n the fowl administered the effective amount of the fowl supplement exhibits at least a 1% decrease in feed conversion ratio, at least a 1% se in weight, and or at least a 1% decrease in pathogen-associated lesion formation in the gastrointestinal tract, as compared to fowl not having been administered the supplement.

The method according to claim 46, wherein the fowl administered the effective amount of the fowl supplement exhibits at least a l0% decrease in feed conversion ratio, at least a % increase in weight, and / or at least a l0% decrease in patliogenmassociated lesion formation in the gastrointestinal tract, as ed to fowl not having been administered the supplement, 66. A shelf~stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion ion in the intestinal tract of fowl, comprising: a) a purified population of ,Li:ictoliacillus bacteria comprising bacteria with a l6$ nucleic acid sequence that is at least about 97% identical to SEQ ID N0: 1; and b) a stable carrier suitable for fowl administration, n the purified population oflactobacillus bacteria of a) is present in the supplement in an amount effective to decrease feed con version ratio, increase fowl weight, or decrease patl’iogen—associated lesion ion in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement.

The shelf—stable fowl supplement according to claim 66, n the purified population of Lacmbacz’llus bacteria comprises bacteria with a loS nucleic acid sequence that is at least about 99% identical to SEQ ID N011, l‘x) l‘x) i_.

WO 81203 68. The shelf—stable fowl supplement according to claim 66, wherein the purified tion of Lnflobacfllus bacteria comprises bacteria with a 163 nucleic acid sequence comprising SEQ ID NO: 1.

The shelf—stable fowl supplement according to claim 66, wherein the purified population of Lactobczcz’iius ia comprises bacteria with a 168 nucleic acid sequence comprising SEQ ll) NO: 1,, and wherein the bacteria are as ted as PATENTS-101703004. \1.0 The shelf—stable fowl supplement according to claim 66, further comprising: (i) a ed population of bacteria comprising a 168 nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NO: L50 and 59385, and/or (ii) a purified population of fungi sing an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NO:51—58. 71. The shelf—stable fowl supplement according to claim 70. wherein the purified population of bacteria comprises ia with a 168 nucleic acid, sequence that is at least about 99% identical to a nucleic acid sequence selected from the grou 3 consisting of: SEQ ID NO: l ~ 50 and 59—385.

The shelf—stable fowl supplement according to claim 70. wherein the purified population of fungi comprises fungi with an ITS c acid sequence that is at least about 99% identical to a c acid sequence selected from the group ting of: SEQ 1]) N05] «58‘ 73. The shelfmstable fowl ment according to claim 7Q wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence selected from the group consisting of SEQ ID NO: l —50 and 59—385.

The shelf-stable fowl supplement according to claim 70, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID NOE—58 The shelf—stable fowl supplement according to claim 70, wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ll) N03. 76. The shelf—stable fowl supplement according to claim 70, wherein the purified population of bacteria comprises bacteria with a 16S nucleic acid sequence that is at least about 99% identical to SEQ ID N03. \1\1 The shelf—stable fowl supplement according to claim 70, wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence comprising SEQ ID 78. The shelf—stable fowl supplement according to claim 70, wherein the purified tion of bacteria comprises SEQ ID N03, and wherein the bacteria are as deposited as PATENTZOI 70’ GOT£44 , The stable fowl supplement according to claim 70, wherein both a purified population of bacteria (i) and a ed population of fungi (ii) are present in the supplement. 80. The shelf—stable fowl supplement according to claim 66, ated for administration to a broiler 81. The shelf—stable fowl ment according to claim 66, n the supplement is stable under t conditions for at least one week.

The shelf—stable fowl supplement according to claim 66, ated as an: encapsulation, tablet, capsule, pill, feed additive, food ingredient, food additive, food ation, food supplement, water additive, waternmixed, additive, heatmstabilized additive, moisteruren stabilized additive, consumable solution, consumable spray additive, consumable solid, able gel, injection, suppository, drench, or combinations thereof83. The shelf—stable fowl ment according to claim 66, wherein the purified population of Lactobacz’llus bacteria is present in the fowl supplement at a concentration of at least l 02 cells, to to w WO 81203 84. The shelf—stable fowl supplement according to claim 66, wherein the fowl administered the supplement exhibits an increase in weight as compared to fowl not having been administered the supplement. 85. The shelf—stable fowl supplement ing to claim 66, wherein the fowl administered the supplement exhibits a decrease in pathogennassociated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 86. The shelf—stable fowl supplement according to claim 66, wherein the fowl administered the supplement ts a decreased incidence of Closm’dium pegfrr‘ngcnsnassociated lesion formation in the gastrointestinal tract as ed to fowl not having been administered the supplement.

O!) >1 The stable fowl supplement according to claim 66, wherein the fowl stered the supplement ts a 1% decreased incidence of Closrridium perfrz’ngens~associated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 88. The shelf—stable fowl supplement according to claim 66, wherein the fowl administered the supplement exhibits a 10% decreased incidence of Clostridium peiji‘ingenyassociated lesion ion in the gastrointestinal tract as compared to fowl not having been administered the supplement. 89. The shelf-stable fowl ment according to claim 66, wherein the fowl stered the supplement exhibits a 20% decreased incidence of Clostridium peiji‘ingenyassociated lesion formation in the gastrointestinal tract as compared to fowl not having been administered the supplement. 90. A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry supplement con'iprising: i) a ed microbial population that comprises a bacterium with a l68 nucleic acid sequence, and/or a fungus with an {TS nucleic acid sequence, which is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: l 685, and said bacterium and/or fungus have a MIC score of at least about 0.2; and l‘x) l‘x) 4; ii) a shelf—stable carrier suitable for poultry administration, wherein the bird stered the effective amount of the shelf—stable poultry supplement exhibits a se in the number of ic enteritis—causing ia in the gastrointestinal tract, as compared to a bird not having been administered the supplement. 91. The method of claim 90, wherein the bird is a broiler.

The method ing to claim 90, wherein the poultry supplement is stable under ambient conditions for at least one week. 93. The method according to claim 90, wherein the poultry supplement is formulated as an: encapsulation, tablet, capsule, pill, feed additive, food ingredient, food additive, food preparation, food supplement, water additive, water—mixed additive, heat—stabilized additive, moisterure—stabilized additive, consumable solution, consumable spray additive, consumable solid, consumable gel, ion, suppository, drench, or combinations thereof94. The method according to claim 90, wherein the poultry supplement is encapsulated in a polymer or ydrate. 9s, The method according to claim 90, wherein administering comprises: feeding the poultry supplement to a bird. 96. The method, ing to claim 90, wherein administering comprises: spraying the poultry supplement onto a bird.

The method according to claim 90, wherein the purified microbial population is t in the poultry supplement at a concentration of at least if)2 cells. 98. The method according to claim 90, wherein the purified microbial population ses a bacterium with a 168 nucleic acid sequence that is at least about 97% identical to a c acid sequence selected from the group consisting of: SEQ TD N0s:l~50 and 59— 99. The method according to claim 90, wherein the purified microbial population comprises a fungus with an ITS c acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:5l —5 8. 100. The method ing to claim 90, wherein the purified microbial population comprises a bacterium with a 168 nucleic acid sequence that is at least about 99% identical to a l‘x) l‘x) U} nucleic acid sequence selected from the group consisting of: SEQ ID NOs;1—50 and 59_ 101. The method according to claim 90, wherein the purified microbial population comprises a fungus with an lTS nucleic acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of: SEQ ID NOs:51n58.

The method according to claim 90, wherein the ed ial population comprises a bacterium with a 168 nucleic acid sequence selected from the group consisting of: SEQ 1D NOs:1—50 and 59—385. 103. The method according to claim 90, wherein the purified microbial population comprises a fungus with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID 104. The method according to claim 90, wherein the purified ial tion comprises a bacterium with a 168 nucleic acid sequence and a fungus with an US nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of: SEQ 11) N05: 1—385. 105. The method according to claim 90, wherein the purified microbial population comprises a ia with a 168 nucleic acid sequence that is at least about 97% cal to SEQ 11) 106. The method according to claim 90, wherein the purified ial population comprises a bacterium with a 16S nucleic acid sequence comprising SEQ 11) N01, and wherein the bacterium is as deposited as PATENT201703004. 107. The method according to claim 90, wherein the purified microbial population only contains organisms that are members of a group selected from: Laczobacii’lus, Closrrirtfium, Faecahbacter, Hydrogenaanaerobaclermm, Acrocarpospom, Bacillus, Subdoligranuhzm, Lemxmostoc, Lachnospimcea, Airzaerqfilum, ,Microbacterizmz, Verrucosispora, Aizaerqfilum, Blaulia, Pseudommzas, Spomliacrer, Corynebaclerizmz, ococcus, Paracoccus, Cellulosz'lyliwm, Rzmiinococcus, m, Bacferoides, Filobasz’dizmz, lla, Alarmpora, Pichia, and Candida. 108. The method according to claim 90, wherein the bird administered the effective amount of the poultry supplement exhibits at least a 1% decrease in the number of necrotic enteritis~ g bacteria in the intestinal tract, as compared to a bird not having been administered the supplement. 109. The method according to claim 90, n the necrotic enteritis—causing ia is Closrrirtt’z'um perfi‘z’ngens. 110. A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf—stable poultry supplement comprising: i) a purified microbial population of Lacrobacz’llus bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID N01, and said bacterium has a MIC score of at least about 0.2; ii) a shelfvstable carrier suitable for poultry administration, wherein the poultiy stered the effective amount of the shelf-stahle poultry supplement exhibits a decrease in the number of necrotic enteritis—causing bacteria in the gastrointestinal tract, as compared to a bird not having heen administered the supplement. l l l. The method of claim 1 10, wherein the bird is a r. 112. The method according to claim 110, wherein the poultry supplement is stahle under ambient ions for at least one week. 113 The method according to claim 110, wherein the poultry supplement is ated as an: encapsulation, tahlet, capsule, pill, feed additive, food ingredient, food additive, food preparation, food supplement, water additive, vvatervmixed additive, heat—stabilized additive, moisture—stabilized ve, consumable solution, consumable spray additive, consumable solid, consumable gel, ion, suppository, drench, or combinations thereof.

H4. The method according to claim I l0, wherein the poultry supplement is encapsulated in a polymer or carbohydrate. h) h) \3 115 The method to claim wherein 3 according 110, administering ses: feeding the poultry supplement to a bird. 116. The method according to claim 110, wherein administering ses: spraying the poultry supplement onto a bird 117. The method according to claim 110, wherein the purified microbial population is t in the poultry supplement at a tration of at least 102 cells. 118. The method according to claim 110, further comprising: (i) a purified population of bacteria comprising a 163 nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1—50 and 59—385, and/or (ii) a purified population of fungi comprising an ITS nucleic acid sequence that is at least about 97% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOS:51—58. 119. The method according to claim 118, wherein the purified population of bacteria comprises ia with a 16S c acid sequence that is at least about 99% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NOS:1—50 and 59 120. The method according to claim 118, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence that is at least about 99% identical to a c acid sequence selected from the group consisting of SEQ ID NOsz51—58. 121. The method according to claim 118, wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence selected from the group consisting of SEQ ID NO:1~50 and 59~385 122. The method according to claim 118, wherein the purified population of fungi comprises fungi with an ITS nucleic acid sequence selected from the group ting of SEQ ID NO:51~58. 123. The method according to claim 118, wherein the purified tion of bacteria comprises bacteria with a 168 c acid sequence that is at least about 97% identical to SEQ ID N01. l‘x) l‘x) 00 124. The method according to claim 118, wherein the purified population of bacteria comprises bacteria with a 16S nucleic acid sequence that is at least about 9 % cal to SEQ ID NO: 1. 125. The method according to claim 118, wherein the purified population of bacteria comprises bacteria with a 168 nucleic acid sequence comprising SEQ 11) N01. 126. The method according to claim 118, wherein the purified population of bacteria comprises SEQ 11) N01, and n the bacteria are as ted as PA'I'ENT201703 001i 127. The method according to claim 118, wherein the purified population of bacteria and/or fungi only contain organisms that are members of a group selected from; Lactobacillus, Clostrz'dz‘um, Faccalz‘bacrer, HydrogenOrtnaerobacrerium, rpospom, Bacillus, Subdoltgrcmm’um, Leuconostoc, ospimcea, Anczerqfiium, rlficrobacrerium, osz'spora, Anaerofilum, Biattrz'a, Pseudomomts, Sporobacter, Corynebacrerz’um, Streptococcus, Paraceccus, (jellztloiriliiric:uin, Ruminococcus, Roscbura, Bacremz'des, Filobasidz’um, Gibberella, Alatospora, Pichz'a, and Candida. 128. The method according to claim 110, n the bird administered the ive amount of the poultry supplement exhibits at least a 1% decrease in feed conversion ratio, at least a 1% increase in weight, or at least a 1% decrease in the number of necrotic enteritis" causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement. 129. The method according to claim 1 10, wherein the fowl stered the effective amount of the fowl supplement exhibits at least a 10% decrease in the number of necrotic enteritis—causing ia. in the gastrointestinal tract, as compared to a bird not having been administered the supplement. 130. The method according to claim 110, wherein the necrotic enteritis~causing bacteria is Closl'ridium peiji‘mgens 131. A method for decreasing feed conversion ratio, increasing fowl weight, and / or decreasing pathogenmassociated lesion formation in the gastrointestinal tract of fowl, the method comprising: 1‘4 1‘4 KO a) administering to a fowl an effective amount of a stable fowl supplement comprising; i) a ed microbial population of Eubacrerz'um bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ll) NOz346, and, said bacterium has a MIC score of at least about 0.2; ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in weight, or a decrease in pathogen-associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement, 132 A method for decreasing feed conversion ratio, increasing fowl weight, and ,I’or decreasing pathogenmassociated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) stering to a fowl an effective amount of a shelf~stable fowl supplement con'iprising: i) a purified microbial population of Bacillus bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID NOzl3, and said bacterium has a MIC score of at least about O2; and ii) a shelf-stable carrier le for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in , or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. 133. The shelf—stable fowl ment according to claim 66, wherein the fowl administered the supplement exhibits a se in feed conversion ratio as compared to fowl not having been administered, the supplement.

NU) 0 134. The shelf—stable fowl supplement according to claim 21, wherein the fowl administered the supplement exhibits a se in feed sion ratio as compared to fowl not having been administered the supplement. 135. A method for decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising; a) administering to a fowl an effective amount of a shelfnstahle fowl supplement comprising: i) a purified microbial population that comprises a ium with a 168 nucleic acid ce at least about 97% identical to SEQ ID NO:346, and said bacterium has a MlC score of at least about 0.2; and ii) a shelfvstable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogenmassociated lesion formation in the gastrointestinal tract, as compared to a fowl not having been stered the supplement, 136 A shelf—stable fowl supplement capable of decreasing feed sion ratio, sing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population that comprises a ium with a léS nucleic acid sequence at least about 97% identical to SEQ ID NO:346, and b) a shelf-stable carrier suitable for fowl administration, wherein the purified population of bacteria, of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, and or decrease pathogenmassociated lesion formation in the intestinal tract of fowl, as compared to a fowl not having been administered the supplement. 137. A method for decreasing feed conversion ratio, increasing fowl weight, and or decreasing en—associated lesion formation in the gastrointestinal tract of fowl, the method comprising: l‘x) U) i_. a) administering to a fowl an effective amount of a shelfustahle fowl supplement comprising; i) a purified microbial population of Eubacrerz'um ia comprising ia with a 163 nucleic acid sequence of SEQ ID NO:346, and said bacterium has a MIC score of at least about 0.2; and ii) a stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in , or a decrease in pathogen—associated lesion formation in the intestinal tract, as compared to a fowl not having been administered the ment 13% A shelf—stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or sing pathogen~associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population ofE"bacterium bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID NO:346; and h) a shelf-stable carrier suitable for fowl administration, wherein the purified population cterium bacteria. of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, or se pathogen-associated lesion formation in the intestinal tract of fowl, as compared to a fowl not having been administered the supplement~ HQ A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry supplement con'iprising: i) a purified microbial population that comprises a bacterium with a 168 nucleic acid sequence at least about 97% identical to SEQ ID NO:346, and said bacterium has a l‘s/IlC score of at least about 0.2; and ii) a shelf—stable carrier suitable for poultry administration, wherein the bird stered the effective amount of the stable poultry supplement exhibits a decrease in the number of necrotic enteritis—causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement. 140. A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf—stable poultiy supplement comprising: i) a purified microbial population of Eubacterz’um bacteria comprising bacteria with a 163 nucleic acid ce of SEQ ID NO:346, and said bacterium has a MIC score of at least about 0.2; and ii) a shelfvstable r suitable for poultry administration, wherein the poultiy administered the effective amount of the shelf-stable poultry supplement exhibits a decrease in the number of ic enteritis—causing bacteria in the intestinal tract, as compared to a bird not having been administered the supplement. 141. A method for decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogenmassociated lesion formation in the gastrointestinal tract of fowl, the method sing: a) administering to a fowl an effective amount of a shelf~stable fowl supplement comprising: i) a purified microbial population that comprises a ium with a l 68 nucleic acid sequence at least about 97% identical to SEQ ID NO: l 3, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as ed to a fowl not having been administered the supplement. 142. A stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or sing pathogennassociated lesion formation in the gastrointestinal tract of fowl, comprising: to U) do a) a purified population that comprises a bacterium with a 168 nucleic acid sequence at least about 979/6 cal to SEQ ID N013; and b) a shelf—stable carrier suitable for fowl administration, wherein the purified population of bacteria of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, and, or decrease pathogen-associated lesion ion in the gastrointestinal tract of fowl, as ed, to a fowl not having been administered the supplement. 143. A method for decreasing feed conversion ratio, increasing fowl weight, and or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a stable fowl supplement comprising: i) a purified microbial population of Bacillus bacteria comprising bacteria with a 168 nucleic acid sequence of SEQ ID NO: 13, and said bacterium has a MIC score of at least about 02; and ii) a shelfvstable carrier suitable for fowl administration, n the fowl administered the ive amount of the shelfvstable fowl supplement exhibits an decrease in feed sion ratio, an increase in , or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. 144, A shelf~stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population of Bacillus bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID NO:13; and b) a shelf—stable carrier suitable for fowl administration, wherein the purified population of Bacillus bacteria of a) is present in the supplement in an amount ive to decrease feed conversion ratio, se fowl weight, or decrease l‘x) U) .1; pathogen—associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement. 145. A method of treating poultry for necrotic tis, the method comprising: a) administering to a bird an effective amount of a shelf—stable poultry supplement comprising: i) a purified microbial population that comprises a bacterium with a 168 nucleic acid sequence at least about 97% cal to SEQ ID N013, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for poultry administration, n the bird administered the effective amount of the shelfnstable poultry supplement exhibits a decrease in the number of necrotic enteritis—causing bacteria in the gastrointestinal tractfi as compared to a bird not having been administered the supplement 146 A method of treating poultry for necrotic tis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry supplement comprising: i) a purified microbial population ofBacilius bacteria comprising bacteria with a 168 nucleic acid sequence of SEQ ID N013, and said bacterium has a MlC score of at least about 0.2; and ii) a stable carrier suitable for poultry stration, wherein the y administered the effective amount of the shelf—stable y supplement exhibits a decrease in the number of necrotic ei'iteritis—causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the ment 147. A method for decreasing feed conversion ratio, sing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelfustable fowl supplement comprising; l‘x) U) {I} WO 81203 i) a purified microbial population that comprises a ium with a 168 nucleic acid sequence at least about 97% identical to SEQ ID N019, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the ive amount of the shelf—stable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. 148 A shelf—stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl , or decreasing pathogen~associated lesion ion in the gastrointestinal tract of fowl, comprising: a) a purified population that comprises a bacterium with a 168 nucleic acid sequence at least about 97% identical to SEQ ID NO:19; and h) a shelf-stable carrier suitable for fowl administration, wherein the purified population of bacteria of a) is present in the ment in an amount effective to decrease feed conversion ratio, increase fowl weight, and or se pathogenessociated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having 1oeen administered the supplement.

Mg A method for decreasing feed conversion ratio, increasing fowl weight, and or decreasing pathogen—associated lesion ation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelf—stable fowl supplement comprising; i) a purified microbial population of Lactobacilius bacteria comprising bacteria with a 168 nucleic acid sequence of SEQ ID N019, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for fowl stration, n the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in weight, or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. : 0. A nstable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing patliogen~associated lesion formation in the gastrointestinal tract of fowl, comprising: a) a purified population of Bacillus bacteria comprising ia with a 163 c acid sequence that is at least about 97% identical to SEQ ID N019; and, b) a shelf—stable carrier suitable for fowl administration, wherein the purified population of Lacrobacilius bacteria of a) is present in the supplement in an amount effective to se feed conversion ratio, increase fowl weight, or decrease pathogen—associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement. ,l, A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry ment comprising: i) a purified microbial population that ses a bacterium with a I68 nucleic acid sequence at least about 97% identical to SEQ II) NO: I9, and said bacterium has a MIC score of at least about 02.; and ii) a shelf-stable carrier suitable for poultry administration, wherein the bird administered the effective amount of the stable poultry supplement exhibits a decrease in the number of necrotic enteritis-causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement, to A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry ment comprising; i) a purified microbial population of Lactobacilius bacteria comprising bacteria with a res nucleic acid sequence of SEQ ID N019, and said bacterium has a MIC score of at least about 0.2; and ii) a stable carrier suitable for poultry administration, wherein the poultry administered the ef"ective amount of the shelf—stable poultry supplement exhibits a decrease in the number of necrotic tis—causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the supplement. 153. A method for decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion formation in the gastrointestinal tract of fowl, the method comprising; a) administering to a fowl an effective amount of a shelfnstable fowl supplement comprising: i) a purified microbial tion that ses a bacterium with a loS nucleic acid sequence at least about 97% identical to SEQ ll) N022, and said bacterium has a MIC score of at least about 0.2; and ii) a shelfvstable carrier suitable for fowl administration, wherein the fowl administered the ive amount of the shelf—stable fowl supplement exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogenmassociated lesion formation in the gastrointestinal tract, as ed to a fowl not having been administered the supplement. l54, A shelf~stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen—associated lesion ion in the gastrointestinal tract of fowl, comprising: a) a purified population that comprises a bacterium with a loS nucleic acid sequence at least about 979/6 identical to SEQ ID N022; and b) a shelf—stable carrier suitable for fowl administration, n the purified population of bacteria of a) is present in the ment in an amount effective to decrease feed conversion ratio, increase fowl weight, and or decrease genmassociated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement. 155. A method for decreasing feed conversion ratio, increasing fowl weight, and or decreasing pathogen—associated lesion formation in the intestinal tract of fowl, the method comprising: l‘x) U) 00 a) stering to a fowl an effective amount of a shelfustahle fowl ment comprising; i) a purified microbial population of Lacrobaciiius bacteria comprising bacteria with a 163 nucleic acid sequence of SEQ ID N022, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for fowl administration, n the fowl administered the effective amount of the shelf—stable fowl supplement exhibits an decrease in feed conversion ratio, an increase in weight, or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement ,6~ A shelf—stable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen~associated lesion formation in the intestinal tract of fowl, sing: a) a purified tion of Bacillus bacteria comprising bacteria with a 168 nucleic acid sequence that is at least about 97% identical to SEQ ID N022; and h) a shelf-stable carrier suitable for fowl administration, wherein the ed population of Lacrobaciiius bacteria of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, or decrease pathogen-associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement~ A method of treating y for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf-stable poultry ment con'iprising: i) a purified microbial population that comprises a bacterium with a 168 nucleic acid sequence at least about 97% cal to SEQ ID N022, and said bacterium has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for poultry administration, l‘x) U) KO wherein the bird administered the effective amount of the shelf—stable poultry supplement exhibits a decrease in the number of necrotic enteritis—causing bacteria in the gastrointestinal tract, as compared to a bird not having been administered the ment. 158. A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective amount of a shelf—stable poultiy ment comprising: i) a purified microbial population of Lacrobaciiius bacteria comprising bacteria with a 163 nucleic acid ce of SEQ ID N022, and said bacterium has a MIC score of at least about 0.2; and ii) a shelfvstable carrier suitable for poultry administration, wherein the poultiy administered the ive amount of the shelf-stable y supplement exhibits a decrease in the number of necrotic enteritis—causing bacteria in the intestinal tract, as compared to a bird not having been administered the supplement.

