WO2022169933A2

WO2022169933A2 - Compositions for gut health

Info

Publication number: WO2022169933A2
Application number: PCT/US2022/015047
Authority: WO
Inventors: Tanja GRUBER; Ryan FRISCH; Felipe Bendezu; Gerda SAXER QUANCE
Original assignee: Dupont Nutrition Biosciences Aps
Priority date: 2021-02-03
Filing date: 2022-02-03
Publication date: 2022-08-11
Also published as: WO2022169933A3

Abstract

Provided herein, inter alia, are compositions of organic acid-producing microorganisms and methods of making and using the same to inhibit pathogenic bacterial populations in the gastrointestinal tracts of an animal and additionally promote improvement of one or more metrics in an animal, such as increased bodyweight gain, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces.

Description

COMPOSITIONS FOR GUT HEALTH

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Patent Application No. 17/166,015, filed February 3, 2021, the disclosure of which is incorporated by reference herein in its entirety.

INCORPROATION BY REFERENCE OF THE SEQUENCE LISTING

[0002] The sequence listing provided in the file named “20220202_NB41585WOPCT[2]_Seq. List_ST25.txt” with a size of 23.7 KB which was created on February 2, 2022 and which is filed herewith, is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

[0003] Provided herein, inter alia, are multi- strain direct fed microbial bacterial consortia useful for improving animal gut health and/or performance as well as methods of making and using the same.

BACKGROUND

[0004] In monogastric animal species such as birds, the gastrointestinal tract and intestinal- associated microflora are not only involved in digestion and absorption but also interact with the immune and central nervous system to modulate health. The inside of the intestinal tract is coated with a thin layer of sticky, viscous mucous, and embedded in this mucus layer are millions and millions of bacteria and other microbes. When the intestinal bacteria are in balance (i.e., the good bacteria outnumber the bad bacteria), the gut is said to be healthy. A healthy microbiota provides the host with multiple benefits, including colonization resistance to a broad spectrum of pathogens, essential nutrient biosynthesis and absorption, and immune stimulation that maintains a healthy gut epithelium and an appropriately controlled systemic immunity. In settings of “dysbiosis” or disrupted symbiosis, microbiota functions can be lost or deranged, resulting in increased susceptibility to pathogens, altered metabolic profiles, or induction of proinflammatory signals that can result in local or systemic inflammation or autoimmunity. Thus, the intestinal microbiota of poultry plays a significant role in the pathogenesis of many diseases and disorders, including a variety of pathogenic infections of the gut such as coccidiosis or necrotic enteritis.

[0005] Over the past several years, there has been increasing governmental and consumer pressure applied to the animal feed industry to decrease or curtail the use of antibiotics as components of animal nutrition feeding regimens. This pressure is due in large part to the recognition that use of such antibiotics contribute to the rise of antibiotic-resistant pathogenic microorganisms. However, this “No Antibiotics Ever” consumer trend, especially in the poultry industry, has led to the re-emergence of bacterial diseases, particularly necrotic enteritis (Poultry Science, Volume 97, Issue 6, 1 June 2018, 1929-1933). Necrotic enteritis is caused by certain toxin-producing Clostridium perfringens strains. Under certain conditions C. perfringens produces toxins which cause lesions in the small intestines and ultimately result in reduced growth or death of the infected birds. Accordingly, there is currently a recognized need for products and methods capable of reducing pathogenic bacterial populations in the digestive tracts of domesticated animals such as birds without the use of traditionally-used antibiotics.

[0006] The subject matter disclosed herein addresses these needs and provides additional benefits as well.

SUMMARY

[0007] Provided herein, inter alia, are multi- strain direct fed microbial bacterial consortia of organic acid-producing microorganisms and methods of making and using the same to inhibit pathogenic bacterial populations in the gastrointestinal tracts of an animal (such as birds, for example, chickens) and additionally promote improvement of one or more metrics in an animal such as increased bodyweight gain, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces.

[0008] In additional aspects, provided herein is a biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267. [0009] In further aspects, provided herein is a biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147268.

[0010] In other aspects, provided herein is a biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147269.

[0011] In another aspect, provided herein is a biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147270.