A method for decreasing feed conversion ratio, increasing fowl weight, or decreasing pathogen-associated lesion formation in the gastrointestinal tract of fowl, the method comprising: a) administering to a fowl an effective amount of a shelf—stable fowl supplement rising: i) a purified microbial population that comprises a bacterium with a 168 nucleic acid sequence, and/or a fungus with an {TS nucleic acid sequence, which is at least about 97% identical to any one of the ces disclosed in Table l, and said bacterium and/or fungus has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for fowl administration, wherein the fowl administered the effective amount of the shelf—stable fowl ment exhibits a decrease in feed conversion ratio, an increase in weight, and/or a decrease in pathogen—associated lesion formation in the gastrointestinal tract, as compared to a fowl not having been administered the supplement. 160. A slielfustable fowl supplement capable of decreasing feed conversion ratio, increasing fowl weight, or decreasing patliogenuassociated lesion formation in the intestinal tract of fowl, comprising: a) a ed ial population that comprises a ium with a 168 nucleic acid sequence, and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% identical to any one of the sequences disclosed in Table l; and b) a shelf—stable carrier suitable for fowl administration, wherein the purified population of bacteria of a) is present in the supplement in an amount effective to decrease feed conversion ratio, increase fowl weight, and, or decrease pathogen~associated lesion formation in the gastrointestinal tract of fowl, as compared to a fowl not having been administered the supplement, 161. A method of treating poultry for necrotic enteritis, the method comprising: a) administering to a bird an effective. amount of a. shelfvstable poultiy supplement comprising: i) a purified microbial tion that comprises a bacterium with a res nucleic acid sequence, and/or a fungus with an ITS nucleic acid sequence, which is at least about 97% identical to any one of the sequences disclosed in Table l, and said bacterium and/or fungus has a MIC score of at least about 0.2; and ii) a shelf—stable carrier suitable for poultry administration, whereii'i the bird administered the effective amount of the f—stable poultry supplement exhibits a decrease in the number ot‘necrotic enteritis—causing bacteria in the gastroii'itestinal tract, as compared to a bird not having been administered the supplement.