[0012] In still further aspects, provided herein is a feed additive composition comprising a direct fed microbial (DFM) comprising one or more biologically pure strains of Lactobacillus reuteri selected from the group consisting of (a) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; and (d) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270. In some embodiments, the composition further comprises a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923. In some embodiments, the composition comprises a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at WFDB under number CBS 147267; a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923. In some embodiments of any of the embodiments disclosed herein, the feed additive composition comprises one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); and/or (d) L. reuteri strain S2a (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147270). In some embodiments, the composition further comprises L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 (CBS 145923). In some embodiments of any of the embodiments disclosed herein, the composition produces one or more organic acids selected from the group consisting of lactate, butyrate, isobutyrate, propionate, acetate, isovalerate, and valerate. In some embodiments of any of the embodiments disclosed herein, the feed additive composition further comprises one or more enzymes. In some embodiments, the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase, and a beta-glucanase. In some embodiments of any of the embodiments disclosed herein, the feed additive composition further comprises one or more essential oils. In some embodiments of any of the embodiments disclosed herein, each strain is present at a concentration of at least about 1 x 10³ CFU/g feed additive composition to at least about 1 x 10¹⁵ CFU/g feed additive composition. In some embodiments of any of the embodiments disclosed herein, the composition inhibits at least one pathogen selected from avian pathogenic Salmonella sp., Escherichia coli, Clostridium perfringens and Enterobacteriaceae in a gastrointestinal tract of a bird having ingested an effective amount of said direct fed microbial composition. In some embodiments of any of the embodiments disclosed herein, the composition is formulated for delivery to an animal via waterline.

[0013] In another aspect, provided herein is bacterial consortium comprising one or more of (a) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; (d) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and/or (e) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923.

[0014] In some embodiments, the consortium comprises one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); (d) L. reuteri strain S2b (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2b (CBS 147270);(e) L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 (CBS 145923) either (A) alone; or (B) in combination with a culture supernatant derived from one or more of these strains. In some embodiments of any of the embodiments disclosed herein, a) the 16S ribosomal RNA sequence of L. reuteri strain S1a and S1b comprises the nucleotide sequence of SEQ ID NO:7; (b) the 16S ribosomal RNA sequence of L. reuteri strain S2a and S2b comprises the nucleotide sequence of SEQ ID NO:8; and (c) the 16S ribosomal RNA sequence of L. reuteri strain S3 comprises the nucleotide sequence of SEQ ID NO:9. In some embodiments of any of the embodiments disclosed herein, the consortium produces one or more organic acids selected from the group consisting of lactate, butyrate, isobutyrate, propionate, acetate, isovalerate, and valerate. In some embodiments of any of the embodiments disclosed herein, each strain is present at a concentration of at least about 1 x 10³ CFU/animal/day to at least about 1 x 10¹⁵ CFU/animal/day in the consortium. In some embodiments of any of the embodiments disclosed herein, the consortium inhibits at least one pathogen selected from avian pathogenic Salmonella sp., Escherichia coli, Clostridium perfringens and Enterobacteriaceae in a gastrointestinal tract of a bird having ingested an effective amount of said direct fed microbial composition. [0015] In additional aspects, provided herein is a premix comprising any of the feed additive compositions disclosed herein or any of the bacterial consortia disclosed herein and at least one mineral and/or at least one vitamin.

[0016] In still further aspects, provided herein any of the feed additive compositions disclosed herein or any of the bacterial consortia disclosed herein or any premix disclosed herein.

[0017] In one aspect, provided herein is a kit comprising a)(i) any of the feed additive compositions disclosed herein; (ii) any of the bacterial consortia disclosed herein; or (iii) any premix disclosed herein; and b) written instructions for administration to an animal. In some embodiments, the kit further comprises one or more enzymes. In some embodiments, the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase and a beta-glucanase.