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Embree, Mallory Tarasova, Janna Picking, Luke Gogul, Grant Vanderlinden, Kayla <120> METHODS FOR IMPROVING AGRICULTURAL PRODUCTION OF FOWL BY ADMINISTRATION OF MICROBIAL CONSORTIA OR PURIFIED STRAINS THEREOF <130> ASBI‐003/03WO <150> 62/323305 <151> 2016‐04‐15 <150> 559 <151> 2016‐05‐12 <150> 62/425480 <151> 2016‐11‐22 <160> 385 <170> PatentIn version 3.5 <210> 1 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 1 agatttgatc tggctcagca cgaacgctgg cggcgtacct aatacatgca agtcgagcga 60 gcggaactaa cagatttact tcggtaatga cgttaggaaa gcgagcggcg gatgggtgag 120 gtgg tgcc ccatagtctg ggataccact tggaaacagg tgctaatacc 180 ggataagaaa gcagatcgca tgatcagctt ttaaaaggcc gcgt 224 <210> 2 <211> 224 <212> DNA <213> Unknown <220> <223> s rRNA from Lachnospiraceae (Clostridium Cluster XIVa) Page 1 747203 ‐ Sequence Listing.txt <400> 2 agatttgatc ctggctcagg atgaacgctg gcggcgtgct atgc aagtcgagcg 60 aagcgctttt gcggatttct tcggattgaa gcaattgtga ctgagcggcg gacgggtgag 120 taacgcgtgg ggaacctggc aggg ggataacagt tagaaatgac tgctaatacc 180 gcataagcgc acggaaccgc atggttttgt gtgaaaaact ccgg 224 <210> 3 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 3 agatttgctc ctggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc ggatgggtga 120 gtaacacgtg gggaacctgc cccatagtct gggataccac ttggaaacag gtgctaatac 180 cggataagaa agcagatcgc atgatcagct aggc ggcg 224 <210> 4 <211> 224 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 4 agagtttgat tcag gatgaacgcc ggcggtgtgc ctaatacatg gagc 60 gcactggccc aactgatatg acgtgcttgc actgaattga cgttggatta ccagtgagcg 120 gcggacgggt gagtaacacg tgggcaacct gccctggagc taac atctggaaac 180 aggtgctaat accgcataac aacgaaaacc acatggtttt cgtt 224 <210> 5 <211> 224 <212> DNA <213> Unknown Page 2 747203 ‐ Sequence g.txt <220> <223> Encodes 16S rRNA from Lactobacillus <400> 5 agatttgatc ctggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgagcg 60 cactggccca atga cgtgcttgca ctgaattgac gttggattac cagtgagcgg 120 cggacgggtg agtaacacgt gggcaacctg ccctggagcg ggggataaca tctggaaaca 180 ggtgctaata ccgcataaca acgaaaacca catggttttc gttt 224 <210> 6 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 6 agagtttgat cctggctcag gacgaacgct gtgc ctaatacatg caagtcgagc 60 gagcttgcct agatgatttt agtgcttgca ctaaatgaaa acaa gcgagcggcg 120 gacgggtgag taacacgtgg gtaacctgcc caagagactg ggataacacc tggaaacaga 180 tgctaatacc agataacaac actagacgca tgtctaaagt atga 224 <210> 7 <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from ibacterium <400> 7 agatttgatc atggctcagg acgaacgctg gcggcgcgcc taacacatgc aagtcgaacg 60 gaatacggag aggatttatc ttttctgtgt ttagtggcga acgggtgagt aacgcgtgag 120 gaacctgcct caaagagggg gacaacagtt ggaaacgact gctaataccg cataagccca 180 cggggccgca tggccctgag ggag aaatccgctt tgag 224 <210> 8 <211> 224 <212> DNA Page 3 747203 ‐ Sequence Listing.txt <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 8 agatttgatc ctggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 ccta gatgatttta gtgcttgcac taaatgaaac tagatacaag cgagcggcgg 120 acgggtgagt aacacgtggg taacctgccc aagagactgg gataacacct ggaaacagat 180 gctaataccg gataccaaca ctagacgcat gtctatagtt tgaa 224 <210> 9 <211> 224 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Hydrogenoanaerobacterium <400> 9 agatttgatc atggctcagg acgaacgctg gcggcgtgcc atgc aagtcgaacg 60 gagataagcg ctgatgattt ctag agattcttgc ttatcttagt cggg 120 tgagtaacgc gtgagcaacc tgcctttcag agggggataa cgtcttgaaa aggacgctaa 180 taccgcatga tattatggag ccacatggct ctataatcaa agga 224 <210> 10 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Peptostreptococcaceae (Clostridium Cluster <400> 10 agatttgatc ctggctcagg gctg gcggcgtgcc taacacatgc aagtcgagcg 60 aactcttcgg agtgagcggc ggacgggtga gtaacgcgtg ctgc cctgtacaca 120 tggataacat accgaaaggt atgctaatat aagataaaat atatttatcg catgatagct 180 atatcaaagc gttagcggta catgatggac ccgcgtctga ttag 224 Page 4 747203 ‐ ce Listing.txt <210> 11 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from rpospora <400> 11 agatttgatc cagg acgaacgctg gcggcgtgct taacacatgc aagtcgagcg 60 gaaaggccct tcggggtact cgagcggcga acgggtgagt aacacgtgag taacctgccc 120 ctgactctgg gataagcctg cggg tctaataccg gatacgacca ccggccgcat 180 ggcctggtgg tggaaagatt catcggttgg ggatgggctc gcgg 224 <210> 12 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 12 agatttgatc atggctcagg gctg gcggcgtgcc taatacatgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgctgggga cgcgagcggc ggatgggtga 120 gtaacacgtg ctgc cccatagtct gggataccac ttggaaacag gtgctaatac 180 cggataagaa agcagatcgc atgatcagct tataaaaggc ggcg 224 <210> 13 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 13 agatttgatc atggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 gacagatggg ctcc ctgatgttag cggcggacgg gtgagtaaca cgtgggtaac 120 ctgcctgtaa gactgggata actccgggaa accggggcta ataccggatg gttgtctgaa 180 ccgcatggtt cagacataaa aggtggcttc ggctaccact taca 224 Page 5 747203 ‐ Sequence Listing.txt <210> 14 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 14 agatttgatc ctggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgaacg 60 cgttggtccg actgattgat gatgcttgca tctgattgac gacggtttac gtgg 120 cggacgggtg agtaacacgt aggcaacctg cccagaagcg ggggacaaca tttggaaaca 180 agtgctaata ccgcataaca acca catggttttc gttt 224 <210> 15 <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Subdoligranulum <400> 15 agatttgatc atggctcagg acgaacgctg gcggcgcgcc taacacatgc aagtcgaacg 60 gagttaattt tgttgaagtt ttcggatgga atta acttagtggc gaacgggtga 120 gtaacgcgtg ctgc cccgaagtgg gggacaacag ttggaaacga ctgctaatac 180 cgcataagcc cacggcaccg catggtgctg agggaaaagg gctt 224 <210> 16 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Subdoligranulum <400> 16 agatttgatc atggctcagg acgaacgctg gcggcgcgcc taacacatgc aagtcgaacg 60 gaacttgaga gctt tttcaagttt agtggcgaac gtaa cgcgtgagta 120 acctgccctg gagtggggga caacagttgg aaacgactgc taataccgca taagcccacg 180 Page 6 747203 ‐ Sequence Listing.txt gtaccgcatg gtactgaggg aaaaggattt attcgcttca ggat 224 <210> 17 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiraceae (Clostridium Cluster XIVa) <400> 17 agatttgatc atggctcagg atgaacgctg tgcc taacacatgc aagtcgaacg 60 aagcgcttta ctttgatttc ttcgggatga agattttgtg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcatacagg gggataacag ttagaaatga ctgctaatac 180 agac cacagcttcg catggagcag tggtaaaaac tccg 224 <210> 18 <211> 224 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 18 agatttgatc cagg atgaacgccg gcggtgtgcc taatacatgc aagtcgaacg 60 cgttggcccg actgattgat gatgcttgca tgac gacggtttac caacgagtgg 120 cggacgggtg agtaacacgt cctg cccagaagcg ggggacaaca tttggaaaca 180 agtgctaata ccgcataaca acgaaaacca catggttttc gttt 224 <210> 19 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 19 agatttgatc atggctcagg acgaacgctg gcggtgtgcc taatacatgc aagtcgtacg 60 cactggccca actgattgat ggtgcttgca cctgattgac ttac cagtgagtgg 120 Page 7 747203 ‐ Sequence g.txt cggacgggtg agtaacacgt cctg ccccggagcg ggggataaca tttggaaaca 180 gatgctaata ccgcataaca acaaaagcca catggctttt gttt 224 <210> 20 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Leuconostoc <400> 20 agatttgatc atggctcagg atgaacgctg gcggcgtgcc taatacatgc aagtcgaacg 60 cacagcgaaa ggtgcttgca cctttcaagt gagtggcgaa cgggtgagta acacgtggac 120 aacctgcctc aaggctgggg ataacatttg gaaacagatg ctaataccga ataaaactta 180 gtgtcgcatg acacaaagtt aaaaggcgct tcggcgtcac ctag 224 <210> 21 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea ae sedis <400> 21 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 gaagcacttt attc ttcggatgaa gaagactgtg actgagtggc ggacgggtga 120 gtaacgcgtg ggcaacctgc cctgtacagg gggataacag atga ctgctaatac 180 agcg cacgaggacg catgttcttg tgtgaaaaac tccg 224 <210> 22 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 22 agatttgatc atggctcagg gccg gcggtgtgcc taatacatgc aagtcgtacg 60 Page 8 747203 ‐ Sequence g.txt ccca actgattgat ggtgcttgca tgac tcac cagtgagtgg 120 cggacgggtg agtaacacgt aggtaacctg ccccggagcg ggggataaca tttggaaaca 180 gatgctaata ccgcataaca acaaaagtcg catggctttt gttt 224 <210> 23 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Anaerofilum <400> 23 agatttgatc atggctcagg acgaacgctg gcggcgcgcc taacacatgc aagtcgaacg 60 gagctgcttt gacagattcc ttcgggatga cgttgattta gcttagtggc gaacgggtga 120 gtaacacgtg agcaacctac ctttcagagg gggacaacag ttggaaacga ctgctaatac 180 cgcataagac cacgctatgg catcgtagag gggtcaaagg agaa 224 <210> 24 <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lachnospiracea invertae sedis <400> 24 gacc tggctcagga tgaacgctgg cggcgtgctt aacacatgca agtcgaacga 60 agcattggag aacggagatt tcggttgaag ttttcctttg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc cctgtacagg gggataacag ttagaaatga ctgctaatac 180 cgcataagcg cacagcttcg catggagcgg tgtgaaaaac tgag 224 <210> 25 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiraceae (Clostridium Cluster XIVa) Page 9 747203 ‐ Sequence Listing.txt <400> 25 agatttgatc atggctcagg atgaacgctg gcggcgtgcc taacacatgc aagtcgaacg 60 aagcgatttg gttt tcggatggaa tccaaattga ctgagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc tcacactggg ggacaacagc tggaaacggc tacc 180 gcataagcgc acagcttcgc atgaagcagt gtgaaaaact ccgg 224 <210> 26 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Microbacterium <400> 26 agatttgatc atggctcagg acgaacgctg gcggcgtgct taacacatgc aagtcgaacg 60 atgaagctgg tgcttgcact ggtggattag tggcgaacgg gtgagtaaca cgtgagtaac 120 ctgcccctga gata actgctggaa acggtagcta atactggata tgaaccgtac 180 gggcatctgt tgcggttgga aagttttttc ggttggggat gggc 224 <210> 27 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Verrucosispora <400> 27 agatttgatc ctggctcagg acgaacgctg gcggcgtgct taacacatgc aagtcgagcg 60 gaaaggccct tcggggtact cgagcggcga gagt aacacgtgag gccc 120 taggctttgg gataaccctc ggaaacgggg gctaataccg cact tgctgccgca 180 tggtggtggg gatt tttcggcttg ggatgggctc gcgg 224 <210> 28 <211> 224 <212> DNA <213> Unknown <220> Page 10 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Anaerofilum <400> 28 gatc atggctcagg acgaacgctg gcggcgcgcc taacacatgc aacg 60 gagcattgag agcttgcttt ttag tggcgaacgg gtgagtaacg cgtgagtaac 120 ctgcccttga gaca acagttggaa acgactgcta ataccgcata agaccacaga 180 gccgcatggc tcggaggtaa aaggatttat tcgctcaagg atgg 224 <210> 29 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 29 agatttgatc atggctcagg acgaacgctg gcggcgtgcc taacacatgc aagttgagcg 60 gagatatgag aagcttgctc tttctatttt agcagcgaac gggtgagtaa cacgtagata 120 atttgtccta tactggggga taggccgatg aaaattggat taataccgca tacagctatt 180 taaccgcatg gatagatagt gaaaggggaa acttgatata ggag 224 <210> 30 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 30 agatttgatc ctggctcaga ttgaacgctg ggcc taacacatgc aagtcgagcg 60 agcagaacta gcagatttac ttcggtaatg acgctgggga cggc ggatgggtga 120 gtaacacgtg gggaacctgc gtct gggataccac ttggaaacag gtgctaatac 180 cggataagaa agcagatcgc atgatcagct tataaaaggc ggcg 224 <210> 31 <211> 224 <212> DNA <213> Unknown Page 11 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from Lactobacillus <400> 31 agatttgatc cagg acgaacgctg gcggcgtgcc taatacatgc aagtcgaacg 60 aaactttctt aatg cttgcattca ccgtaagaag ttgagtggcg gacgggtgag 120 taacacgtgg gtaacctgcc aagg ggataacact tggaaacagg tgctaatacc 180 gtatatcttt cgca ttag atgaaagatg gttc 224 <210> 32 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiraceae (Clostridium Cluster XIVa) <400> 32 agatttgatc ctggctcagg atgaacgctg gcggcgtgct taacacatgc aagtcgagcg 60 aagcgcttaa acagatttct tcggaatgaa gtttttgcga ctgagcggcg gacgggtgag 120 taacgcgtgg gcaacctgcc ccataccggg ggataacagc tggaaacggc tgctaatacc 180 gcataagcgc acagtgccgc atggcacggt gtgaaaaact ccgg 224 <210> 33 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from a <400> 33 agatttgatc atggctcagg atgaacgctg gcggcgtgct taacacatgc aagtcgaacg 60 ggaaacattt tattgaagct tcggcagatt tagcttgttt ctagtggcgg acgggtgagt 120 aacgcgtggg taacctgccc cacacggggg gataacaacc agaaatggct gctaataccg 180 cataagcgca cggggccgca tggccatgtg tgaaaaactc cggt 224 <210> 34 <211> 224 Page 12 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 34 agatttgatc ctggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgagcg 60 cactggccca actgatatga cgtgcttgca ctgaattgac gttggattcc cagtgagcgg 120 ggtg acgt gggcaacctg ccccaaagcg ggggataaca tttggaaaca 180 ggtgctaata aact tggaaaacca catggttttc caat 224 <210> 35 <211> 224 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 35 agatttgatc ctggctcagg acgaacgctg gcggcgtgcc atgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc ggatgggtga 120 gtaacacgtg gggaacctgc cccatagtct gggataccac ttggaaacag atac 180 cgcataacaa caaaagccac atggcttttg tttgaaagat ggct 224 <210> 36 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 36 agatttgatc atggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgtacg 60 cactggccca actgattgat ggtgcttgca cctgattgac ttac cagtgagtgg 120 cggacgggtg agtaacacgt gggtaacctg cctaaaagaa ggggataaca cttggaaaca 180 ggtgctaata ccggataaga aagcagatcg catgatcagc tttt 224 Page 13 747203 ‐ Sequence Listing.txt <210> 37 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Pseudomonas <400> 37 agatttgatc ctggctcaga ttgaacgctg gcgacaggcc taacacatgc aagtcgagcg 60 gatgagagga gcttgctcct tgatttagcg gcggacgggt gggtaatgcc taggaatctg 120 agtg ggggataacg ttccgaaagg aata ccgcatacgt cctacgggag 180 aaagcagggg accttcgggc ctat cagatgagcc tagg 224 <210> 38 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiraceae (Clostridium Cluster XIVb); Potential human pathogen (currently unconfirmed pathogen status) <400> 38 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 ggagttttac gagagcttgc ttttgtaaaa ggcg gacgggtgag taacgcgtgg 120 gtaacctgcc ctatacacag ggataacatt gagaaattga tgctaatacc tgataagcta 180 acagctaggc atctagcagt tagaaaaact gaggtggtat agga 224 <210> 39 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from acter <400> 39 gatc atggctcagg acgaacgctg gcggcgtgcc taacacatgc aagtcgaacg 60 gagccaatcg aatgaatttt tcggaaggat tttgaggaag cttagtggcg gacgggcgag 120 taacgcgtga tgcc cataagaggg ggataatcca tggaaacgtg gactaatacc 180 Page 14 747203 ‐ Sequence Listing.txt gcatattgag cattaaccgc atggttgatg gttgaaagat ttat 224 <210> 40 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 40 gatc atggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc gtga 120 gtaacacgtg gggaacctgc cccatagtct gggataccac ttggaaacag gtgctaatac 180 cgcataacaa ccac atggttttcg tttaaaagat ggtt 224 <210> 41 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 41 agatttgatc atggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgaacg 60 aaactttctt acaccgaatg cttgcattca ccgtaagaag ttgagtggcg tgag 120 taacacgtgg gtaacctgcc taaaagaagg ggataacatt tggaaacaga tgctaatacc 180 gcataacaac aaaagccaca tggcttttgt ttgaaagatg gctt 224 <210> 42 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 42 agatttgatc cagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 acca gcagatttac ttcggtaatg acgctgggga cgcgagcggc ggatgggtga 120 Page 15 747203 ‐ Sequence Listing.txt gtaacacgtg gggaacctgc cccatagtct gggataccac acag atactaatac 180 cgcataacaa caaaagccac atggcttttg tttgaaagat ggct 224 <210> 43 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 43 agatttgatc cagg atgaacgctg tgct taacacatgc aagtcgaacg 60 aagcactggg gaacggagat ttcggttgaa gttttccttt gactgagtgg cggacgggtg 120 agtaacgcgt gggtaacctg ccctgtacag ggggataaca gttagaaatg actgctaata 180 aagc gcacagcttc gcatggagcg gtgtgaaaaa ctga 224 <210> 44 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 44 agatttgatc atggctcagg acgaacgctg gcggcgtgcc taatacatgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc ggatgggtga 120 gtaacacgtg gggaacctgc cccatagtct acat ttggaaacag atgctaatac 180 cgcataacaa caaaagccac atggcttttg tttgaaagat ggct 224 <210> 45 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 45 gatc cagg atgaacgccg gcggtgtgcc taatacatgc aagtcgagcg 60 Page 16 747203 ‐ Sequence Listing.txt cattggccca atga cgtgcttgca ctgaattgac gttggattac cagtgagcgg 120 cggacgggtg agtaacacgt gggcaacctg ccctgaagcg ggggataaca tctggaaaca 180 gatgctaata ccgcataaca acaaaagcca catggctttt gttt 224 <210> 46 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Peptostreptococcaceae (Clostridum Cluster <400> 46 gatc atggctcagg atgaacgctg gcggcgtgcc taacacatgc aagtcgagcg 60 aactcttcgg agtgagcggc ggacgggtga cgtg ggtaacctgc cctgtacaca 120 tggataacat accgaaaggt atgctaatac aagataaaat atatttatcg catgatagat 180 atatcaaagc ggta caggatggac ccgcgtctga ttag 224 <210> 47 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA of Lactobacillus <400> 47 agatttgatc atggctcagg acgaacgctg gcggcgtgcc atgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc ggacgggtga 120 gtaacacgtg ggtaacctgc ccaagagact gggataacac ctggaaacag gtgctaatac 180 cggataagaa agcagatcgc atgatcagct tttaaaaggc ggcg 224 <210> 48 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA of Lactobacillus Page 17 747203 ‐ Sequence Listing.txt <400> 48 agatttgatc ctggctcagg acgaacgctg tgcc taatacatgc aagtcgagcg 60 agcttgccta gatgatttta gcac taaatgaaac tagatacaag cgagcggcgg 120 gagt aacacgtggg taacctgccc aagagactgg gataacacct ggaaacagat 180 gctaataccg aaca aaagccacat ggcttttgtt tgaa 224 <210> 49 <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lactobacillus <400> 49 agatttgatc atggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgtacg 60 cactggccca actgattgat ggtgcttgca cctgattgat gatggatcac cagtgagtgg 120 cgaacgggtg agtaacacgt aggtaacctg ccccggagcg ggggataaca tttggaaaca 180 ggtgctaata ccgcataaca acgaaaacca catggttttc gttt 224 <210> 50 <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lactobacillus <400> 50 agatttgatc atggctcagg acgaacgctg gcggcgtgcc atgc aagtcgagcg 60 agcggaacta acagatttac ttcggtaatg acgttaggaa agcgagcggc ggacgggtga 120 gtaacacgtg ggtaacctgc cctgaagcgg gggataacat ctggaaacag gtgctaatac 180 cgcataacaa caaaagccac atggcttttg tttgaaagat ggct 224 <210> 51 <211> 225 <212> DNA <213> Unknown <220> Page 18 747203 ‐ Sequence Listing.txt <223> Encodes ITS region from Nectriaceae <400> 51 tccgtaggtg aacctgcgga gggatcatta ttac aactcccaaa tgaa 60 cataccaatt gttgcctcgg cggatcagcc cgctcccggt aaaacgggac ggcccgccag 120 aggaccccta aactctgttt ctatatgtaa cttctgagta aaaccataaa taaatcaaaa 180 ctttcaacaa cggatctctt ggca tcgatgaaga acgca 225 <210> 52 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes ITS region from Filobasidium floriforme <400> 52 tccgtaggtg aacctgcgga aggatcatta atgaatttag attgaaccat aggcgaaagc 60 cagtggttct tctttcatat ccataacacc tgtgcactgt tggatgcttg catccacttt 120 taaactaaac attattgtaa caaatgtagt cttattataa aaaa ctttcaacaa 180 cggatctctt ggctctcgca tcgatgaaga cgaa atgcg 225 <210> 53 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes ITS region from Gibberella zeae <400> 53 ggtg aacctgcgga gggatcatta ccgagtttac aactcccaaa cccctgtgaa 60 cataccttat gttgcctcgg cggatcagcc cgcgccccgt aaaaagggac ggcccgccgc 120 aggaacccta aactctgttt ttagtggaac ttctgagtat aaaaaacaaa taaatcaaaa 180 ctttcaacaa cggatctctt ggca tcgatgaaga acgca 225 <210> 54 <211> 225 <212> DNA <213> Unknown Page 19 747203 ‐ Sequence Listing.txt <220> <223> Encodes ITS region from Alatospora <400> 54 ggtg cgga ggagcatatc aataagcgga ggaccttccg taggtgaacc 60 tgcggacgca tatcattaag acat atcaataagc ggaggacctt ccgtaggtga 120 acctgcggac gcatatcaat aagcggagga tcttccgtag ctgc ggaaggatca 180 ttatgaataa gcatatcaat aagcggagga tcgtccgtag gtgaa 225 <210> 55 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes ITS region from Hypocreaceae <400> 55 tccgtaggtg cgga aggatcatta tgaattataa atatttgtga atttaccaca 60 gcaaacaaaa atcatacaat caaaacaaaa ataattaaaa cttttaacaa tggatctctt 120 ggttctcgta tcgatgaaga acgcagcgaa acgcgatatt tcttgtgaat tgcagaagtg 180 aatcatcagt ttttgaacgc acattgcact ttggggtatc cccca 225 <210> 56 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes ITS region from Pichia Fermentans <400> 56 ggtg aacctgcgga aggatcatta ctgtgattta tatcttatac acatgcgtga 60 gcgcaccaaa cacctaaaat tgtaataata ccagtcagta agttttaaca aaacaaaact 120 ttcaacaacg gatctcttgg ttctcgcatc gatgaagagc aaat gcgataccta 180 gtgtgaattg cagccatcgt gaatcatcga gttcttgaac gcaca 225 <210> 57 <211> 225 Page 20 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes ITS region from Candida railenensis <400> 57 tccgtaggtg aacctgcgga aggatcatta cagtattctt ttgccagcgc ttaattgcgc 60 aaac cttacacact atgttttttt aatttgaaac tattgctttg gtctggctta 120 gaaataggtt gggccaaagg ttttatcaaa acttcaatat ttattattga attgttattt 180 ttaattttat gtcaatttgt tgattatatc aaaaatcttc aaaac 225 <210> 58 <211> 225 <212> DNA <213> Unknown <220> <223> s ITS region from Hypocreaceae <400> 58 tccgtaggtg aacctgcgga aggatcatta agaattataa atatttgtga aatttacaca 60 gcaaacaata attttatagt caaaacaaaa aaaa cttttaacaa tggatctctt 120 ggttctcgta tcgatgaaga cgaa acgcgatatt tcttgtgaat tgcagaagtg 180 aatcatcagt ttttgaacgc acattgcact tatc cccca 225 <210> 59 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVb <400> 59 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gcgtctgatt tgatgcttgc gaaa gatgagcggc ggacgggtga gtaacgcgtg 120 ggtaacctgc cctatacaca acat actgaaaagt ttactaatac atgataatat 180 atatttacgg catcgtagat atatcaaagt gttagcggta tagga 225 Page 21 747203 ‐ Sequence Listing.txt <210> 60 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from er <400> 60 agagtttgat catggctcag cgcc ggcggtgtgc ctaatacatg gaac 60 ggtaacagga agcagcttgc tgcttcgctg acgagtggcg gacgggtgag gtga 120 gtaacctgcc ccgaagtggg ggacaacagt tggaaacgac tgctaatacc gcataagccc 180 acagagccgc atggctcaga gggaaaagga cttcggtttg cttcg 225 <210> 61 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 61 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggaaaggcct tgca actc gagtggcgaa cgggtgagta acacgtgggt 120 aacctgccca agagactggg ataacacctg gaaacagatg ctaataccgg ataacaacac 180 tagacgcatg tctagagttt gaaagatggt tctgctatca ctctt 225 <210> 62 <211> 185 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XI <400> 62 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctattgcaca atgggcgaaa 60 gcctgatgca gcaacgccgc gtgagcgaag aaggccttcg ggtcgtaaag ctctgtcata 120 taggaagata atgacggtac ttgaggagga agccccggct aactacgtgc cagcagccgc 180 ggaat 185 Page 22 747203 ‐ Sequence Listing.txt <210> 63 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from licoccus <400> 63 agagtttgat catggctcag cgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcgaagatca ggagcttgct cctgagattc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ctaataccgg atacgacatt 180 taag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 64 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 64 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagttgagc 60 ggagatatga ggagcttgct ttttatatct tagcagcgaa agta acacgtgggg 120 aacctgcccc atagtctggg ataccacttg gaaacaggtg ctaataccgg ataagaaagc 180 agatcgcatg atcagctttt aaaaggcggc gtaagctgtc gctat 225 <210> 65 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 65 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcatcggccc aactgattga agatgcttgc atccgattga cgatggttta ccgatgagcg 120 gcggacgggt gagtaacacg taggtaacct gcccagaagc gggggataac acctggaaac 180 Page 23 747203 ‐ Sequence Listing.txt agatgctaat accgcatagg tcatttgacc gcatggtcaa atgat 225 <210> 66 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 66 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagttgttt gaggaagttt tcggatggaa tcagatgact tagtggcgga agta 120 acgcgtggga aacctgccct gtactggggg ataacacttg gaaacaggtg ctaataccgg 180 ataagaaagc agatcgcatg atcagctttt aaaaggcggc gtaag 225 <210> 67 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Jeotgalicoccus <400> 67 agagtttgat tcag gatgaacgct ggcggcgtgc ctaatacatg gagc 60 gcgagcgtta gaagcttgct tctaacaatc gagcggcgga agta gggc 120 agcctacctt tgagattggg ataactaccg gaaacggtag ctaataccgg ataggacatg 180 attacataag tagtgatgtt aaaaggcgga tttatctgcc gttca 225 <210> 68 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 68 tgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gaaactttct tacaccgaat gcttgcattc atcgtaagaa gttgagtggc ggacgggtga 120 Page 24 747203 ‐ Sequence Listing.txt gtaacacgtg gggaacctgc cccatagtct gggataccac ttggaaacag gtgctaatac 180 cggataagaa agcagatcgc atgatcagct tttaaaaggc ggcgt 225 <210> 69 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Jeotgalicoccus <400> 69 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 atca ggagcttgct attc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ctaataccgg atacgacatt 180 taag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 70 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 70 tgat catggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgagc 60 gcactggccc aacagaaatg acgtgcttgc actgatttga cgttggattc agcg 120 gcggacgggt gagtaacacg tgggcaacct gccccaaagc gggggaagat ggta 180 cccaaggagg aagccacggc taactacgtg ccagcagccg cggta 225 <210> 71 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 71 agagtttgat catggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgagc 60 Page 25 747203 ‐ Sequence Listing.txt gcactggccc aacagaaatg acgtgcttgc actgatttga attc ccagtgagcg 120 gcggacgggt gagtaacacg tgggcaacct gccccaaagc gggggatcgc atgatcctta 180 gatgaaagat ggttctgcta tcgcttttag atggacccgc ggcgt 225 <210> 72 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 72 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gaacagataa ggagcttgct cctttgacgt tagcggcgga cgggtgagta acacgtgggt 120 aacctaccta taagactggg ataacttcgg gaaaccggag ctaataccgg ataagaaagc 180 agatcgcatg atcagcttat aaaaggcggc tgtc gctat 225 <210> 73 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from bacterium <400> 73 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gaaactttct tacaccgaat gcttgcattc accgtaagaa gttgagtggc gtga 120 gtaacacgtg ggtgatctgc cctgcactgt gggataagcc tgggaaactg ggtctaatac 180 catataggac ttgg atggtgtggt cttt tgcgg 225 <210> 74 <211> 197 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Microbacterium Page 26 747203 ‐ Sequence Listing.txt <400> 74 agagtttgat cctggctcag actcctacgg gaggcagcag tggggaatat tgcacaatgg 60 gggaaaccct gatgcagcaa cgccgcgtga gggatgacgg ggtt gtaaacctct 120 tttggcaggg aagaagcgag agtgacggta gaaa aagcgccggc taactacgtg 180 ccagcagccg cggtaat 197 <210> 75 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from licoccus <400> 75 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcgaagatca ggagcttgct cctgagattc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ctaataccgg atacgacatt 180 taag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 76 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from licoccus <400> 76 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcgaagatca ggagcttgct cctgagattc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ccgg catt 180 cctgcataag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 77 <211> 225 <212> DNA <213> Unknown <220> Page 27 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Glycomyces <400> 77 agagtttgat catggctcag gacgaacgct ggcggcgtgc ttcacacatg caagtcgaac 60 ggaaaggctc gagt gctcgagtgg cgaacgggtg agtaacacgt gggtaacctg 120 cccccatctc tgggataact gctggaaacg gtggctaata ccggatacta ctgctggtcg 180 catggcctgg aaag cttttgcggt gggg ctcgc 225 <210> 78 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Streptomyces <400> 78 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgaaccgg ggtt ggggattagt ggcgaacggg acac gtgggtaatc 120 tgccctgcac tctgggataa gcctgggaaa ctgggtctaa tactggatat gaccttctct 180 cgcatggggg ttggtggaaa gcttttgcgg tgcaggatgg gcccg 225 <210> 79 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Saccharopolyspora <400> 79 agagtttgat cctggctcag gcggtcagtc cgagccgctc cattcgggtg tcgg 60 cgatgagatc ggtgtgcacg gcctcgatct gcgagaccat ccgctgcacc tcgtcgtcac 120 gctcgagcgt cgagtcgcgc agcgcccgca gcaccggctc gtcgagcacc atgagcgccc 180 ggcaccacag caacgcgtcg ccgacgaccc gccgccccca catgg 225 <210> 80 <211> 225 <212> DNA <213> Unknown Page 28 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from acterium <400> 80 agagtttgat cctggctcag gacgaacgct gtgc ttaacacatg caagtcgaac 60 ggaaaggcct catccttttt tgggtggggt gctcgagtgg cgaacgggtg agtaacacgt 120 gagtaacctg cccctgactc tgggataagc ctgggaaact gggtctaata ctggatatga 180 tgcctggccg catggtctgg gtgtggaaag ttttttcggt tggga 225 <210> 81 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Microbacterium <400> 81 agagtttgat cctggctcag cgct ggcggcgtgc catg caagtcgaac 60 ggtgaagcca agcttgcttg gtggatcagt ggcgaacggg tgagtaacac gtgagcaacc 120 tgccctggac tctgggataa gcgctggaaa cggcgtctaa tactggatat gagcctcttc 180 cgcatggtgg gggttggaaa gattttttgg tctgggatgg gctcg 225 <210> 82 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acinetobacter <400> 82 agagtttgat catggctcag cgct aggc ttaacacatg caagtcgagc 60 ggagagaggt agcttgctac cgatcttagc ggcggacggg tgagtaatgc ttaggaatct 120 gcctattagt gggggacaac atttcgaaag gaatgctaat accgcatacg tcctacggga 180 gaaagcaggg cgga ccttgcgcta atagatgagc ctaag 225 <210> 83 <211> 225 Page 29 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactococcus <400> 83 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagttgagc 60 gctgaaggtt ggtacttgta ggat gagcagcgaa cgggtgagta acgcgtgggg 120 aatctgcctt tgagcggggg acaacatttg gaaacgaatg ctaataccgc ataaaaactt 180 taaacacaag ttttaagttt gaaagatgca attgcatcac tcaaa 225 <210> 84 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from bacterium <400> 84 tgat cctggctcag cgct agcgggaggc ctaacacatg caagccgagc 60 ggtattgttt cttcggaaat gagagagcgg cgtacgggtg cggaacacgt gtgcaacctg 120 cctttatctg agcc tttcgaaagg aagattaata ctccataata tattgattgg 180 catcaattaa tattgaaagc tccggcggat agagatgggc acgcg 225 <210> 85 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Mycobacterium <400> 85 agagtttgat catggctcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggaaaggccc cttcgggggt gctcgagtgg cgaacgggtg agtaacacgt gggtgatctg 120 ccctgcactc tgggataagc ctgggaaact gggtctaata ccggatagga ccacatgtcg 180 catggtgtgt ggtggaaagc ttttgcggtg tgggatgggc ccgcg 225 Page 30 747203 ‐ Sequence Listing.txt <210> 86 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Leucobacter <400> 86 agagtttgat catggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagctc tgct gggggtggat gagtggcgaa cgggtgagta acacgtgagt 120 aacctgcccc gaactctggg ataagcgctg gcgt ctaatactgg atatgtccta 180 tcaccgcatg gtgtgtaggt ggaaagaatt ttggttcggg atgga 225 <210> 87 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 87 agagtttgat catggctcag gatgaacgct ggcggcatgc cttacacatg ggac 60 gggaagtggt gtttccagtg gcggacgggt gagtaacacg tgggtaacct gcctaaaaga 120 taac acttggaaac aggtgctaat accgtatatc tctaaggatc gcatgatcct 180 tagatgaaag atggttctgc tatcgctttt agatggaccc gcggc 225 <210> 88 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Rothia <400> 88 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gccc agcttgctgg gtggattagt cggg tgagtaatac gtgagtaacc 120 tgcctttaac tctgggataa gccttggaaa cggggtctaa taccggatac ttcc 180 cgcatgggat gctggtggaa agggatatgt actggtttta gatgg 225 Page 31 747203 ‐ Sequence Listing.txt <210> 89 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 89 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagagagcgg cggacgggtg agtaacacgt ggggaacctg ccccatagtc 120 tgggatacca cttggaaaca ggtgctaata ccggataaga aagcagatcg catgatcagc 180 tttttaaaag gcggcgtaag ctgtcgctat gccc cgcgg 225 <210> 90 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clavibacter <400> 90 agagtttgat tcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gtca gagcttgctc tggcggatca aacg ggtgagtaac acgtgagtaa 120 cctgcccccg actctgggat aactgctaga aatggtagct aataccggat atgacgactg 180 gccgcatggt ctggtcgtgg aaagaatttc ggttggggat ggact 225 <210> 91 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 91 agagtttgat catggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggggatattt aagagcttgc ttttgaatat tctagtggcg gacgggtgag taacgcgtga 120 gtaacctgcc aggg ggataacagt tggaaacagc tgctaatacc gcataacata 180 Page 32 747203 ‐ Sequence Listing.txt tacaattcgc atgggaagta tatcaaagag ctga aagac 225 <210> 92 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Howardella <400> 92 tgat cctggctcag gatgaacgct ggcggcgtgc catg caagtcgaac 60 ggacaaagag gggcttgctc ctctttgtta gtggcggacg ggtgagtaac acgtgagcaa 120 cctgcccata tctggggaat aacacagtga aaattgtgct aataccgcat aagaccacga 180 ggaggcatct ccttgcggta aaagatttat cggatatgga tgggc 225 <210> 93 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Clostridium sensu stricto <400> 93 agagtttgat tcag gacgaacgct ggcggcgtgc catg caagtcgaac 60 ggacgaggag gtgcttgcac ctccaagtta gtggcggacg ggtgagtaac gcgtgagcaa 120 cctgcctcaa agagggggat aacgtctgga cgct aataccgcat gatatattga 180 ataggcatct atttaatatc aaaggagcaa tccgctttga gatgg 225 <210> 94 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 94 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 gaagcggttt tggaagtctt cggacggaag agagcgactg agcggcggac gggtgagtaa 120 Page 33 747203 ‐ Sequence Listing.txt cgcgtgggta acctgcctcg tacaggggga taacagttgg aaacgactgc taataccgca 180 taagcccacg gggtcgcatg gctctgaggg aaaaggattt attcg 225 <210> 95 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 95 agagtttgat tcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 attt aagagcttgc atat tctagtggcg gacgggtgag taacgcgtga 120 gtaacctgcc tttcagaggg ggataacagc tggaaacagc tgctaatacc gcataacata 180 tacaattcgc atgggaagta tatcaaagag atatcgctga aagat 225 <210> 96 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Papillibacter <400> 96 tgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagtttgag aagcttgctt ctta gtggcggacg ggtgagtaac gcgtgagtaa 120 cctgcctttc agagggggat aacgtctgga aacggacgct aataccgcat aacgtaccga 180 gtgggcatcc acttgatacc aaaggagcaa tccgctgaaa gatgg 225 <210> 97 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 97 agagtttgat tcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 Page 34 747203 ‐ Sequence Listing.txt ggggatattt aagagcttgc ttttgaatat tctagtggcg gacgggtgag taacgcgtga 120 gtaacctgcc tttcagaggg ggataacagc tggaaacagc tgctaatacc gcataacata 180 tacaattcgc atgggaagta tatcaaagag atatcgctga aagat 225 <210> 98 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Eubacterium <400> 98 tgat cctggctcag gacgaacgct ggcggcgcgc ctaacacatg gaac 60 ggggttattt tggaaagttc tttcggggac tggaatcttt aacctagtgg cggacgggtg 120 agtaacgcgt gagcaatctg cctttaggag ggggataaca gtcggaaacg gctgctaata 180 ccgcataatg catcaatttc gcatgttatt gatgccaaag gagca 225 <210> 99 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Turicibacter <400> 99 agagtttgat catggctcag gatgaacgct ggcggcgtgc catg caagtcgagc 60 gaaccacctt gagc ggcggacggg tgagtaacac gtaggtaacc tgcccataag 120 atggggacaa gaaa cggtggctaa taccgcataa gcccacgggg ccgcatggcc 180 ctgagggaaa aggagcacac gaga tggcctcgcg tccga 225 <210> 100 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Page 35 747203 ‐ Sequence Listing.txt <400> 100 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gaaccacctt ggtggtgagc ggcggacggg tgagtaacac gtaggtaacc tgcccataag 120 atggggacaa ccaccggaaa cggtggctaa taccgcataa cgtaccgagt gggcatccac 180 ttgataccaa aggagcaatc cgctgaaaga tgggctcgcg tccga 225 <210> 101 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Asaccharobacter <400> 101 agagtttgat cctggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggttaaggcg ccttcgggcg cgaatagagt ggcgaacggg acac gtgaccaacc 120 tgcccccctc cccgggataa cgcgaggaaa cccgcgctaa taccggatac tccgcccctc 180 ccgcatggga ggggcgggaa agccccgacg gagggggatg gggtc 225 <210> 102 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Faecalibacterium <400> 102 agagtttgat tcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gcgagccttc gggctcgagt cggg tgagtaacgc aacc tgcctcaaag 120 agggggacaa cagttggaaa cgactgctaa taccgcataa gcccacgggg ccgcatggct 180 gaaa aatc gaga tggcctcgcg tccga 225 <210> 103 <211> 225 <212> DNA <213> Unknown <220> Page 36 747203 ‐ Sequence g.txt <223> Encodes 16S rRNA from Clostridium XlVa <400> 103 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaagcggttt cgatgaagtt ttcggatgga ttcggaattg actgagcggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcacactgg acag ctggaaacga ctgctaatac 180 cgcataacgc atgaccggtg catcccggac atgccaaaga tttat 225 <210> 104 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 104 agagtttgat cctggctcag gatgaacgct ggcggcatgc ctaatacatg gaac 60 ggaatgcgga ttat cttttctgtg tttagtggcg aacgggtgag taacgcgtga 120 gcaacctgcc cttcagaggg cgtc tggaaacgga cggtaatacc gcataacgta 180 cagggaccgc atgatctttg taccaaaact gaggtgctga aggat 225 <210> 105 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 105 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagatttga gctt tcaaatctta gtggcggacg ggtgagtaac gcgtgagtaa 120 cctgcctcat acagggggat aacagttaga aatgactgct aataccgcat aagcgcacag 180 taccgcatgg tacggtgtga aaaactccgg tggtatggga tgggc 225 <210> 106 <211> 225 <212> DNA <213> Unknown Page 37 747203 ‐ Sequence g.txt <220> <223> Encodes 16S rRNA from Clostridium XlVb <400> 106 agagtttgat cctggctcag gatgaacgct gtgc catg caagtcgagc 60 ggagatattc agaaagcttg ctttttgaat atcttagcgg cggacgggtg agtaacgtgt 120 cctg acag agggataatc atgtgaaaac gtgactaata ccgcatgtca 180 ttaccgaagg ttag gtaagaaaag gagcaatccg gtatg 225 <210> 107 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 107 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacttattt tggaaagttc actg gaatctataa gttagtggcg gacgggtgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc tggaaacggc tgctaatacc 180 gcataatgca ttctggtcgc atggcctaaa tgccaaaggc ttgct 225 <210> 108 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sporobacter <400> 108 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagatacag gggcttgccc ctgtatctta gtggcggacg ggcgagtaac gcgtgaggaa 120 cctgcccttc agtggggaat aacggctgga aacggtcgct aataccgcat gacacattgg 180 taccgcatga tactgatgtc aaaggagcaa tccgctgaag gatgg 225 <210> 109 <211> 225 Page 38 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 109 agagtttgat catggctcag gatgaacgct ggcggcgtgt ctaacacatg caagtcgaac 60 ggggtaccct gaaacgaggc ttcggccaag cggaaggact acctagtggc gtga 120 gtaacgcgtg agcaacctgc ctttcagatg gggataacgg ctggaaacgg ccgctaatac 180 cgcataacgc ataactgggg catcccggca aaga tttat 225 <210> 110 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 110 agagtttgat catggctcag cgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggaaatgatt gaagtttact ttggtcattt tagtggcgga cgggtgagta gagc 120 aacctgcctt tcagaggggg ataacgtttg gaaacgaacg ctaataccgc ataacgtata 180 cggatggcat cgtctgtata ccaaaggagg aatccgctga aagat 225 <210> 111 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Anaerofilum <400> 111 agagtttgat cctggctcag cgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggagcttgct tgtcagatcc ggtg tgta agcttagtgg cgaacgggtg 120 agtaacacgt gagtaacctg ccccagagtg ggggacaaca gttggaaacg actgctaata 180 ccgcataagc ccacggaacc gcctggttca gagggaaaaa gagca 225 Page 39 747203 ‐ Sequence Listing.txt <210> 112 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 112 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagtttgtt ggatcgatcc ttcgggtgat tgaaaataaa gtgagtggcg gacgggtgag 120 taacacgtga gcaacctgcc tttcagagcg ggataacagt tggaaacgac tacc 180 gcataagacc acgctatggc atcgtagagg ggtcaaagga gaaat 225 <210> 113 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from idium XlVa <400> 113 agagtttgat tcag gatgaacgct gtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg cggacgggtg agtaacgcgt gggtaacctg actg 120 ggggataaca gatagaaata tctgctaaaa ccgcataagc gcacgaggtc gcatgaccat 180 gtgtgaaaaa tggt gtgagatgga cccgcgtctg attag 225 <210> 114 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 114 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 ttcg gagtgagcgg cggacgggtg agtaacgcgt gggtaacctg ccctgtacag 120 ggggataaca gttagaaatg actgctaata ccgcataagc gcacagcttc gcatgaagcg 180 gtgtgaaaaa ctgaggtggt acaggatggg cccgcgttgg attag 225 Page 40 747203 ‐ Sequence Listing.txt <210> 115 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 115 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg cggacgggtg agtaacgcgt gggtaacctg cctcatacag 120 ggggataaca gttagaaatg actgctaata ccgcataaga ccacagcacc gcatggtgca 180 ggggtaaaaa ctccggtggt tgga cccgcgtctg attag 225 <210> 116 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 116 tgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg gaac 60 gggcttattt tggaaagttc ttcggaactg gaatctataa gttagtggcg tgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc tggaaacggc tgctaatacc 180 gcatgatgca ttctggtcgc atggcctaaa tgccaaaggc ttgct 225 <210> 117 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Pediococcus <400> 117 agagtttgat catggctcag gatgaacgct ggcggcatgc catg caagtcgaac 60 gaggtggccc taag aaggaaagtt gaaaagcttg cttggatgct ggaattctta 120 tgacgtggat cttccaccta gtggcaaacg ggtgagtaac acgtgggtta cctacctcta 180 Page 41 747203 ‐ Sequence Listing.txt agttggggat aacaattgga aacgattgat aataccgaat aagct 225 <210> 118 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acetanaerobacterium <400> 118 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg ggtg agtaacacgt gagtaacctg cctttcagag 120 tggaataacg tttggaaacg aacgctaata ccgcataaca tgagagaacg gcatcgttct 180 ttcatcaaag attttatcgc tgagagatgg gctcgcggcc gatta 225 <210> 119 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Hydrogenoanaerobacterium <400> 119 agagtttgat catggctcag gatgaacgct ggcggcacgc ctaacacatg gaac 60 gaagttattt tgatcgaagt tttcggatgg acattgattt aacttagtgg cggacgggtg 120 agtaacacgt gagcaatctg agag tgggataccg tttggaaacg aacgttaata 180 ccgcataacg cagcgaggcc gcatgacctt gctgccaaag attta 225 <210> 120 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Butyricicoccus <400> 120 agagtttgat tcag gatgaacgct ggcggcgtgc ataacacatt caagtcgaac 60 ggagttatac gagtagcaat ataa cttagtggcg gacgggtgag taacgcgtga 120 Page 42 747203 ‐ ce Listing.txt gcaacctacc tttcaaagcg ggataacaca tggaaacgtg tgctaatacc gcataacgta 180 tcgatgtcgc atgacaacga taccaaaagg gcaacctgat gaaag 225 <210> 121 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 121 tgat tcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg cggacgggtg agtaacgcgt gggtaacctg cctcatacag 120 ggggataaca aatg actgctaata ccgcataaga ccacagcttc gcatggagca 180 gtggtaaaaa ctccggtggt atgagatgga cccgcgtctg attag 225 <210> 122 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from elotrichaceae ae sedis <400> 122 agagtttgat cctggctcag gatgaacgct ggcggcgtgc catg caagtcgaac 60 gggaatcttc ggattccagt ggcgaacggg tgaggaatac ataggtaacc tgcccctccg 120 agggggacaa cagacggaaa catctgctaa gaccgcatag ccacagggaa ggcatcttcc 180 ctgtgccaaa tgtcctttcg gggacagcgg ggggatggac ctatg 225 <210> 123 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 123 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 Page 43 747203 ‐ Sequence Listing.txt gaactcttcg gagtgagcgg cggacgggtg attaacgcgt gggtaacctg cctcatacag 120 ggggataaca gttagaaatg actgctaata ccgcataaga ccccagcttc gcatgaagcg 180 gtggtaaaaa ctccggtggt tgga tcag attag 225 <210> 124 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 124 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacattttt tggaaacttc ttcggaagtg gaatctaaat gttagtggcg gacgggtgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc cggaaacggc tgctaatacc 180 gcataatgta tgagagtcgc atggctttta aggc ttgct 225 <210> 125 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from cicoccus <400> 125 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacttattt gttc ttcggaactg gaatctataa gttagtggcg tacgggtgag 120 gtga gcaatctgcc tcggagtggg cagc cggaaacggc tgctaatacc 180 gcataatgta tgagagtcgc atggctttta taccaaaggc ttgct 225 <210> 126 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus Page 44 747203 ‐ Sequence Listing.txt <400> 126 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 gaacttattt tggaaagttc ttcggaactg gaatctataa gttagtggcg gacgggtgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc cggaaacggc tgctaatacc 180 gcataatgta tgagagtcgc atggctttta taccaaaggc ttgca 225 <210> 127 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 127 agagtttgat catggctcag cgct ggcggcgtgc catg gaac 60 ggagttattt tggaaagtct ttcgggactg gaatctataa cttagtggcg gacgggtgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc cggaaacggc tgctaatacc 180 gcataatgca tcgc atggttgaaa tgccaaaggc ttgct 225 <210> 128 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 128 agagtttgat cctggctcag cgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggagttattt tggaaagtct ttcgggactg gaatctataa cttagtggcg gacgggtgag 120 taacgcgtga gcaatctgcc tcggagtggg ggataacagc cggc tgctaatacc 180 gcataatgca ttctggtcgc atgacctaaa tgccaaaggc ttgct 225 <210> 129 <211> 225 <212> DNA <213> Unknown <220> Page 45 747203 ‐ Sequence g.txt <223> s 16S rRNA from Lachnospiracea incertae sedis <400> 129 agagtttgat tcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg cggacgggtg agtaacgcgt gggtaacctg cctcacacag 120 ggggataaca gttagaaatg actgctaata ccgcataaga ccacagcacc gcatggtgca 180 gtggtaaaaa ctccggtggt atgagatgga cccgcgtctg attag 225 <210> 130 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Howardella <400> 130 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ataacacatt caagtcgaac 60 ggagacttat gcgtagcaat acaagtaagt cttagtggcg gacgggtgag taacgcgtga 120 tacc tttcaaagcg ggataacaca tggaaacgtg tgctaatacc gcataacgta 180 ccgacaccgc atgatgatgg taccaaaagg gcaacctgat gaaag 225 <210> 131 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 131 agagtttgat catggctcag cgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg ggtg agtaacgcgt gggtaacctg cctcatacag 120 ggggataaca gttagaaatg actgctaata ccgcataaga ccccagcttc gcatgaagcg 180 gtggtaaaaa tggt atgagatgga cccgcgtctg attag 225 <210> 132 <211> 225 <212> DNA <213> Unknown Page 46 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from Clavibacter <400> 132 agagtttgat catggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggtgatgtca gagcttgctc tggcggatca gtggcgaacg ggtgagtaac acgtgagtaa 120 cctgcccccg actctgggat taga aatggtagct aataccggat atgacgactg 180 gccgcatggt ctggtcgtgg aaagaatttc ggttggggat ggact 225 <210> 133 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 133 agagtttgat tcag gatgaacgct ggcggcgtgc ataacacatt caagtcgaac 60 ggagacttat gcgtagcaat acaagtaagt ggcg gacgggtgag taacgcgtga 120 gcaacctacc tttcaaagcg ggataacgtc tggaaacgga cgctaatacc gcataacgta 180 ccgc atgatgatgg taccaaaagg gcaacctgat gaaag 225 <210> 134 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 134 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacgagcag gctt ctgcgagtaa gtggcggacg ggtgagtaac gcgtgagcaa 120 cctgcctttc agagggggat aacgtctgga cgct aataccgcat aagctccgag 180 gatcgcatgg tctcaggagc aaaggaggaa tccgctgaaa gatgg 225 <210> 135 <211> 225 Page 47 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Spiroplasma <400> 135 agagtttgat catggctcag gatgaacgct ggcggcatgc ctaagacatg caagtcgtac 60 gaaggagccc attgatattt attgaagttt gaagtgcttg cacggatgac ggatttattt 120 ggatttggat tctctcctta gtggcaaacg ggtgagtaac acgtgggtta tcca 180 agatggggat aacaattgga aacgattgat aataccgaat gtgct 225 <210> 136 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 136 agagtttgat cctggctcag gacgaacgct ggcggcgcgc catg caagtcgaac 60 taca ttttgaagtt tgga cgaatgtaag cttagtggcg gacgggtgag 120 taacgcgtgg gcaacctacc ttatacaggg ggataacagt tgac tgctaatacc 180 gcataagacc acagcttcgc atggagcagt ggtaaaaact ccggt 225 <210> 137 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Jeotgalicoccus <400> 137 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gagatggccc aatgaagttt gagtgcttgc acaatttctg atttggattt tccatctagt 120 ggcggacggg acac gtgggtgacc tacctttgag tctgggacaa ctactggaaa 180 cggtagctaa taccggatga tatacagttt catttctgta ttaaa 225 Page 48 747203 ‐ Sequence Listing.txt <210> 138 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from phomonas <400> 138 tgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacgaggcc ccttcgggga ccgagttagt ggcggacggg tgagtaacgc gtgagcaacc 120 tgcctttcag tgggggacaa cagttggaaa cgactgctaa taccgcataa gcgcacagga 180 ccgcatggtc gaaa aactccggtg gtatgagatg gaccc 225 <210> 139 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 139 agagtttgat cctggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggagcattga gagcttgctt ttaatgctta gtggcggacg ggtgagtaac gcgtgaggaa 120 cctgcctcgg agtggggaat aacagcccga aagggttgct aataccgcat gatgcagttg 180 ggccgcatgg ctctgactgc caaagattta tcgctctgag atggc 225 <210> 140 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from spiracea incertae sedis <400> 140 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggactgattt gagagcttgc tcttgaagaa agttagtggc ggacgggtga gtaacgcgtg 120 agtaacctgc ctttcagagg gggataacat cctgaaaagg atgctaatac agcg 180 cacagcttcg catgaagcgg tgtgaaaaac tccggtggta tggga 225 Page 49 747203 ‐ Sequence Listing.txt <210> 141 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 141 agagtttgat catggctcag gacgaacgct ggcggcgcgc ctaacacatg gaac 60 gggactattt ggccggaagt tttcggatgg aaggcgggat agtttagtgg cggacgggtg 120 agtaacacgt gagcaacctg cctctgagag gggaataacg gctggaaacg gtcgctaata 180 ccgcataacg tatcgggggg acatccccct ggtaccaaag atttt 225 <210> 142 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Oscillibacter <400> 142 tgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg gagc 60 gaagcaccct tgactgaggt ttcggccaaa tgataggaat gcttagtggc gtga 120 gtaacgcgtg aggaacctgc gagg gggacaacag ttggaaacga ctgctaatac 180 cgcataagcg cacagggccg catggcccgg tgtgaaaagc tccgg 225 <210> 143 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 143 agagtttgat catggctcag gatgaacgct ggcggcgtgc catg caagtcgaac 60 gagaatctaa ggacggagtt ttcggacaac tgaattagag gaaagtggcg gacgggtgag 120 taacgcgtga ggaacctgcc ttggagtggg gaataacagt cagc tgctaatacc 180 Page 50 747203 ‐ Sequence Listing.txt gcataatgca tttggatcgc atggtcctga atgccaaaga tttat 225 <210> 144 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sporobacter <400> 144 agagtttgat tcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 gaga ggagcttgct tttcttgact tagtggcgga cgggtgagta acgcgtgagc 120 aatctgcctc ggagtggggg ataacagctg gaaacggctg ctaataccgc ataatgcatt 180 ctggtcgcat ggtcggaatg ccaaaggctt gctgctctga gatga 225 <210> 145 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from occus <400> 145 tgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg ggac 60 gcaatgcttc ggcattgagt ggcgaacggg tgagtaatac ataagcaacc tgcccctgtg 120 agggggataa ctgctggaaa cggcagctaa gaccgcataa gcgcacggta ggta 180 cagtgtgaaa aactccggtg gtatgggatg gacccgcgtc tgatt 225 <210> 146 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sporobacter <400> 146 agagtttgat cctggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 ggacttattt tggaaagttc ttcggaactg gaatctataa gttagtggcg gacgggtgag 120 Page 51 747203 ‐ Sequence Listing.txt taacgcgtga gcaatctgcc tcggagtggg ggataacagc tggaaacggc tgctaatacc 180 gcataatgca ttctggtcgc atggcctaaa aggc ttgct 225 <210> 147 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 147 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gaaccaataa gaagcttgct ttttgttggt tagcggcgga cgggtgagta gggt 120 aacctgcctg taagatcggg ataactccgg gaaaccggtg ctaataccgg atagattatc 180 tttccgcttg gagagataag gaaagatggc tattgccatc actta 225 <210> 148 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Cellulomonas <400> 148 tgat tcag gacgaacgct ggcggtatgc ctaacacatg caagtcgaac 60 gaggttcttc ggaacctagt cggg tgagtaacac gtgagcaacc tgccttacac 120 tttcggatac ctacgggaaa ctgtagtcaa tacggtataa gctg tcgcatgaca 180 gagggataaa agatttatcg gatg ggctcgcgtc gcatt 225 <210> 149 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Syntrophomonas <400> 149 agagtttgat cttggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 Page 52 747203 ‐ Sequence Listing.txt ggagattaaa gttaacaccg agagccacga ggctgccggt ggagcgtgtt caaaaaatac 120 aaagtatttt ttgaactagg ctttaaagag gtgactgaca ctgagttgag cggaatggtt 180 ttgggtattg actttaatct tagtggcgga cgggtgagta acgcg 225 <210> 150 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Cryptanaerobacter <400> 150 agagtttgat catggctcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggactttcca ggacagattc gatg aagacctggc gagttagtgg cggacgggtg 120 agtaacgcgt ggataatctg cccaacagac cgggacaaca gttggaaacg actgctaata 180 ccggataacg tagttttgcg gcatcgcaag attaccaaag gaggc 225 <210> 151 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sporobacter <400> 151 tgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg gaac 60 ggggctcttt agac ttcggtcaag tgaatttgag cttagtggcg gacgggtgag 120 gtga gcaacctgcc tttcagaggg cagt tggaaacgac tgctaatacc 180 gcataacgtg tcgaggaggc atctctttga caccaaagat ttatc 225 <210> 152 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium Page 53 747203 ‐ Sequence Listing.txt <400> 152 agagtttgat catggctcag cgct ggcggcgcac ataagacatg caagtcgaac 60 ggaagtcgtt gtaatgaaat tggactggac agagaacttg ttcgaaggaa agaaagatag 120 acttacaaca ttag tggcggactg gtgagtaacg cgtgagcaac ctgcctatta 180 gaggggaata acagtgagaa atcattgcta ataccgcata tacca 225 <210> 153 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 153 agagtttgat catggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 gaagtttgcc atcc ttcgggtgat tgattgtaaa cttagtggcg gacgggtgag 120 taacacgtga gcaacctgcc ttacagaggg ggataacgtt tggaaacgaa cgctaatacc 180 gcataacacc tttaagggac atcccttggg ggtcaaagga gcaat 225 <210> 154 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 154 agagtttgat tcag gataaacgct ggcggcgcac ataagacatg caagtcgaac 60 ggacttaact ttta gattgagagc ggttagtggc ggactggtga gtaacatgta 120 agcaatctgc ctattagagg ggaataacag tgagaaatca ttgctaatac tgcc 180 ataaaaacca catggtttta gtgggaaagg agcaatccgc taata 225 <210> 155 <211> 225 <212> DNA <213> Unknown <220> Page 54 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Spiroplasma <400> 155 agagtttgat tcag gatgaacgct ggcggcatgc ctaagacatg caagtcgaac 60 gaggtggccc atagaagatg gagtgcttgc acaaaatcgg acatggattc ccacctagtg 120 gcagacgggt gagtaacacg tgggtgacct acctttaaga tggggataac agttggaaac 180 gattgctaat accgaataag atataactgt cgtggttata tagaa 225 <210> 156 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Erysipelotrichaceae incertae sedis <400> 156 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 tcga ggaagcttgc agag acttagtggc gaacgggtga gtaacacgta 120 ggtaacctgc ccatgtgtcc gggataactg ctggaaacgg tagctaaaac ggta 180 tacagagcgc atgctcagta tattaaagcg cccatcaagg cgtga 225 <210> 157 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Pseudoflavonifractor <400> 157 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggagagctat ggaaagagga ttcgtccaat tgaaatagtt tcttagtggc ggacgggtga 120 gtaacgcgtg aggaacctgc cttggagtgg acag ttagaaatga ctgctaatac 180 cgcataatat accg catggtagtg gacatcaaag attta 225 <210> 158 <211> 225 <212> DNA <213> Unknown Page 55 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from idium XlVa <400> 158 tgat tcag cgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg ggtg agtaacgcgt gggcaacctg ccccataccg 120 ggggataaca gagagaaatt tctgctaata ccgcataagc gcacgaggac cgcatggtcc 180 ggtgtgaaaa gccgagacgg tatacgatgg acccgcgtct gatta 225 <210> 159 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Mogibacterium <400> 159 aagtttgatc ctggctcagg atgaacgctg gcggcgtgcc taacacatgc aagtcgagcg 60 agaaatgtat ttatgaaact tcggtagatt agatacatgg aaagcggcgg acgggtgagt 120 aacgcgtagg caacctgccc cttgcagagg gatagccatt ggaaacgatg attaaaacct 180 cataacgctg cattgtcaca tgatagagca gccaaagatt tatcg 225 <210> 160 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 160 agagtttgat catggctcag gatgaacgct gtgc ctaacacatg caagtcgagc 60 gaactcttcg gagtgagcgg cggacgggtg agtaacacgt gagtaacctg cctttcagag 120 tggaataacg tttggaaacg aacgctaata ccgcataaca tagtttccgg gcatccggag 180 actatcaaag attttatcgc tgagagatgg gctcgcggcc gatta 225 <210> 161 <211> 225 Page 56 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 161 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagcttttc tgaggaagtt tgga atcagttagg cttagtggcg gacgggtgag 120 taacgcgtga gcaacctgcc tttcagaggg ggataacgtt ctgaaaagaa cgctaatacc 180 gcataacata ttttctccgc atggagggga tatcaaagga gcaat 225 <210> 162 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Citrobacter <400> 162 aagttacctg gctcaggatg aacgctggcg gcgtgcctaa tacatgcaag tcggacgcaa 60 ggca ttgagtggcg tgag taagacataa tgcc cctgtgaggg 120 ggataactac tggaaacggt agctaatacc gcataacgtc gcaagaccaa agagggggac 180 cttcgggcct cttgccatcg ccca gatgggatta gctag 225 <210> 163 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Hydrogenoanaerobacterium <400> 163 agagtttgat cctggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 gaagttattt tgatcgaagt tttcggatgg acattgattt aacttagtgg cggacgggtg 120 agtaacacgt gagcaatctg cctttcagag tgggataccg tttggaaacg aacgttaata 180 ccgcataacg cagcgaggcc cctt gctgccaaag attta 225 Page 57 747203 ‐ Sequence Listing.txt <210> 164 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 164 agagtttgat catggctcag gatgaacgct gtgc ttaacacatg caagtcgaac 60 gaagcacata ggcagatttc ttcggattga agtatatgtg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctttcacagg gggacaacag ctggaaacgg ctgctaatac 180 cgcataaccc gccg ccag acggaaaagg agcaa 225 <210> 165 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 165 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaagcacaga tttc ttcggattga agtttctgtg actgagtggc gtga 120 gtaacgcgtg ggtaacctgc ctttcacagg gggacaacag ctggaaacgg atac 180 cgcataaccc gctagggccg catggcccag acggaaaagg agcaa 225 <210> 166 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 166 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggacgaggag gtgcttgcac ctccaagtta gtggcggacg ggtgagtaac gcgtgagcaa 120 cctgcctcaa agagggggat aacgtctaga aacggacgct aataccgcat gatgtattcg 180 atct attggatacc aaaggagcaa tccgctttga gatgg 225 Page 58 747203 ‐ Sequence Listing.txt <210> 167 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Erysipelotrichaceae incertae sedis <400> 167 agagtttgat catggctcag cgct ggcggcatgc ctaatacatg caagtcgaac 60 ggacggaaga tgagcttgct cattggaagt cagtggcgaa cgggtgagta acacgtaggg 120 aatctgccca tgtgcccggg acaacagatg gaaatgtctg ctaaaaccgg ataggtggca 180 atgaggcatc ttcttgcgat taaaggggct acggccttga acatg 225 <210> 168 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVb <400> 168 tgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 ggagatattc ggaaagcttg ctttttggat atcttagcgg cggacgggtg agtaacgtgt 120 gggcaacctg cctcatacag agggatagtc atgtgaaaac gtgactaata ccgcatgtca 180 ttaccaaagg gcatccttcg gtaagaaaag gagcaatccg gtatg 225 <210> 169 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVb <400> 169 agagtttgat tcag gatgaacgct ggcggcgtgc ttaacacatg gagc 60 ggagatattc ggaaagcttg ggat atcttagcgg cggacgggtg gtgt 120 gggcaacctg cctcatacag actc atgtgaaaac gtgactaata ccgcatgtca 180 Page 59 747203 ‐ Sequence Listing.txt ttactgcagg gcatccttcg gtaagaaaag gagaaatccg gtatg 225 <210> 170 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Butyricicoccus <400> 170 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagcaccct agtt ttcggacaag agagaggaat gcttagtggc ggacgggtga 120 gtaacgcgtg agcaatctgc ctttcagagg gggacaacag agggaaactt ctgctaatac 180 cgcataacgt ggcg catgctctgg ataccaaaga tttga 225 <210> 171 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Pediococcus <400> 171 agagtttatc ctggctcagg gctg gcggcgtgcc taatacatgc gacg 60 caatgcttcg gcattgagtg gcgaacgggt gagtaagaca taagcaacct gcccctgtga 120 gggggataac tgctggaaac ggcagctaat accgcataag cgcacagggc cgcatggcct 180 agtgtgaaaa actccggtgg tgtgggatgg gcccgcgttg gatta 225 <210> 172 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sphingomonas <400> 172 agagtttgat catggctcag gatgaacgct ggcggcatgc catg caagtcgaac 60 gaagtggccc gatg ttgc actgattcgg acttggattc ccacttagtg 120 Page 60 747203 ‐ Sequence Listing.txt gcgaaagggt gagtaacacg tgggttatct gccttcgagt ctggaataac agttagaaat 180 gattgctaat tgat atatgttagg atacgtccta atata 225 <210> 173 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 173 agagtttgat cctggctcag gatgaacgct ggcggcatgc ctaagacatg caagtcgaac 60 gaagtggccc aaggaagtag agtgcttgca cgaagcggaa ttggattccc acttagtggc 120 agacgggtga gtaacacgtg ggtaacctac cgaagagact gggataacag ttagaaatga 180 ctgctaatac cggatgattc atctttacat aagtagagat gctaa 225 <210> 174 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 174 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagttatca gacggaagtt ttcggatgga ataa cttagtggcg gacgggtgag 120 taacgcgtga gtaacctgcc tttcagaggg ggataacgtt ttgaaaagaa tacc 180 gcataacaca gatggaccgc tgtc tgtcaaagga gcaat 225 <210> 175 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 175 tgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 Page 61 747203 ‐ Sequence Listing.txt gaagcggcgc agaggaagtt ttcggatgga atcggcgctg actgagtggc ggacgggtga 120 gtaacgcgtg ctgc ctcgcacagg gggataacag ttagaaatga ctgctaatac 180 cgcataaccc gctagggccg catggcctgg acggaaaaga tttat 225 <210> 176 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 176 agagtttgat catggctcag gatgaacgct gtgc ttaacacatg gaac 60 gaagcggcgc ggaggaagtt tgga atcggcgctg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcacacagg gggataacag ttagaaatga ctgctaatac 180 cgcataaccc gctagggccg catggcccgg acggaaaaga tttat 225 <210> 177 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Methylobacterium <400> 177 agagtttgat catggctcag agcgaacgct ggcggcaggc ttaacacatg gaac 60 gctcgtcttc ggacgggagt ggcagacggg acac gtgggaacgt accctttggt 120 tcggaataac gcagggaaac ttgcgctaat accggatacg cccttttggg gaaaggttta 180 ctgccgaagg atcggcccgc gtctgattag ctagttggtg gggta 225 <210> 178 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Salana Page 62 747203 ‐ Sequence Listing.txt <400> 178 agagtttgat cctggctcag cggt aatacgtagg gcgcgagcgt tgtccggaat 60 cattgggcgt aaagagctcg taggcggttt gtcgcgtctg ctgtgaaagc ctggggctca 120 actccgggat tgcagtgggt acgggcagac tagagtgcgg taggggagac tggaattcct 180 ggtgtagcgg gcgc agatatcagg aagaacaccg atggc 225 <210> 179 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Petrobacter <400> 179 agagtttgat cctggctcag tttgcgggag cgtggtgact ttgt agcgctgctt 60 gtcgtcgttg ccgtagaagg tgcccgtcac catcaggttg cgcgtgttcg acagcagtac 120 gctc aatgacaacc cgagccgttg cgtgtcggtc aggtagcgcg attgatagcc 180 cagttgctcc agcggcagat tctcgggcat atag tgcga 225 <210> 180 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 180 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg gagc 60 ggactttaaa agcttgcttt taaagttagc ggcggacggg tgagtaacac gtgggcaacc 120 tgcctgtaag ataa cttcgggaaa ccggagctaa taccggataa tccttttcct 180 ctcatgagga aaagctgaaa gacggtttac gctgtcactt acaga 225 <210> 181 <211> 225 <212> DNA <213> Unknown <220> Page 63 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Thermovibrio <400> 181 agagtttgat cctggctcag cgaaggtagc gtcaggcacg tcgaggtctt ccagatgttc 60 ggtgtgagaa cctccatcat cggaagacct cgacccctac ccagtgcccg acgcgccgac 120 caccatcaca ctac accccggatt gtgatgagcc cctgaaacca ccgtactgat 180 aagcagtact tctgcacact caacgagacc agcagggcca gcgga 225 <210> 182 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Erysipelotrichaceae incertae sedis <400> 182 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 ggagcacctt ggtgctcagt ggcgaacggg tgaggagaac ataggtaacc tgcccctccg 120 agggggacaa cagctggaaa cggctgctaa gaccgcatag acgcattcag ggcatcctgg 180 atgcgctaaa tgaccggatg gtcagcgggg ggatggacct atgca 225 <210> 183 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Selenomonas <400> 183 agagtttgat catggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gata tttagcttgc tattttgaag ccgagtggca aacgggtgag gtag 120 acaacctgcc atgg ggacaacagt ccgaaaggac tacc gaatgttgtc 180 agattcccgc gact gattaaagat ggcctctact tgtaa 225 <210> 184 <211> 225 <212> DNA <213> Unknown Page 64 747203 ‐ Sequence Listing.txt <220> <223> s 16S rRNA from Glaciecola <400> 184 agagtttgat catggctcag attgaacgct ggcggcaggc ctaatacatg caagtcgaac 60 ggtaacatgg aagtagcaat acttttgatg acgagtggcg gacgggtgag taatatttgg 120 gaatctacct atcagagggg gatagcaact ggaaacggtt gataagaccg cgtacgctct 180 gaggaggaaa gtaatgggat acca ttagctgata gatga 225 <210> 185 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from acillus <400> 185 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gagttttgtt atca aggtgcttgc agaa ttagaatgaa acgagtggcg 120 gacgggtgag taacacgtgg gtaacctacc ctaaagtggg ggataacatt tggaaacaga 180 tgctaatacc gcataacgaa cgaagccaca tggctttgtt ctgaa 225 <210> 186 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Eubacterium <400> 186 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggttaagt gaaattttcg gatggagctt aacttagtgg cggacgggtg agtaacgcgt 120 ggataacctg cctcacactg ggggatagca gctggaaacg aata ccgcataaga 180 cacc gcatggtgca ggggtaaaag atttatcggt gtgag 225 <210> 187 <211> 225 Page 65 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Thermomicrobium <400> 187 agagtttgat cctggctcag ccacacggtg tgctcggggt cgcgcacggt gacgtcgtcg 60 acctcgtcgg gcgtgctgac gatctgcacc cggtcgggcg cctcgccgct gacg 120 tcgt ggccacggtg gccgatgagc acgatgtcgt agtcctgcct cgcataccgg 180 cgcacctccc ggtgcacctt cgtgacgagc gggcaggtcg cgtcg 225 <210> 188 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acidobacteria <400> 188 agagtttgat cctggctcag tgaaaggccc ttcctagcgg cagggcaacg tcaattgttg 60 agtggaattt gaca gatttgcctc aatgaaaggc ccttcctagc ggaagggcaa 120 ccagttcccc aacaagtgtg gcgtctccta cagtcgcctc aatgaaaggc ccttcctagc 180 ggaagggcaa acga aacg ctctggagag gagca 225 <210> 189 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Chlorobaculum <400> 189 agagtttgat cctggctcaa agtaaaagta atcctcctca ttct ggctggaagg 60 ctgtttttga tgatgaatac cagacttggt attatgtaga tttatctacg aacagctctc 120 agtgggaacc accaagggga acaacatggc caagacccaa aggtcctcca ccagatgtta 180 acaatgagaa gagttctcgt caacaggcag accaggctcc tccac 225 Page 66 747203 ‐ Sequence Listing.txt <210> 190 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Rothia <400> 190 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgaagcct agcttgctag tagt ggcgaacggg tgagtaatac gtgagtaacc 120 tacctttaac tctgggataa gcctgggaaa ctgggtctaa taccggatac gaccaatctc 180 gggt gttggtggaa agcgttatgt agtggttata gatgg 225 <210> 191 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Selenomonas <400> 191 tgat catagctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaggtgattg aaagcttgct tttgagaacc gggtggcaaa cgggtgagta acgcgtagac 120 aacctgccgc aaagatgggg gtcc gaaaggactg ctaataccga atgttgtgca 180 acttccgcat gggagatgca ttaaagatgg cctctacttg taagc 225 <210> 192 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 192 agagtttgat catggctcag gatgaacgct gtgc ctaacacatg caagtcgaac 60 ggggttaagt ttcg gatggatctt aacttagtgg cggacgggtg agtaacgcgt 120 ggataacctg cctcacacag ggggatagca gctggaaacg gctggtaata ccgcataaga 180 ccacggcccc gcatggggct gtagtaaaag atttatcggt gtgag 225 Page 67 747203 ‐ ce Listing.txt <210> 193 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Virgibacillus <400> 193 agagtttgat catggctcat ctcgagcagg agggcaagag cgagggcgac gccg 60 aggagatccg cggcgatgtc gagcgcggca tccgcaccca gctgctgctc gacaaggtcg 120 tcgaggagct cggcgtgcag ctgagccagg acgagctgtc acagtacctg gtgcagcagt 180 cgatgcagta cggcatcgac ccgaacgagt tcttccgcat catca 225 <210> 194 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Sphingomonas <400> 194 agagttgatc caga gctg gcggcatgcc taacacatgc aagtcgaacg 60 tcgg gtctagtggc gcacgggtgc gtaacgcgtg ggaatctgcc cttgggttcg 120 gaataacttc gggaaactga agctaatacc ggatgatgac gtaagtccaa agatttatcg 180 cccaaggatg agcccgcgta ggattagcta gttggtgagg taaag 225 <210> 195 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Citricoccus <400> 195 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagctc ctagcttgct gggggtggat gagtggcgaa cgggtgagta tcacgtgagt 120 aacctgccct tgactctggg ataagcctgg gggt ctaataccgg atgatcactt 180 Page 68 747203 ‐ Sequence Listing.txt ctctccgcat tggt gtaaagattg tatcggtctt ggatg 225 <210> 196 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Catenibacterium <400> 196 agagtttgat cctggctcag aaaa ccacatgccc aacccggcat gggttggccg 60 cttaaactca atgtcattgg cgctcggcgc cgcgtttctc gagggtctta ccgggcgcac 120 tggatagcgc aagaaccggg cccctagaaa agagcgctgc tttataccag aaagccctgg 180 gagcaacaag gaaaaacgca ggataaaacc caaccccgag ccagc 225 <210> 197 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Amycolatopsis <400> 197 agagtttgat catggctcag gcggttggga ttgc cggttaaggt ggagcgattc 60 tggcgggggg ctcctgacag gtca ggagcgttca ggagggtggc aaagcgtgtt 120 gcagattgcc caggcagtga ataccgggcg gagggaggag cgattcagtg ccaa 180 cccgccagca gccgcggtaa ctta tacacatctc cgagc 225 <210> 198 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sphingobium <400> 198 agagtttgat cctggctcag aacgaacgct ggcggcatgc ctaatacatg caagtcgaac 60 gagatcttcg gatctagtgg cgcacgggtg cgtaacgcgt gggaatctgc ccttgggttc 120 Page 69 747203 ‐ Sequence Listing.txt ggaataacgt cgggaaactg acgctaatac cggatgatga cgtaagtcca aagatttatc 180 ggat gagcccgcgt aggattagct tggg gtaaa 225 <210> 199 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Actinomyces <400> 199 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagccc ctgg gagt ggcgaacggg tgagtaacac gtgagtaacc 120 tgcccccttc tttgggataa cgcccggaaa cgggtgctaa tactggatat tcactggcct 180 tcgcatgggg gttggtggaa aggttttttc tggtggggga tgggc 225 <210> 200 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Succiniclasticum <400> 200 agagtttgat cctggctcag cgct gtgc ctaacacatg caagtcgaac 60 ggggattttg tttcggcaga atcctagtgg cgaacgggtg agtaacgcgt aggcaacctg 120 ggat tgggacaaca ccccgaaagg ggtgctaata ccggatacga agataacacc 180 gcatggtgat attttgaaag atggcctcta tttataagct atcgc 225 <210> 201 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Beijerinckia <400> 201 agagtttgat cctggctcag aacgaacgct ggcggcaggc ttaacacatg caagtcgaac 60 Page 70 747203 ‐ Sequence Listing.txt caag gggagtggca gacgggtgag taacgcgtgg gaacataccc tttcctgcgg 120 tccg tgga attaataccg ccct acgggggaaa tcgg 180 ggaaggattg gcccgcgttg gattagctag ttggtggggt aaagg 225 <210> 202 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bosea <400> 202 agagtttgat cctggctcag agcgaacgct ggcggcaggc ttaacacatg caagtcgaac 60 gggcacttcg gtgctagtgg cagacgggtg agtaacacgt gggaacgtac ctttcggttc 120 ggaataatcc actt ggactaatac cggatacgcc cttcggggga aagatttatc 180 gccgatagat cggcccgcgt ctgattagct agttggtgag gtaat 225 <210> 203 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sporobacter <400> 203 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagattaag accg aacacttgat gctgttaaag taagcgcatc aaaaacgcga 120 agcgtttttg attaggctta ttttgagtga caaacacaaa agatatcgag tagtcggtgt 180 tgaacttaat cttagtggcg gacgggtgag taacgcgtga gtaac 225 <210> 204 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Facklamia Page 71 747203 ‐ Sequence g.txt <400> 204 agagtttgat cctggctcag cgct ggcggcgtgc ctaatacatg caagtcgaac 60 gcactgacgg agaacttgtt ctcttgacgt gagtggcgca cgggtgagta acacgtggga 120 aacctaccct tcagcggggg atcg gaaacgatga ctaataccgc atagacgaca 180 gaaccgcctg gttcaatcgg gaaagacggc ttcggctgtc actga 225 <210> 205 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acinetobacter <400> 205 agagtttgat cctggctcag cgct ggcggcaggc ttaacacatg caagtcgagc 60 ggggaagggt agcttgctac ctgacctagc ggcggacggg tgagtaatgc ttaggaatct 120 gcctattagt gggggacaac attccgaaag gaatgctaat accgcatacg gggg 180 gaaagcaggg gatcttcgga ccttgcgcta atagatgagc ctaag 225 <210> 206 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Brevundimonas <400> 206 agagtttgat catggctcag agcgaacgct ggcggcaggc ctaacacatg caagtcgaac 60 ggacccttcg gggttagtgg cggacgggtg agtaacacgt gggaacgtgc gttc 120 ggaatagctc ctggaaacgg gtggtaatgc cgaatgtgcc ggga aagatttatc 180 gcctttagag cggcccgcgt ctgattagct agttggtgag gtaac 225 <210> 207 <211> 225 <212> DNA <213> Unknown <220> Page 72 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Ochrobactrum <400> 207 agagtttgat cctggctcag aacgaacgct ggcggcaggc ttaacacatg gagc 60 gccccgcaag gggagcggca gacgggtgag taacgcgtgg gaatctacct acgg 120 aataactcag ggaaacttgt gctaataccg tatgtgccct tcgggggaaa gatttatcgg 180 caaaggatga gcccgcgttg gattagctag ttggtggggt aaagg 225 <210> 208 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from genes <400> 208 agagtttgat cctggctcag attgaacgct atgc tttacacatg caagtcgaac 60 ggcagcgcga ttgc tctcttggcg gcgagtggcg gacgggtgag taatatatcg 120 gaacgtgccc agtagcgggg tact cgaaagagtg gctaataccg catacgccct 180 acgggggaaa gggggggatc gcaagacctc tcactattgg agcgg 225 <210> 209 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Pseudochrobactrum <400> 209 agagtttgat catggctcag aacgaacgct ggcggcaggc ttaacacatg caagtcgaac 60 ggtctcttcg gaggcagtgg cagacgggtg agtaatgcat gggaatctac cgttctctac 120 ggaataactc actt gtgctaatac cgtatacgcc cttttgggga aagatttatc 180 ggagaatgat gagcccatgt tggattagct agttggtagg gtaaa 225 <210> 210 <211> 225 <212> DNA <213> Unknown Page 73 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from Jeotgalicoccus <400> 210 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcgagcgtta gaagcttgct tctaacaatc gagcggcgga cgggtgagta gggc 120 cctt tgagattggg ataactaccg gtag ctaataccgg ataggacatg 180 attacataag tagtgatgtt aaaaggcgga tttatctgcc gttca 225 <210> 211 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from licoccus <400> 211 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gcgaatctca ggagcttgct cctgagattc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ctaataccgg atacgacatt 180 cctgcataag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 212 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from obacter <400> 212 agagtttgat catggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 ggggcgaagg tagcttgcta ctggaaccta gcggcggacg ggtgagtaat acttaggaat 120 ctgcctatta gtgggggaca acgttccgaa aggagcgcta ataccgcata acgg 180 gggaaagcag gggatcactt gtgaccttgc gctaatagat gagcc 225 <210> 213 <211> 225 Page 74 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sphingobacterium <400> 213 agagtttgat catggctcag gatgaacgct agcggcaggc ctaatacatg caagtcgaac 60 cagg tgttagcttg ctaacatttg gtgagagtgg cgcacgggtg cgtaacgcgt 120 gagcaaccta cccatatcag ggggatagcc cgaagaaatt cggattaaca ccgcataaga 180 ctacgagatg gcatcatcaa gtagttaaat atttatagga tatgg 225 <210> 214 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea <400> 214 agagtttgat cctggctcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggagttattt agcc ttcgggtgga ataa cttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc aggg ggataacagc cggaaacggt tgctaatacc 180 gcataagcgc acagtattgc atgatacagt gtgaaaagat ttatc 225 <210> 215 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from rillum <400> 215 agagtttgat cctggctcag aacgaacgct ggcggcatgc ctaacacatg caagtcgaac 60 ttcg gccttagtgg cgcacgggtg agtaacacgt gggaacctgc ctttcggttc 120 ggaataacgt ctggaaacgg acgctaacac cggatacgcc cttcggggga aagttcacgc 180 cgagagaggg gcccgcgtcg gattaggtag ttggtgtggt aacgg 225 Page 75 747203 ‐ Sequence Listing.txt <210> 216 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 216 agagtttgat cctggctcag gacgaacgtt ggcggcgtgc ctaatacatg caagtcgaac 60 gaagtcgccc aattgattct tagtgcttgc actaagatga ttttggatcc gactgagtgg 120 ggtg agtaacacgt gggtaacctg cccagaagaa ggggataaca aaca 180 gatgctaata ccgtataaca acaagaacca catggttctt gtttg 225 <210> 217 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Clavibacter <400> 217 tgat cctggctcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggtgatgtca gagcttgctc tggcggatca gtggcgaacg ggtgagtaac acgtgagtaa 120 cctgcccccg actctgggat aactgctaga aatggtagct aataccggat atgacgactg 180 gccgcatggt ctggtcgtgg aaagaatttc ggttggggat ggact 225 <210> 218 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Clostridium XlVa <400> 218 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg gaac 60 ggagttattt tacggaagcc ttcgggtgga agtaaaataa cttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tgctaatacc 180 gcataagcgc acagtattgc atgatacggt gtgaaaagat ttatc 225 Page 76 747203 ‐ Sequence Listing.txt <210> 219 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 219 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggagttattt tatggaagcc ttcgggtgga aataaaataa cttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tgctaatacc 180 gcataagcgc acagtattgc atgatacagt agat ttatc 225 <210> 220 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 220 agagtttgat catggctcag gacgaacgct gtgc ttaacacatg caagtcgaac 60 gatgaagctg gtgcttgcac tggtggatta gtggcgaacg ggtgagtaac acgtgggtaa 120 cttg aagtagggga taacacttgg aaacaggtgc taataccgta taacaaccaa 180 aaccacctgg ttttggttta aaagacggct tcggctgtca cttta 225 <210> 221 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 221 agagtttgat tcag cgct ggcggcgtgc ctaacacatg gaac 60 ggagttatgc tgaaacctag tgaggcataa cttagtggcg gacgggtgag taacgcgtgg 120 gcaacctgcc ccacacaggg ggataacact tagaaatagg tgctaatacc gcataagcgc 180 Page 77 747203 ‐ Sequence Listing.txt acagcttcgc atgaagcagt gtgaaaagct gcggcggtgt gggat 225 <210> 222 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 222 agagtttgat cctggctcag gacgaacgct ggcggcgtgc catg caagtcgagc 60 gaaccaataa gaagcttgct ttttgttggt tagcggcgga cgggtgagta acacgtgggt 120 aacctgcctg taagaccggg ccgg gaaaccggtg ctaataccgg atagattatc 180 tttccgcctg gagagataag gaaagatggc catc actta 225 <210> 223 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Methanoplanus <400> 223 agagtttgat cctgccagta gtcatatgct tgtctcaaag attaagccat gcaa 60 gtatgaacta attcgaactg tgaaactgcg aatggctcat taaatcagtt atagtttgtt 120 tgatggtacg tgctactcgg ataaccgtag taattctaga gctaatacgt gcaacaaacc 180 tccg ggaggggcgc atttattaga taaaaggctg acgcg 225 <210> 224 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Mogibacterium <400> 224 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gagaaatgta tttatgaaac ttcggtagat tagatacatg ggcg gacgggtgag 120 Page 78 747203 ‐ Sequence Listing.txt taacgcgtag gcaacctgcc ccttgcagag ggatagccat tggaaacgat gattaaaacc 180 tcataacgct gcattgtcac gagc agccaaagat ttatc 225 <210> 225 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Brachybacterium <400> 225 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgacggtg gtgcttgcac cgcctgatta gtggcgaacg ggtgagtaac acgtgagtaa 120 cctgccctcc acttcgggat ggga ggct aataccggat atgagcactc 180 atcgcatggt tgga aagatttatc ggtgggggat ggact 225 <210> 226 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Facklamia <400> 226 agagtttgat tcag gacgaacgct ggcggcgtgc catg caagtcgaac 60 gcactgacgg agaacttgtt ctcttgacgt gagtggcgca cgggtgagta acacgtggga 120 aacctaccct tcagcggggg ataaccatcg gaaacgatga ctaataccgc atagacgaca 180 gaaccgcctg gttcaatcgg gaaagacggc ttcggctgtc actga 225 <210> 227 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 227 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 Page 79 747203 ‐ Sequence Listing.txt ggagttattt tatggaagcc ttcgggtgga agtaaaataa cttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tacc 180 gcataagcgc acagtattgc atgataccgt agat ttatc 225 <210> 228 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 228 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggacttattt tatggaagcc ttcgggtgga aataaaataa gttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tgctaatacc 180 gcgc acagtattgc atgataccgt gtgaaaagat ttatc 225 <210> 229 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from phomonas <400> 229 agagtttgat cctggctcag cgct ggcggcgtgc ctaacacatg gaac 60 ggaagtaaga gcttcggttt ttactttagt ggcgaacggg tgagtaacgc aacc 120 tgcctttcag tgggggacaa cagttggaaa cgactgctaa taccgcataa tgtttccggt 180 ctgcatggac tggaaaccaa agctttatgt gctgaaagat ggcct 225 <210> 230 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Beijerinckia Page 80 747203 ‐ Sequence Listing.txt <400> 230 agagtttgat tcag aacgaacgct ggcggcaggc ttaacacatg caagtcgaac 60 gccccgcaag gggagtggca gacgggtgag taacgcgtgg accc tttcctgcgg 120 aatagctccg ggaaactgga accg catacgccct acgggggaaa gatttatcgg 180 ggaaggattg gcccgcgttg gattagctag ttggtggggt aaagg 225 <210> 231 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 231 agagtttgat catggctcag gacgaacgct atgc ttaacacatg caagtcgaac 60 gggaagtggt gtttccagtg gcgaacgggt cacg tggggaacct gccccatagt 120 ctgggatacc acttggaaac aggtgctaat accggataag aaagcagatc gcatgatcag 180 cttttaaaag taag ctgtcgctat gggatggccc cgcgg 225 <210> 232 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 232 agagtttgat catggctcag gatgaacgct ggcggcatgc ttaacacatg caagtcgaac 60 gggaagtggt gtttccagtg gcggacgggt gagtaacacg tggggaacct gccccatagt 120 ctgggatacc acttggaaac aggtgctaat accggataag aaagcagatc gcatgatcag 180 cttataaaag gcggcgtaag ctat gggatggccc cgcgg 225 <210> 233 <211> 225 <212> DNA <213> Unknown <220> Page 81 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Lactobacillus <400> 233 agagtttgat tcag gatgaacgct ggcggcatgc ttaacacatg caagtcgaac 60 gggaagtggt gtttccagtg gcggacgggt cacg tgggtaacct gcccaagaga 120 ctgggataac aaac agatgctaat accggataac aacactagac gcatgtctag 180 aaag atggttctgc tatcactctt ggatggacct gcggt 225 <210> 234 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Erysipelotrichaceae incertae sedis <400> 234 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 ggagcacctt ggtgctcagt ggcgaacggg tgaggagaac ataggtaacc tgcccctccg 120 agggggacaa cagctggaaa cggctgctaa gaccgcatag acgcattcag ggcatcctgg 180 atgcgctaaa tgaccggatg gtcagcgggg ggatggacct atgca 225 <210> 235 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Rummeliibacillus <400> 235 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gaatgatgag gagcttgctc ctctgattta gcggcggacg ggtgagtaac acgtgggcaa 120 cctgccctgt ggat aacttcggga agct aataccggat aattctttta 180 tggc tttaagctaa aaggcgcttc ggcgtcacta cagga 225 <210> 236 <211> 225 <212> DNA <213> Unknown Page 82 747203 ‐ ce Listing.txt <220> <223> Encodes 16S rRNA from Acinetobacter <400> 236 agagtttgat catggctcag attgaacgct aggc ttaacacatg caagtcgagc 60 ggggataggg tgcttgcacc tgattcctag cggcggacgg gtgagtaatg cttaggaatc 120 tgcctattag tgggggacaa cgttccgaaa gggacgctaa taccgcatac gtcctacggg 180 agaaagcagg ggatcttcgg cgct aatagatgag cctaa 225 <210> 237 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactococcus <400> 237 agagtttgat cctggctcag gacgaacgct gtgc ctaatacatg caagttgagc 60 gctgaaggtt ggtacttgta ccgactggat gagcagcgaa cgggtgagta acgcgtgggg 120 aatctgcctt tgagcggggg acaacatttg gaaacgaatg ctaataccgc actt 180 taaacacaag ttttaagttt tgca attgcatcac tcaaa 225 <210> 238 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Propionibacterium <400> 238 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgtac 60 ggtaaggccc tttcgggggt acacgagtgg cgaacgggtg agtaacacgt gagtaacctg 120 cccacaactt tgggataacg ctaggaaact ggtgctaata ctggatatgt gctcctgctg 180 catggtgggg gttggaaagc tccggcggtt gtggatggac tcgcg 225 <210> 239 <211> 225 Page 83 747203 ‐ Sequence Listing.txt <212> DNA <213> n <220> <223> s 16S rRNA from idium sensu stricto <400> 239 agagtttgat catggctcag gataaacgct gcac ataagacatg caagtcgaac 60 ggacttaatc gaaatattta tattttgaag cggttagtgg cggactggtg agtaacgcgt 120 aaggaacctg cctgttagag gggaataaca gtgagaaatc actgctaata ccgcatatgc 180 tacc acatggtaat agtgggaaag gagcaatccg ctgac 225 <210> 240 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 240 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ccca ggacgaagcc tacgggcaga ggaatggggg actgagtggc ggacgggtga 120 gtaacgcgtg aggaacctgc ctcatacagg gggataacag ttagaaatga ctgctaatac 180 cgcataagcg cacgagaccg catgggaacg tgtgaaaaac tgagg 225 <210> 241 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Rummeliibacillus <400> 241 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gaatgacgag aagcttgctt ctctgattta gcggcggacg ggtgagtaac acgtgggcaa 120 cctgccctgt agactgggat aacttcggga aaccggagct aataccggat aattctttta 180 gcctcatggc tttaagctaa aaggcgcttc ggcgtcacta cagga 225 Page 84 747203 ‐ Sequence Listing.txt <210> 242 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Ralstonia <400> 242 agagtttgat cctggctcag attgaacgct ggcggcatgc cttacacatg caagtcgaac 60 atga ttgc tagattgatg gcgagtggcg aacgggtgag taatacatcg 120 gaacgtgccc tgtagtgggg gataactagt cgaaagatta gctaataccg catacgacct 180 gagggtgaaa gtgggggacc gcaaggcctc atgctatagg agcgg 225 <210> 243 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Brachybacterium <400> 243 tgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgacgatg gtgcttgcac cgtctgatta gtggcgaacg ggtgagtaac acgtgagtaa 120 cctgccctcc tcttcgggat aaccgccgga aacggtggct ggat atgaatgcct 180 gccgcatggt gggtgttgga aagatttatc ggtgggggat ggact 225 <210> 244 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Ruminobacter <400> 244 agagtttgat cctggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgtac 60 ggtaacagag ggaagcttgc ttctctgctg acgagtggcg tgag taatgtctgg 120 gaagctgcct gggg gatagcggag cgaaagttcc gataataccg cgtaagcccg 180 agaggggaaa gtgcgggacc gcaaggccgc acgcgagcag atgcg 225 Page 85 747203 ‐ ce Listing.txt <210> 245 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Glycomyces <400> 245 agagtttgat catggctcag gcggttggcc aggtacaccg agcggtggtg accaccggtg 60 cagccaatgg cgatggtcac ataggcgcgg ttgctggcgg cgaagcgtgg cagccatttt 120 tccaggtagg cgaggatgtc ctgatacatc tcctcgacct ccggttgcgc ggccaggtag 180 tcgatcactg gttgatccag cccggagtgg tcgcgcagtt ccggc 225 <210> 246 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Psychrobacter <400> 246 agagtttgat catggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 attt ctagcttgct agaagatgac gagcggcgga cgggtgagta atacttagga 120 atctacctag tagtggggga tagctcgggg aaactcgaat cgca tacgacctac 180 aagg cttg ttgctctcgc tattagatga gccta 225 <210> 247 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Yaniella <400> 247 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagctc ccagcttgct gggggtggat gagtggcgaa cgggtgagta tcacgtgagt 120 ccct tgactctggg ataagcccgg gaaactgggt ctaatactgg ataggactgg 180 Page 86 747203 ‐ Sequence g.txt ccatcgcatg gtggttggtt gaaagctttt gcggttttgg atgga 225 <210> 248 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 248 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagttatta gagtgaagtt tgga atgataataa cttagtggcg gacgggtgag 120 taacgcgtga gtaacctgcc catgagaggg ggataacgtt ctgaaaagaa cgctaatacc 180 gcataacata tttagttcgc atggactgaa tatcaaagga gcgat 225 <210> 249 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 249 agagtttgat tcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gatgatatcc cttcggggat gcgg cggacgggtg agtaacacgt gggtaacctg 120 cctcaaagag ggggatagcc ctccgaaagg aggattaata ccgcataaag ttgagagttc 180 gcatgaacat tcaaccaaag gagcaatccg ctttgagatg gaccc 225 <210> 250 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 250 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggacttattt tacggaagcc tgga agtaaaataa gttagtggcg gacgggtgag 120 Page 87 747203 ‐ Sequence Listing.txt taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tgctaatacc 180 gcataagcgc acagtattgc atgatacagt gtgaaaagat ttatc 225 <210> 251 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 251 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gagggacttc ggtccctagc ggcggacggg tgagtaacac aacc tgcctcatag 120 agggggatag cctcccgaaa gggagattaa taccgcataa catcatgctt tcgcatggaa 180 gtatgatcaa aatc gaga tggacccgcg gcgca 225 <210> 252 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 252 tgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggagttattt tacggaagcc tgga agtaaaataa cttagtggcg gacgggtgag 120 taacgcgtgg gtaacctgcc ttatacaggg ggataacagc cggaaacggt tacc 180 gcataagcgc acagtattgc atgatacggt gtgaaaaaga ttaaa 225 <210> 253 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Cohnella <400> 253 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 Page 88 747203 ‐ Sequence Listing.txt ggatctctga tggagcttgc tcctgatgag gttagcggcg gacgggtgag taacacgtag 120 gcaacctgcc atcg ggataacatt cggaaacgaa tgctaagacc ggatacacgg 180 tttggtcgca tgatcggatc gggaaacacg gagcaatctg tggct 225 <210> 254 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Chthonomonas/Armatimonadetes gp3 <400> 254 agagtttgat cctggctcag cagtttccgt attgaacaaa tggactgccc caccgaacag 60 acgctgattc aagacaaact gagcaagctg gctggcatag acaagctcga tttcaatctg 120 atcaatcgcg ttcttggggt atggcacagc ttgccgtcga ccgctcttat tgaagcggcg 180 atctcatccc tgca agcagaaccg ctctctgctg agggg 225 <210> 255 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Streptophyta <400> 255 agagtttgat cctggctcag gatgaacgct ggcggcatgc cttacacatg caagtcggac 60 gggaagtggt gtttccagtg gcggacgggt gagtaacgcg taagaaccta cccttgggag 120 aaca gctggaaacg actgctaata ccgcataagc ggcc gcatggctct 180 gagggaaaag gagcaatccg ctttgagatg gcctcgcgtc cgatt 225 <210> 256 <211> 225 <212> DNA <213> n <220> <223> s 16S rRNA from Acinetobacter Page 89 747203 ‐ Sequence Listing.txt <400> 256 agagtttgat cctggctcag cgct ggcggcaggc catg caagtcgagc 60 ggggaaaggt agcttgctac ctgacctagc ggcggacggg tgagtaatgc ttaggaatct 120 gcctattagt gggggacaac atctcgaaag taat accgcatacg tcctacggga 180 gaaagcaggg gaccttcggg ccttgcgcta atagatgagc ctaag 225 <210> 257 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Clostridium XlVb <400> 257 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 ggagatattc ggaaagcttg ctttttggat atcttagcgg cggacgggtg agtaacgtgt 120 gggcaacctg acag agggataatc atgtgaaaac gtgactaata ccgcatgtca 180 ttactgaagg gcatccttcg gtaagaaaag gagaaatccg gtatg 225 <210> 258 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Neisseria <400> 258 agagtttgat catggctcag attgaacgct ggcggcatgc tttacacatg gaac 60 ggcagcgagg agaagcttgc ttctctgtcg gcgagtggcg aacgggtgag tatagcatcg 120 gaacgtgcca agtagtgggg caaa cgaaagtttg gctaataccg cgtaagctcc 180 aaggaggaaa gtaggggacc taaataaggc cttacgctat ttgat 225 <210> 259 <211> 225 <212> DNA <213> Unknown <220> Page 90 747203 ‐ Sequence g.txt <223> Encodes 16S rRNA from Butyricicoccus <400> 259 tgat cctggctcag gatgaacgct ggcggcacgc ctaacacatg caagtcgaac 60 gaagttattt tgatcgaagt tttcggatgg acattgattt aacttagtgg cggacgggtg 120 agtaacacgt gagcaatctg cctttcagag tgggataccg tttggaaacg aacgttaata 180 ccgcataacg cagcgaggcc cctt gctgccaaag attta 225 <210> 260 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from acter <400> 260 agagtttgat tcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagatatat tgaatgaaga tttcggttgg aatttgatat atcttagtgg cggacgggtg 120 agtaacgcgt gagtaacctg ccgatgagag tggaataacg ttctgaaaag aacgctaata 180 ccgcataaca tatgggagcc gcatgactct gatatcaaag atttt 225 <210> 261 <211> 225 <212> DNA <213> n <220> <223> s 16S rRNA from Sporobacter <400> 261 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggctcttt ggatcgagac ttcggtcaag tgaatctgag cttagtggcg gacgggtgag 120 taacgcgtga gcaacctgcc tttcagaggg ggacaacagt tggaaacgac tgctaatacc 180 gcataatgtg ttttgggggc atccccgaaa caccaaagat ttatc 225 <210> 262 <211> 225 <212> DNA <213> Unknown Page 91 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from phomonas <400> 262 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggctcttt ggatcgagac ttcggtcaag tgaaactgag cttagtggcg gacgggtgag 120 taacgcgtga gcaacctgcc aggg ggacaacagt tggaaacgac tgctaatacc 180 gcataacgtg tcgaggaggc atctctttga caccaaagat ttatc 225 <210> 263 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Desulfotomaculum <400> 263 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 actg tgaaggagtt cttcggaacg aatttatttt aacctagtgg cggacgggcg 120 agtaacgcgt cctg cccataagag ggggataaca cagagaaatt tgtgctaata 180 ccgcatattg aagtatttct gcatggagat gctttgaaag attta 225 <210> 264 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Streptophyta <400> 264 agagtttgat cctggctcag gatgaacgct ggcggcatgc catg caagtcgaac 60 gggaagtggt gtttccagtg gcgaacgggt gcgtaatgcg tgggaatctg ccgaacagtt 120 cgggccaaat cctgaagaaa aagc gctgtttgat gagcctgcgt agtattaggt 180 agttggtcag gtaaaggctg accaagccaa tgatgcttag ctggt 225 <210> 265 <211> 225 Page 92 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acetomicrobium <400> 265 agagtttgat catggctcag gacgaacgct gtgc ctaacacatg caagtcgagc 60 ggggacacgg ggcttcggcc ctgtgttcta gcggcggacg ggtgagtaac gcgtgaacaa 120 tctgtcccag acagggggat aacaactgga aacagttgct aataccgcat aagaccacgg 180 atgg ggctggggta aaagtgggaa cacggtttgg ggtga 225 <210> 266 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from obacter <400> 266 agagtttgat catggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 ggggaagggt ctac ctgacctagc ggcggacggg tgagtaatgc ttaggaatct 120 gcctattagt caac attccgaaag gaatgctaat accgcatacg ccctacgggg 180 gaaagcaggg gatcttcgga ccttgcgcta atagatgagc ctaag 225 <210> 267 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Erysipelotrichaceae incertae sedis <400> 267 agagtttgat catggctcag gatgaacgct ggcggcatgc ctaatacatg caagtcgaac 60 gaagtttcga ttgc ttccaaagag acttagtggc gaacgggtga gtaacacgta 120 ctgc ccatgtgtcc gggataactg ctggaaacgg tagctaaaac cggataggta 180 tacagagcgc atgctcagta tattaaagcg cccatcaagg cgtga 225 Page 93 747203 ‐ Sequence Listing.txt <210> 268 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Jeotgalicoccus <400> 268 agagtttgat cctggctcag gatgaacgct gtgc catg caagtcgagc 60 gcgaagatca tgct cctgagattc gagcggcgga cgggtgagta acacgtaggc 120 aacctaccct tgagattggg ataactaccg gaaacggtag ctaataccgg atacgacatt 180 cctgcataag taagaatgtt aaaaggcgga tttatctgcc gctca 225 <210> 269 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Selenomonas <400> 269 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gagacgattt agaagcttgc ttttattgag tcgagtggca aacgggtgag gtag 120 acaacctgcc gcaaagatgg ggacaacagt ccgaaaggac tgctaatacc gaatgttgta 180 tctcctccgc gaga tattaaagat ggcctctact tgtaa 225 <210> 270 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Howardella <400> 270 tgat cctggctcag gatgaacgct ggcggcgtgc catg caagtcgaat 60 gtagtttact acatggcgga cgggtgagta acgcgtgagc aatctgccca tatctggggg 120 ataacagttg gaaacgactg ataataccgc ataatattgt ttgaaggcat cttcttacaa 180 tcaaagattt atcggatatg gatgagctcg cgtctgatta gctag 225 Page 94 747203 ‐ Sequence Listing.txt <210> 271 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 271 agagtttgat cctggctcag cgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagttatgc tgaaaccagg cggtgcttgc actgccttgt gatgaataac ttagtggcgg 120 acgggtgagt tggg caacctgccc cacacagggg gataacactt agaaataggt 180 gctaataccg cataagcgca cagcttcgca tgaagcagtg tgaaa 225 <210> 272 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 272 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 atat agatgatttc ggtctgaaat atatcatagt ggcggacggg acgc 120 gtggataacc tgccccgtac tgggggatag cagctggaaa cggctggtaa taccgcataa 180 gcgcacgagg gggcctcccc ttgtgtgaaa atcg gtacg 225 <210> 273 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 273 agagtttgat tcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 gggactattt agagatgttt tcggactgat ctttttagtt tagtggcgga cgggtgagta 120 acgcgtggac aacctgcctt tcacaggggg atagcagctg gaaacggctg gtaataccgc 180 Page 95 747203 ‐ Sequence Listing.txt atacgctcaa gcat ggtgtgatga ggaaagattt atcgg 225 <210> 274 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 274 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggttaaga gaaattttcg gatggacctt aacttagtgg cggacgggtg agtaacgcgt 120 ggataacctg cctcacacag ggggatagca gctggaaacg gctggtaata ccgcataaga 180 cccc gcatggagct gtagtaaaag atttatcggt gtgag 225 <210> 275 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 275 agagtttgat catggctcag gatgaacgct gtgc ctaacacatg caagtcgaac 60 gaagcacttc tggtttgaga ttcgtcaaga accggatttg acttagtggc ggacgggtga 120 gtaatgtatg agcaacctgc ctttcagagg gggacaacag acga ctgctaatac 180 cgcataatgt attttaaggg catccttgga aagg agcaa 225 <210> 276 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 276 agagtttgat catggctcag cgct ggcggcgtgc ctaatacatg caagtcgagc 60 ggatgaagaa gagcttgctc tttggattca gcggcggacg ggtgagtaac acgtgggcaa 120 Page 96 747203 ‐ Sequence Listing.txt cctgcctgta ggat aacttcggga aaccggagct aataccggat aaaaactttc 180 ttcacatgaa ggaaggataa gttt tgctgtcact tacag 225 <210> 277 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Paenibacillus <400> 277 agagtttgat catggctcag gacgaacgct ggcggcgtgc catg caagtcgagc 60 ggagttactt tgaaagcttg ctttcaaagt aacttagcgg cggacgggtg agtaacacgt 120 aggcaacctg cccctcagac tgggataact accggaaacg gtagctaata ccggataatt 180 tcttttttct cctgagagaa gaatgaaaga cggagcaatc tgtca 225 <210> 278 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Eubacterium <400> 278 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggttaagg ttcg gatggaactt aacttagtgg cggacgggtg agtaacgcgt 120 ggataacctg cctcacactg ggggatagca aacg gctggtaata ccgcataaga 180 ccacagcacc gcatggtgca ggggtaaaag atttatcggt gtgag 225 <210> 279 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Amphibacillus <400> 279 agagtttgat cctggctcag cgct ggcggcgtgc ctaatacatg caagtcgagc 60 Page 97 747203 ‐ ce Listing.txt gcgtgaagct taactgatct cttcggagtg acgttaagtg gatcgagcgg cggatgggtg 120 agtaacacgt gggcaacctg cctataagac tgggataact tacggaaacg tgagctaata 180 ccggatgaaa ccttttgtca cctggcaaaa ggatgaaagg tggct 225 <210> 280 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Staphylococcus <400> 280 agagtttgat cctggctcag gatgaacgct ggcggcatgc ctaagacatg caagtcgaac 60 gggatggccc actgatagtt gttt ggagagcttg ctcaaagaat ggaaaaagct 120 tgacgtggat tttccatcca gtggcagacg ggtgagtaac gtaa cctaccccag 180 ggat aactgttgga agct aataccggat aaacc 225 <210> 281 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Paenibacillus <400> 281 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 attt tgaaagcttg ctttcaaaat aacttagcgg cggacgggtg agtaacacgt 120 aggcaacctg cccctcagac tgggataact accggaaacg gtagctaata ccggataatt 180 tcttttttct cctgagagaa gaatgaaaga aatc tgtca 225 <210> 282 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV Page 98 747203 ‐ Sequence g.txt <400> 282 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagttgagg agcttgctcc ttaacttagt ggcggacggg tgagtaacgc gtgagtaacc 120 tgcctctgag ataa cgttctgaaa aggacgctaa taccgcataa cacatatttg 180 ccgcatgaca gatatgtcaa agattttatc agat ggact 225 <210> 283 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from ella <400> 283 agagtttgat cctggctcag gatgaacgct agctacaggc ttaacacatg caagtcgagg 60 ggcagcatga agtttgcttg caaactttga tggcgaccgg cgcacgggtg agtaacgcgt 120 atccaacctt ccctatacta gaggatagcc cggcgaaagt cggattaata ctctatgttc 180 ttcgtagaag acatctgaaa tgaagcaaag gtttaccggt atagg 225 <210> 284 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Barnesiella <400> 284 agagtttgat cctggctcag gatgaacgct agcgacaggc ttaacacatg caagtcgagg 60 ggcagcgcgg aggtagcaat acttctggcg gcgaccggcg cactggtgag taacacgtat 120 gcgacctgcc aggg ggataaaccc gggaaactgg gcctaatacc ccataagtat 180 cgaggatgca tgat atgaaagatc cgtcggtccg ggatg 225 <210> 285 <211> 225 <212> DNA <213> Unknown <220> Page 99 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Clostridium XlVa <400> 285 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagatgagt tgatattttc ggatggatac tagt ggcggacggg tgagtaacgc 120 gtggataacc tgcctcgtac tgggggatag cagctggaaa cggctggtaa taccgcataa 180 gcgcacgatg ccgcatggca atgtgtgaaa agatttatcg gtacg 225 <210> 286 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XlVa <400> 286 agagtttgat catggctcag gacgaacgct gtgc ttaacacatg caagtcgaac 60 gaggatcatt agag cttcggcagg attttgaatg attcgagtgg cggacgggtg 120 agtaacgcgt gagcaatctg tcccagacag gggaataaca cttggaaaca ggtgctaata 180 ccgcataaga ccacagtatc gcatggtaca ggggtaaaag gagga 225 <210> 287 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sharpea <400> 287 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaatacatg ggac 60 ggagcgcttc cagt ggcgaacggg tgagtagcac atgggcaacc tgcccttcag 120 agggggacaa cagctggaaa cggctgctaa gaccgcatag gcgcggacgg ccgt 180 ccacgttaaa cgtcctttcg gggacggctg aaggatgggc ctgtg 225 <210> 288 <211> 225 <212> DNA <213> Unknown Page 100 747203 ‐ Sequence Listing.txt <220> <223> Encodes 16S rRNA from spiracea incertae sedis <400> 288 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 ggagtcataa gttgattctt cggatgattt ttatgactta gcggcggatg ggtgagtaac 120 acgtgggtaa tctgccctgc acagggggat tgga aacggctgtt aataccgcat 180 atgcacacgt tatcgcatga tagagtgtgg aaagatttat cggtg 225 <210> 289 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Leucobacter <400> 289 agagtttgat tcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagctc ccagcttgct gggggtggat gagtggcgaa cgggtgagta acacgtgagt 120 aacctgcccc gaactctggg ataagcgctg gaaacggcgt ctaatactgg atatgtccta 180 tcaccgcatg gtgtgtaggt ggaaagaatt ttggttcggg atgga 225 <210> 290 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactonifactor <400> 290 agagtttgat tcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaggttaatt gagcggatta tatg aagcgctttt aactgagtgg cggacgggtg 120 agtaacgcgt gggcaacctg cctcattcag ggggatacca aacg actgttaata 180 ccgcataagc gcacggttcc gcatggaaca gtgtgaaaag ctccg 225 <210> 291 <211> 225 Page 101 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 291 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg gaac 60 gaagcacttc tgaacggaga ttcgtcaaag tttggatttg acttagtggc ggacgggtga 120 gtaatgtatg agcaacctgc ctttcagagg gggacaacag ttggaaacga ctgctaatac 180 cgcataatgt attttggggg tgga ataccaaagg agcaa 225 <210> 292 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Succiniclasticum <400> 292 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggattttg tttcggcaga atcctagtgg cgaacgggtg agtaacgcgt aggcaacctg 120 ccctccggcc aaca ctccgaaagg aata ccggatacga tgcc 180 gcatggtacg gatttgaaag atggcctcta tttataagct atcgc 225 <210> 293 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acidovorax <400> 293 agagtttgat cctggctcag attgaacgct ggcggcatgc cttacacatg caagtcgaac 60 ggtaacagct cttcggaggc tgacgagtgg cgaacgggtg agtaatacat cggaacgtgc 120 ccgatcgtgg gggataacgg agcgaaagct ttgctaatac cgcatacgat ctacggatga 180 aagcagggga ccctcgggcc ttgcgcgaac ggagcggccg atggc 225 Page 102 747203 ‐ Sequence Listing.txt <210> 294 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Acinetobacter <400> 294 agagtttgat cctggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 ggggaaaggt agcttgctac ctaacctagc ggcggacggg tgagtaatgc ttaggaatct 120 tagt gggggacaac attccgaaag gaatgctaat accgcatacg ccctacgggg 180 gaaagcaggg gatcttcgga ccttgcgcta atagatgagc ctaag 225 <210> 295 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Comamonas <400> 295 agagtttgat cctggctcag gacgaacgct atgc tttacacatg caagtcgaac 60 ggcagcacgg acttcggtct ggtggcgagt ggcgaacggg atac acgt 120 gcccagttgt gggggataac tactcgaaag agtagctaat accgcatgag aactgaggtt 180 gaaagcaggg gatcgtaaga ccttgcgcaa cggc cgatg 225 <210> 296 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Prevotella <400> 296 agagtttgat cctggctcag gatgaacgct agctacaggc ttaacacatg caagtcgagg 60 ggcagcatga tcgaagcttg ctttgattga tggcgaccgg cgcacgggtg agtaacgcgt 120 atccaacctt ccctgtagta gagaatagcc cggcgaaagt cggattaatg ctctatgttg 180 gatg acatctgaag aataccaaag gtttaccgct atagg 225 Page 103 747203 ‐ Sequence Listing.txt <210> 297 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium IV <400> 297 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggagtcaaga agcttgcttt ttgacttagt ggcggacggg tgagtaacgc gtgagtaacc 120 tgag aggggaataa cgttctgaaa agaacgctaa taccgcataa cgtatcgaag 180 ccgcatgact ttgataccaa agattttatc agat ggact 225 <210> 298 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 298 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 gagagaatct tgca ccagaggatc tagcggcgga cgggtgagta acacgtgggc 120 aacctgccct aaggagggga ataacaggcc gaaaggtctg ctaataccgc ataatatctt 180 gcat ggagaaaaga attt atcgccttag gatgg 225 <210> 299 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Succiniclasticum <400> 299 agagtttgat catggctcag gacgaacgct ggcggcgtgc catg caagtcgaac 60 ggggattttg tttcggcaga atcctagtgg cgaacgggtg agtaacgcgt aggcaacctg 120 ccctccggcc ggggacaaca ctccgaaagg ggtgctaata ccggatacga agtctgtgcc 180 Page 104 747203 ‐ Sequence Listing.txt gcatggtacg gatttgaaag atggcctctg tttacaagct atcgc 225 <210> 300 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 300 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgaac 60 ggggctgttt gaaagatctt ttcggagtga tttcttacag ggcg gacgggtgag 120 taacgcgtgg ataacctgcc tttcacaggg ggatagcagc tggaaacggc tggtaatacc 180 gcatacgctc ccgc atgatcttaa gaggaaagat ttatc 225 <210> 301 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Pedobacter <400> 301 agagtttgat cctggctcag gatgaacgct agcggcaggc ctaatacatg caagtcgaac 60 gcgattgcgg tgcttgcacc aagt ggcgtacggg tgcgtaacgc gtgagcaacc 120 taccgttgtc tgggggatag cccggagaaa tccggattaa taccgcataa tattagagag 180 cagcattgct ttctgatcaa atgg gacagcgatg ggctc 225 <210> 302 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from idium XII <400> 302 agagtttgat tcag cgct ggcggcgtgc ctaacacatg caagtcgagc 60 gagaaagtct ttacggatcc ttcgggtgaa agaatgactg gacagcggcg gacgggtgag 120 Page 105 747203 ‐ Sequence Listing.txt taacgcgtgg gaaaccttcc aaag ggatagcctc gggaaaccgg gattaatacc 180 ttatgaaact ctagtaccgc atggtacatg agtcaaaact ccggt 225 <210> 303 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Flavobacterium <400> 303 tgat cctggctcag gatgaacgct agcggcaggc ctaacacatg caagtcgagg 60 ggtagagtta taac ttgagaccgg cgcacgggtg cgtaacgcgt atgcaatcta 120 actg agggatagcc cggagaaatc cggattaata ccttatagta tattaaagtg 180 gcatcatttt gatattaaag atttattggt ataagatgag catgc 225 <210> 304 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from idium sensu stricto <400> 304 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg gagc 60 gaggagattc ccttcgggga tgaacctagc ggcggacggg tgagtaacac gtgggcaacc 120 tgccttgtag aggggaatag ccttccgaaa ggaagattaa taccgcataa cattgcttta 180 tcgcatgata aagtaatcaa aggagcaatc cgctacaaga tgggc 225 <210> 305 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Alkaliphilus <400> 305 tgat cctggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 Page 106 747203 ‐ Sequence Listing.txt ggagatgaag aagtttactt ctgattctta gcggcggacg ggtgagtaac gcaa 120 cctaccctgt acagggggat aacaatggga aaccattgct ccat aacgcctttg 180 aggggcatcc cttaaaggtc aaagaatttc ggtacaggat gggcc 225 <210> 306 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Arthrobacter <400> 306 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgaagcct agcttgctgg gtggattagt ggcgaacggg tgagtaacac gtgagtaacc 120 tgcccctgac ttcgggataa gcctgggaaa ctgggtctaa atat cacttcctgc 180 cgcatggtgg gtggttgaaa gatttatcgg ttggggatgg actcg 225 <210> 307 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Flavobacterium <400> 307 agagtttgat cctggctcag gatgaacgct agcggcaggc ctaacacatg caagtcgagg 60 ggtagagtta gcttgctaac ttgagaccgg cgcacgggtg gcgt atgcaatcta 120 ccttatactg agggatagcc cggagaaatc aata ccttatagtt aataaaaaag 180 gcatctttta tattataaag atttattggt tgag catgc 225 <210> 308 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Roseburia Page 107 747203 ‐ Sequence Listing.txt <400> 308 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaagcactta agcggatccc ttcggggtga agcttaagtg acttagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcatacagg gggataacag ttggaaacga ctgctaagac 180 cgcataacaa gaaggaaccg catgatttct tcttcaaata tttat 225 <210> 309 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from acillus <400> 309 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 ggagttcctt tgaaagcttg ctttcaaagg aacttagcgg cggacgggtg acgt 120 cctg agac tgggataact accggaaacg gtagctaata ccggataatt 180 tcttttttct cctgagagaa gaatgaaaga cggagcaatc tgtca 225 <210> 310 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Olivibacter <400> 310 agagtttgat cctggctcag gatgaacgct agcggcaggc ctaatacatg caagtcggac 60 gggattgcag tatagcttgc tatactgcat gagagtggcg cacgggtgcg taacgcgtga 120 gcaacctgcc catgtcaggg cccg ttgaaagacg tacc gcataacaca 180 tagagaccac ctggtttcta tgtcaaatat ttataggaca tggat 225 <210> 311 <211> 225 <212> DNA <213> Unknown <220> Page 108 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Clostridium XII <400> 311 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gagaaagtcg ttacggatcc ttcgggtgaa agaatgactg ggcg tgag 120 taacgcgtgg gaaaccttcc ttatacaaag ggatagcctc gggaaaccgg gattaatacc 180 ttatgaaact ctagtaccgc catg agtcaaaact ccggt 225 <210> 312 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Sphingobacterium <400> 312 agagtttgat cctggctcag gatgaacgct agcggcaggc ctaatacatg caagtcggac 60 gggatccggg ttgc tacttccggt gagagtggcg cacgggtgcg taacgcgtga 120 gcaacctgcc catatcaggg ggatagcccg gagaaatccg gattaacacc gcatgacacg 180 ccgggacggc ccgg cgtcaaatat tcataggata tggat 225 <210> 313 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Sphingobacterium <400> 313 agagtttgat cctggctcag gatgaacgct agcggcaggc ctaatacatg caagtcggac 60 gggatccgtc ggagagcttg ctcgaagacg gtgg cgcacgggtg cgtaacgcgt 120 gagcaaccta cctctatcag ggggatagcc tctcgaaaga gagattaaca ccgcataaca 180 tatctgaccg gcatcggtta gctattaaat atttatagga tagag 225 <210> 314 <211> 225 <212> DNA <213> Unknown Page 109 747203 ‐ Sequence g.txt <220> <223> Encodes 16S rRNA from Anaerosporobacter <400> 314 agagtttgat catggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaagcactta agcggatccc ttcggggtga agcttaagtg acttagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcatacagg gggataacag ttggaaacga agac 180 cgcataaaac agtagtgtcg catgacacaa ctgtcaaata tttat 225 <210> 315 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XII <400> 315 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaagttttca aagcagattt cttcggattg aagttttgat agcg gcggacgggt 120 gagtaacgcg tgagaaacct gcctttcaca aagggatagc aaac taat 180 accttatgat actaattctt cgcatgaaga attagtcaaa gcgta 225 <210> 316 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium XII <400> 316 agagtttgat cctggctcag gacgaacgct ggcggcgtgc catg caagtcgagc 60 gaagttttca aagttgattt cttcggaatg aaactttgat tatcttagcg gcggacgggt 120 gagtaacgcg tgagaaacct gcctttcaca aagggatagc ctcgggaaac tgggattaat 180 accttatgat tctt cacatgaagg aatagtcaaa gcgta 225 <210> 317 <211> 225 Page 110 747203 ‐ Sequence Listing.txt <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 317 agagttatca agga cgaacgctgg cggcgtgcct aacacatgca agtcgagcga 60 ggggagtttc ttcggaaaca aacctagcgg cggacgggtg acgt gggcaacctg 120 ccttgtagag gggaatagcc ttccgaaagg aagattaata ccgcataaca ttgcactttc 180 gcatgagaga aaag gagtaatccg ctacaagatg ggccc 225 <210> 318 <211> 225 <212> DNA <213> n <220> <223> s 16S rRNA from Pedobacter <400> 318 agagtttgat catggctcag gatgaacgct agcggcaggc ctaatacatg caagtcgagg 60 ggtatgggtt gcttgcaacc cagagaccgg cgcacgggtg cgtaacgcgt atgcaatcta 120 ccttaatcag ggggatagcc cggagaaatc cggattaaca ccgcataaca ttaagtaatg 180 gcatcattat ttaatcaaat atttatagga tgag catgc 225 <210> 319 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus <400> 319 agagtttgat cctggctcag gacgaacgct gtgc ctaatacatg caagtcgagc 60 ggattgtgag agaagcttgc ttctcccaca gttagcggcg gacgggtgag taacacgtgg 120 gcaacctgcc tgtaagatcg ggataacttc gggaaaccgg agctaatacc ggataggcga 180 ttttactgca tggtagaatc gagaaagatg ctaaggcatc actta 225 Page 111 747203 ‐ Sequence Listing.txt <210> 320 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Paenibacillus <400> 320 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 ggagttattt tgaaagcttg ctttcgaaat aacttagcgg cggacgggtg agtaacacgt 120 cctg cccctcagac aact accggaaacg gtagctaata ccggataatt 180 ttct cctgaagaaa gaatgaaaga cggagcaatc tgtca 225 <210> 321 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Prevotella <400> 321 agagtttgat catggctcag gatgaacgct agctccaggc ttaacacatg caagtcgagg 60 ggcagcaggg agatagcttg ctatctttgc tggcgaccgg cgcacgggtg agtaacgcgt 120 atccaacctt ccccttacta aggaatagcc cggcgaaagt cggattaatg ccttatgttc 180 tcctttgcag gcatctaacg aggagcaaag attcatcggt aaggg 225 <210> 322 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 322 agagtttgat cctggctcag cgct ggcggcgtgc ctaacacatg caagtcgaac 60 gggactattc tgagatgttt tcggactgat ctaaatagtt tagtggcgga cgggtgagta 120 ggac aacctgcctt tcacaggggg atagcagctg gaaacggctg gtaataccgc 180 tcag tgcaccgcat ttga ggaaagattt atcgg 225 Page 112 747203 ‐ Sequence Listing.txt <210> 323 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from spiracea incertae sedis <400> 323 tgat cctggctcag gatgaacgct gtgc ctaacacatg caagtcgaac 60 gggactattt agagatgttt tcggactgat ctttttagtt tagtggcgga cgggtgagta 120 acgcgtggac aacctgcctt gggg atagcagctg gaaacggctg gtaataccgc 180 atacgctcag tgcaccgcat ggtgtgctga ggaaagattt atcgg 225 <210> 324 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Escherichia/Shigella <400> 324 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctc ccagcttgct gggggtggat gagtggcgaa agta tcacgtgagt 120 aacctgccct taactctggg ataagcccgg gaaactgggt ctaatactgg ataggactga 180 tcatcgcatg gtggttggtt gaaagttttt gacggttttg gatgg 225 <210> 325 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 325 tgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcggaact aacagattta cttcggtaat gacgttagga aagcgagcgg cggatgggtg 120 cattagctag ttggtaaggt aaaggcttac caaggcgatg atgcatagcc gagttgagag 180 Page 113 747203 ‐ Sequence Listing.txt actgatcggc cacattggga ctgagacacg gcccaaactc ctacg 225 <210> 326 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Corynebacterium <400> 326 agagtttgat tcag gatgaacgct ggcggcgtgc catg gaac 60 ggggttaaga ttcg gatggatctt aacttagtgg cggacgggtg agtaacgcgt 120 ggataacctg cctcacacag ggggatagca gctggaaacg gctggtaata ccgcataaga 180 ccacggcccc gcatggagct gtagtaaaag atttatcggt gtgag 225 <210> 327 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 327 agagtttgat catggctcag aacgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 gggcatcttc gggtgtcagc ggcggacggg ttagtaacgc gtgggaacgt gccctttgct 120 tcggaatagc cccgggaaac tgggggtaat accggatgtg ccctgagggg gaaagattta 180 tcggcaaggg atcggcccgc gtctgattag gtagttggtg tggta 225 <210> 328 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lactobacillus <400> 328 agagtttgat tcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcggaaag cgagcggcgg atgggtgagt aacacgtggg gaacctgccc catagtctgg 120 Page 114 747203 ‐ Sequence g.txt gataccactt ggaaacaggt gctaataccg gataagaaag cagatcgcat gatcagcttt 180 taaaaggcgg cgtaagctgt cgctatggga tggccccgcg gtgca 225 <210> 329 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Escherichia/Shigella <400> 329 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgacgatg gtgcttgcac cgtctgatta gtggcgaacg ggtgagtaac acgtgagtaa 120 ctcc tcttcgggat aaccgccgga aacggtggct aataccggat atgaatgcct 180 gccgcatggt gggtgttgga aagatttatc ggtgggggat ggact 225 <210> 330 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 330 agagtttgat catggctcag attgaacgct ggcggcaggc ttaacacatg caagtcgagc 60 ggggagaagg tagcttgcta ctggaaccta gcggcggacg ggtgagtaat gaat 120 ctgcctatta gtgggggaca acgttccgaa aggagcgcta ataccgcata cgccctacgg 180 gcag gggatcactt gtgaccttgc gctaatagat gagcc 225 <210> 331 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 331 agagtttgat cctggctcag cgct gtgc ctaacacatg caagtcgagc 60 Page 115 747203 ‐ Sequence Listing.txt gaagttttta attt cttcggaatg taat tatcttagcg gcggacgggt 120 gagtaacgcg tgagaaacct gcctttcaca aagggatagc ctcgggaaac tgggattaat 180 accttatgac acttaaattt cgcatggaaa ataagttaaa gcgta 225 <210> 332 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 332 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gagacgattt taagcttgct tagatgagtc gagtggcaaa cgggtgagta acgcgtagac 120 aacctgccgc aaagatgggg gtcc gaaaggactg ctaataccga atgttgtcag 180 tttctcgcat ttga ttaaagatgg cctctacttg taagc 225 <210> 333 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 333 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 aact aacagattta cttcggtaat gacgttagga aagcgagcgg cggacgggtg 120 gtgt gggcaacctg cctcacacag ggggataaca gttagaaatg aata 180 ccgcataaga ccacggcacc gcatggtgca ggggtaaaaa ctctg 225 <210> 334 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Page 116 747203 ‐ Sequence Listing.txt <400> 334 agagtttgat tcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaagctc tgct ggat gagtggcgaa cgggtgagta acacgtgagt 120 aacctgcccc gaactctggg gctg gaaacggcgt ctaatactgg atatgtccta 180 tcaccgcatg gtgtgtaggt ggaaagaatt ttggttcggg atgga 225 <210> 335 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus <400> 335 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgatgccc agcttgctgg gcggattagt ggcgaacggg tgagtaatac gtgagtaacc 120 tgcccttgac tctgggataa gcctgggaaa ctgggtctaa tactggatac taccgtccac 180 cgcatggtgg gtggtggaaa gggttttact ggttttggat gggct 225 <210> 336 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 336 agagtttgat tcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgatgctg gtgcttgcac tggtggatta gtggcgaacg ggtgagtaac acgtgagtaa 120 cctgcccctg acttcgggat aagcccggga aactgggtct aataccggat atgacttcct 180 gctgcatggc agggggtgga aagatttatc ggttggggat ggact 225 <210> 337 <211> 225 <212> DNA <213> Unknown <220> Page 117 747203 ‐ Sequence Listing.txt <223> Encodes 16S rRNA from Enterococcus <400> 337 agagtttgat cctggctcag gacgaacgct ggcggcgtgc catg caagtcgaac 60 gcttctttcc tcccgagtgc ttgcactcaa ttggaaagag gagtggcgga cgggtgagta 120 gggt ccca tcagaggggg ataacacttg gaaacaggtg ctaataccgc 180 ataacagttt atgccgcatg gcataagagt gaaaggcgct ttcgg 225 <210> 338 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 338 agagtttgat cctggctcag cgct ggcggcgtgc ttaacacatg caagtcgaac 60 gctgaaacca gagcttgctt tggtggatga gtggcgaacg ggtgagtaac acgtgggtga 120 tctgccctac actttgggat aagcctggga aactgggtct aataccgaat acca 180 ccgtaggggt ggtgtggaaa gctttatgcg gtgtgggatg agcct 225 <210> 339 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Streptococcus <400> 339 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtggaac 60 gcatgattga taccggagct tgctccacca ttaatcatga gtcgcgaacg ggtgagtaac 120 gcgtaggtaa cctacctcat agcgggggat aactattgga aacgatagct aataccgcat 180 aagagtggat tgtt attgatttaa aaggagcaat tgctt 225 <210> 340 <211> 225 <212> DNA <213> Unknown Page 118 747203 ‐ ce g.txt <220> <223> Encodes 16S rRNA from Lactobacillus <400> 340 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gagaatttct gagt gcttgcactc accgtaagaa attcgagtgg cggacgggtg 120 agtaacacgt gggtaacctg cccaaaagaa ggggataaca tttggaaaca aatgctaata 180 aacc atgatgaccg catt atgtaaaagg tggtt 225 <210> 341 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 341 tgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggtaaggccc cagcttgctg gggtacacga gtggcgaacg ggtgagtaac acgtgggtga 120 ccgc acttcgggat aagcctggga aactgggtct aataccggat aggaccgcac 180 cgtgagggtg tggtggaaag tttttcggtg tgggatgggc ccgcg 225 <210> 342 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Peptostreptococcaceae (Clostridium Cluster <400> 342 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gatcttcttc ggaagagagc ggcggacggg tgagtaacgc gtgggtaacc tgccctgtac 120 acacggataa cataccgaaa ggtatgctaa tacgagataa tatgctttta tcgcatggta 180 gaagtatcaa agctccggcg gtacaggatg gacccgcgtc tgatt 225 <210> 343 Page 119 747203 ‐ Sequence Listing.txt <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 343 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gccc ttgcttgcag gggtactcga gtggcgaacg ggtgagtaac acgtgggtga 120 tctgccttgt acttcgggat aagcctggga aactgggtct aataccggat aggaccatgc 180 tttagtgtgt gtggtggaaa gttttttcgg tacaagatga gcccg 225 <210> 344 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Corynebacterium <400> 344 agagtttgat tcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggaaaggcct gtac aggtgctcga gtggcgaacg ggtgagtaac acgtgggtga 120 tctgccctgc actgtgggat aagcccggga aactgggtct aataccatat aggaccactt 180 cttggatgtt gaaa gcttttgcgg tgtgggatga gcctg 225 <210> 345 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiraceae (Clostridium Cluster XlVa) <400> 345 agagtttgat catggctcag gatgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaagcgattc ggatgaagtt ttcggatgga ttttggattg actgagcggc gtga 120 gtaacgcgtg ggtaacctgc ctcatacagg gggataacag atga ctgctaatac 180 cgcataagcg cacagtaccg catggtacgg tgtgaaaaac tccgg 225 Page 120 747203 ‐ Sequence Listing.txt <210> 346 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from spiracea incertae sedis <400> 346 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 gaagcactta cttttgattt cttcggaatg acgaggtctg tgacttagcg gcggacgggt 120 gagtaacgcg tgggcaacct caca taac agttagaaat gactgctaat 180 accgcataag accccggcac cgcatggtgc aggggtaaaa actcc 225 <210> 347 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Ruminococcaceae (Clostridium Cluster III) <400> 347 agagtttgat cctggctcag gacgaacgct ggcggcgtgc catg caagtcgagc 60 ggagatgttc ggagtgcttg cacactgaac atttcagcgg cggacgggtg agtaacgcgt 120 gaacaatctg tcccatacag ggggataaca aaca tctgctaata ccgcataaga 180 ccacgacatc acatgatgat aaag gagcaatccg gtatg 225 <210> 348 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 348 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gaactctggt attgattggt gcttgcatca tgatttacat ttgagtgagt ctgg 120 tgagtaacac gtgggaaacc tgcccagaag cgggggataa cacctggaaa cagatgctaa 180 Page 121 747203 ‐ Sequence Listing.txt ataa caacttggac gtcc gagtttgaaa gatgg 225 <210> 349 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Streptococcus <400> 349 agagtttgat cctggctcag gacgaacgct gtgc ctaatacatg caagtagaac 60 gctgaagaaa ggagcttgct tcttttggat gagttgcgaa cgggtgagta acgcgtaggt 120 aacctgcctt gtagcggggg ataactattg atag ctaataccgc ataacagctt 180 ttgacacatg ttagaagctt gaaagatgca attgcatcac tacga 225 <210> 350 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lachnospiraceae (Clostridium Cluster XlVa) <400> 350 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg gaac 60 gaagcggctg gacggaagtt ttcggatgga agaccggctg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc cgtatacagg gggataacag agagaaattt atac 180 cgcataagcg cacgaagacc gcatggtccg gtgtgaaaag ccgag 225 <210> 351 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 351 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcagaacc agcagattta cttcggtaat gacgctgggg acgcgagcgg cggatgggtg 120 Page 122 747203 ‐ Sequence Listing.txt agtaacacgt ggggaacctg ccccatagtc tgggatacca cttggaaaca ggtgctaata 180 ccggataaga aagcagatcg catgatcagc aagg cggcg 225 <210> 352 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Paracoccus <400> 352 agagtttgat cctggctcag aacgaacgct ggcggcaggc ctaacacatg caagtcgagc 60 ttcg gggttagcgg cggacgggtg agtaacgcgt gggaatatgc ccttctctac 120 ggaatagtct cgggaaactg ggggtaatac cgtatacgcc ctttggggga tatc 180 ggagaaggat tagcccgcgt tggattaggt agttggtggg gtaat 225 <210> 353 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Cellulosilyticum <400> 353 agagtttgat catggctcag gacgaacgct ggcggcgcgc ctaacacatg caagtcgaac 60 gaagctatgt cttg ctggatatat agcttagtgg cggacgggtg agtaacacgt 120 gagtaacctg cctctcagag tggaataacg aacg gacgctaata ccgcataacg 180 tgagaagagg gcatcctctt tttaccaaag atttatcgct gagag 225 <210> 354 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Blautia <400> 354 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 Page 123 747203 ‐ Sequence Listing.txt ggggaatatt ctgacagaga cttcggttga agtcgttata ttcctagtgg cggacgggtg 120 gcgt gggtaacctg ccccacacag ggggataaca accagaaatg gctgctaata 180 ccgcataagc gacc gcatggtttt aaaa ctccg 225 <210> 355 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 355 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 ggaaaggccc ctagcttgct gggggtactc gagtggcgaa agta acacgtgggt 120 gatctgccct gcacttcggg ataagcttgg gaaactgggt ctaataccgg atatgaacgg 180 tctttggtgt gattgttgga aagatttttt cggtgtggga tgagc 225 <210> 356 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lachnospiracea incertae sedis <400> 356 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 agaa gatttcggtt ttctttgtta gtggcggacg ggtgagtaac gcgtgggcaa 120 cctaccttat acagggggat aacagttaga aatgactgat aataccgcat aagcgcccga 180 ggtcgcatga ccttgagtga aaaactccgg aaga tgggc 225 <210> 357 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 357 Page 124 747203 ‐ Sequence Listing.txt agagtttgat cctggctcag gacgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gatgaagctt ctag gtggattagt ggcgaacggg tgagtaacac gtaggtaatc 120 tgccctgcac tttgggataa gcctgggaaa ctgggtctaa taccgaatag gacacactat 180 ctttacggtg gtgtgtggaa agcttttgcg gtgtgggatg agcct 225 <210> 358 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Corynebacterium <400> 358 agagtttgat cctggctcag gatgaacgct ggcggcgtgc catg caagtcgaac 60 ggaaaggcct tgtgcttgca caaggtactc gagtggcgaa cgggtgagta acacgtgggt 120 gatctgccct gcactgtggg ataagcctgg gaaactgggt ccat ataggaccgc 180 actttggatg gtgtggtgga ttgc ggtgtgggat gagcc 225 <210> 359 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Ruminococcus <400> 359 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 taca gacggaagtt ttcggacaga tatg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc cgtatacagg gggataacag ttagaaatgg ctgctaatac 180 cgcataagcg cacagaaccg catggttcgg tgtgaaaagc cgaga 225 <210> 360 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Page 125 747203 ‐ Sequence Listing.txt <400> 360 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcggaacc gacagattca tgat gacgacggga aagcgagcgg cggatgggtg 120 agtaacacgt gggtaaccta cccttaagtc tgggatacca cttggaaaca ggtgctaata 180 ccggatagga attagagctg catggcttta atttaaaagg cggcg 225 <210> 361 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Roseburia <400> 361 agagtttgat catggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaagcacttc agac ttcggtggaa tgagggagtg actgagtggc ggacgggtga 120 gtaacgcgtg ctgc cttacacagg gggataacag ttagaaatga ctgctaatac 180 cgcataagcg accg catggtacag tgtgaaaaac tccgg 225 <210> 362 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from spiracea (Clostridium Cluster XlVa) <400> 362 agagtttgat catggctcag gatgaacgct gtgc ttaacacatg caagtcgaac 60 gaagcgcatg gacagattcc ttcgggttga agaccatgtg acttagtggc ggacgggtga 120 gtaacgcgtg ggtaatctgc cctgcacagg gggataacag acga ctgctaatac 180 cgcataagcc aacagggccg catggcctgg ttggaaaaga tttat 225 <210> 363 <211> 224 <212> DNA <213> Unknown Page 126 747203 ‐ Sequence g.txt <220> <223> Encodes 16S rRNA from Lachnospiracea (Clostridium r XlVb) <400> 363 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgaac 60 gaagaaggtt agaatgagag cttcggcagg atttctatct gtgg cggacgggtg 120 agtaacgtgt gggcaacctg ccctgtactg gggaataatc attggaaacg atgactaata 180 ccgcatgtgg tcctcggaag gcatcttctg aaag gatt 224 <210> 364 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium sensu stricto <400> 364 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaacacatg caagtcgagc 60 gagaagagct ccttcgggag taattctagc ggcggacggg tgagtaacac gtgggcaacc 120 cgccttagtg agggggatag cctcccgaaa gggagattaa taccgcataa cattatttta 180 tcgcatgata gaataatcaa aggagcaatc cgcactaaga tggg 224 <210> 365 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacteroides <400> 365 agagtttgat tcag gatgaacgct agctacaggc ttaacacatg caagtcgagg 60 ggcagcatgg tcttagcttg ctga ccgg cgcacgggtg agtaacacgt 120 atccaacctg ccgtctactc ttggccagcc ttctgaaagg aagattaatc caggatggga 180 tcatgagttc acatgtccgc atgattaaag gtattttccg gtaga 225 <210> 366 <211> 225 <212> DNA Page 127 747203 ‐ Sequence Listing.txt <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 366 agagtttgat cctggctcag gatgaacgcc gtgc ctaatacatg caagtcgtac 60 gcactggccc aactgattga tggtgcttgc accggattga atca ccagtgagtg 120 gcggacgggt gagtaacacg taggtaacct gccccggagc gggggataac atttggaaac 180 agatgctaat accgcataac aacactagac gcatgtctag agttt 225 <210> 367 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 367 agagtttgat cctggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgagc 60 gcactggccc aactgatatt acgtgcttgc actgaattga cgttggatta ccagtgagcg 120 gcggacgggt gagtaacacg tgggcaacct gccctggagc gggggataac atctggaaac 180 taat accgcataac aacaaaagcc acatgacttt tgttt 225 <210> 368 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 368 agagtttgat cctggctcag gatgaacgct gtgc ctaatacatg caagtcgagc 60 gcatcggccc ttga agatgcttgc atccgattga cgatggttta ccgatgagcg 120 gggt gagtaacacg taggtaacct gcccagaagc gggggataac acctggaaac 180 agatgctaat accgcatagg tcatttgacc gcatggtcaa atgat 225 <210> 369 Page 128 747203 ‐ Sequence Listing.txt <211> 224 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lactobacillus (Ascusbbr_5796(B)) <400> 369 tgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcggaact aacagattta cttcggtaat gacgttagga aagcgagcgg cggatgggtg 120 agtaacacgt ggggaacctg agtc tgggatacca aaca ggtgctaata 180 ccggataaga aagcagatcg catgatcagc ttttaaaagg cggc 224 <210> 370 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus (Asbusbbr_5796(C)) <400> 370 agagtttgat cctggctcag gacgaacgct gtgc ctaatacatg caagtcgagc 60 gagcggaact aacagattta cttcggtaat gacgttagga aagcgagcgg cggatgggtg 120 agtaacacgt ggggaacctg ccccatagtc tgggatacca cttggaaaca ggtgctaata 180 ccggataaga aagcagatcg catgatcagc ttttaaaagg cggcg 225 <210> 371 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_14690(B) <400> 371 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gagaatttct tacaccgagt actc accgtaagaa attcgagtgg cggacgggtg 120 agtaacacgt gggtaacctg cccaaaagaa ggggataaca tttggaaaca aatgctaata 180 ccgtataacc accg catt atgtaaaagg tggtt 225 Page 129 747203 ‐ Sequence Listing.txt <210> 372 <211> 225 <212> DNA <213> n <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_14690(C) <400> 372 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg gaac 60 gagaatttct tacaccgagt actc accgtaagaa attcgagtgg cggacgggtg 120 agtaacacgt gggtaacctg cccaaaagaa ggggataaca aaca aatgctaata 180 aacc atgatgaccg catggtcata atgtaaatgg tggtg 225 <210> 373 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_38717(B) <400> 373 tgat cctggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgagc 60 gcactggccc aactgatatg acgtgcttgc actgaattga cgttggatta ccagtgagcg 120 gcggacgggt gagtaacacg tgggcaacct gccctggagc gggggataac atctggaaac 180 aggtgctaat accgcataac aacgaaaacc tttt cgttt 225 <210> 374 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Bacillus Ascusbbr_33(B) <400> 374 agagtttgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 ggacagatgg gagcttgctc cctgatgtta gcggcggacg ggtgagtaac acgtgggtaa 120 cctgcctgta agactgggat aactccggga aaccggggct aataccggat ggttgtctga 180 Page 130 747203 ‐ Sequence Listing.txt accgcatggt tcagacataa aaggtggctt cggctaccac ttaca 225 <210> 375 <211> 224 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_409(B) <400> 375 agagtttgat cctggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgtac 60 gcactggccc aactgattga tggtgcttgc ttga cgatggatca ccagtgagtg 120 gcggacgggt gagtaacacg acct gccccggagc gggggataac atttggaaac 180 taat accgcataac agtc gcatggcttt tgtt 224 <210> 376 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus br_409(C) <400> 376 tgat cctggctcag gatgaacgcc ggcggtgtgc ctaatacatg caagtcgtac 60 gcactggccc aactgattga tggtgcttgc acctgattga cgatggatta ccagtgagtg 120 gcggacgggt gagtaacacg taggtaacct gccccggagc gggggataac atttggaaac 180 taat accgcataac aacaaaagcc acatggcttt tgttt 225 <210> 377 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_409(D) <400> 377 agatttgatc atggctcagg atgaacgccg gcggtgtgcc taatacatgc aagtcgtacg 60 cactggccca actgattgat ggtgcttgca cttgattgac gttggatcac cagtgagtgg 120 Page 131 747203 ‐ ce Listing.txt cggacgggtg agtaacacgt aggtaacctg ccccggagcg ggggataaca tttggaaaca 180 gatgctaata ccgcataaca acaaaagcca catggctttt gtttg 225 <210> 378 <211> 225 <212> DNA <213> Unknown <220> <223> s 16S rRNA from Lactobacillus Ascusbbr_331885(B) <400> 378 agatttgatc ctggctcagg gccg gcggtgtgcc taatacatgc aagtcgtacg 60 cactggccca actgattgat ggtgcttgca ccggattgac gatggatcac cagtgagtgg 120 cggacgggtg agtaacacgt aggtaacctg ccccggagcg ggggataaca tttggaaata 180 gatgctaata ccgcataata gcca catggctttt gtttg 225 <210> 379 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_331885(C) <400> 379 agagtttgat catggctcag gatgaacgcc ggcggtgtgt catg caagtcgtac 60 gcactggccc ttga tggtgcttgc accggattga cgatggatca ccagtgagtg 120 gcggacgggt gagtaacacg taggtaacct gccccggggc gggggataac atttggaaac 180 agatgctaat accgcatgac aacaaaagtc gcatggcttt tgttt 225 <210> 380 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Clostridium Ascusbbr_247(B) <400> 380 agagtttgat cctggctcag gatgaacgct gtgc ctaacacatg caagtcgaac 60 Page 132 747203 ‐ Sequence Listing.txt attt gaaagaagtt ttcggatgga atccaaattg actgagtggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctgg gggacaacag ctggaaacgg ctgctaatac 180 cgcataagcg ttcg catgaagcag tgtgaaaaac tccgg 225 <210> 381 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Chlostridium Ascusbbr_10593(B) <400> 381 agagtttgat catggctcag cgct ggcggcgtgc ctaacacatg caagtcgagc 60 gaagcgattc ggatgaagtt ttcggatgga ttttggattg actgagcggc ggacgggtga 120 gtaacgcgtg ggtaacctgc ctcatacagg gggataacag ttagaaatga ctgctaatac 180 cgcataagcg cacagtaccg catggtacgg tgtgaaaaac tccgg 225 <210> 382 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from ridium Ascusbbr_32731(B) <400> 382 agagtttgat cctggctcag gatgaacgct ggcggcgtgc ttaacacatg caagtcgagc 60 gaagcactta attt cttcggaatg acgaggtatt tgactgagcg gcggacgggt 120 gagtaacgcg tgggcaacct gcctcacaca gggggataac agttagaaat gactgctaat 180 accgcataag accacggcac cgcatggtgc aggggtaaaa actcc 225 <210> 383 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus <400> 383 Page 133 747203 ‐ Sequence Listing.txt tgat cctggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgaac 60 gaaactttct tacaccgaat gcttgcattc accgtaagaa gttgagtggc ggacgggtga 120 cgtg ggtaacctgc gaag gggataacac ttggaaacag gtgctaatac 180 cgtatatctc taaggatcgc atgatcctta gatgaaagat ggttc 225 <210> 384 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus br_42760(B) <400> 384 agagttgatc tggctcagga tgaacgccgg cggtgtgcct tgca agtcgagcgc 60 actggcccaa cagaaatgac gtgcttgcac tgatttgaag ttggattccc agtgagcggc 120 ggacgggtga gtaacacgtg ggcaacctgc cccaaagcgg gggataacat ttggaaacag 180 gtgctaatac cgcataactt ggaaaaccac atggttttcc aataa 225 <210> 385 <211> 225 <212> DNA <213> Unknown <220> <223> Encodes 16S rRNA from Lactobacillus Ascusbbr_265(B) <400> 385 agagtttgat catggctcag gacgaacgct ggcggcgtgc ctaatacatg caagtcgagc 60 gagcagaacc agcagattta cttcggtaat gacgctgggg acgcgagcgg cggatgggtg 120 agtaacacgt ggggaacctg ccccatagtc tgggatacca cttggaaaca ggtgctaata 180 ccggataaga aagcagatcg catgatcagc ttataaaagg cggcg 225 Page 134