[0018] In still other aspects, provided herein is a method for improving one or more metrics in an animal selected from the group consisting of increased body weight gain, intestinal health status, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces comprising administering an effective amount of any of the feed additive compositions disclosed herein, any of the bacterial consortia disclosed herein, any premix disclosed herein, or any feed disclosed herein to the animal, thereby improving the one or more metrics in the animal. In some embodiments, the feed additive composition increases one or more of the lactate, acetate, isobutyrate, butyrate, isovalerate, and/or valerate content of the gastrointestinal tract of the animal. In some embodiments of any of the embodiments disclosed herein, the pathogen is one or more of Clostridium perfringens, Campylobacter jejuni, Enterobacteriaceae, a Salmonela sp., and/or Escherichia coli. In some embodiments of any of the embodiments disclosed herein, the method further treats, prevents, or decreases incidence of necrotic enteritis. In some embodiments of any of the embodiments disclosed herein, the animal is a domesticated bird. In some embodiments, the domesticated bird is selected from the group consisting of chickens, turkeys, ducks, geese, quail, emus, ostriches, and pheasant. In some embodiments, the chicken is a broiler or a layer. In some embodiments of any of the embodiments disclosed herein, the feed additive composition, the bacterial consortium, or the premix is administered by waterline. [0019] In another aspect, provided herein is a method for preparing a feed additive composition or a bacterial consortium comprising combining one or more of (a) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; (d) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and/or (e) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923.

[0020] In some embodiments, the composition or consortium comprises one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); (d) L. reuteri strain S2b (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2b (CBS 147270);(e) L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 (CBS 145923) either (A) alone; or (B) in combination with a culture supernatant derived from one or more of these strains. In some embodiments of any of the embodiments disclosed herein, the method further comprises combining one or more enzyme(s) with the feed additive composition. In some embodiments, the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase and a beta-glucanase. In some embodiments of any of the embodiments disclosed herein, (a) at least about 1 x 10³ CFU/g feed additive composition to at least about 1 x 10¹⁵ CFU/g feed additive composition is combined to form the feed additive composition; or (b) at least about 1 x 10³ CFU/animal/day bacterial consortium to at least about 1 x 10¹⁵ CFU/animal/day is combined to form the bacterial consortium. In some embodiments of any of the embodiments disclosed herein, the method further comprises packaging the feed additive composition.

[0021] In yet another aspect, provided herein is a method for preparing a premix comprising combining any of the feed additive compositions disclosed herein with at least one mineral and/or at least one vitamin. In some embodiments, the method further comprises packaging the premix.

[0022] Each of the aspects and embodiments described herein are capable of being used together, unless excluded either explicitly or clearly from the context of the embodiment or aspect.

[0023] Throughout this specification, various patents, patent applications and other types of publications (e.g., journal articles, electronic database entries, etc.) are referenced. The disclosure of all patents, patent applications, and other publications cited herein are hereby incorporated by reference in their entirety for all purposes.

BRIEF DESCRIPTION OF THE DRAWINGS

[0024] FIG. 1 depicts a graph representing cumulative mortality data over time for all houses in large-scale animal study.

[0025] FIG. 2 depicts a genomic map showing AMR gene deletion in L. reuteri strain S1a compared to parent strain SI. Sequence alignments of strain SI (top) and strain S1a (bottom) show deletions of InuC-l (A), lnuC-2 (B), lnuC-3 (C), lnuC-4 (D) and vatE (E) in strain S1a.

[0026] FIG. 3 depicts a genomic map showing AMR gene deletion in L. reuteri strain S2b compared to parent strain S2. Sequence alignments of strain S2 (top) and strain S2b (bottom) showing the deletions of InuC (A) and vatE (B) in strain S2b.

DETAILED DESCRIPTION

[0027] A variety of microbial species have been shown to have certain degrees of efficacy against gut pathogens either in vitro or in vivo. As described in more detail herein, the inventors have surprisingly discovered that administering specific species of organic acid (such as, lactic acid) -producing microbes to animals (such as domesticated birds, for example, chickens) can improve performance on one or more metrics that include increased bodyweight gain, intestinal health status, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection (such as, but not limited to, infection by Clostridium perfringens). and reduced pathogen shedding in feces. Without being bound to theory, it is believed that metabolites of organic acid-producing bacteria play an important role in the prevention of intestinal inflammation and in the maintenance of intestinal homeostasis. While many bacterial species have the capability to produce organic acids, not all species can provide benefits to animals when administered as a feed additive or as part of a feed. However, as will be described in the Examples section, administration of particular combinations of microbials was discovered to be surprisingly effective in the prevention and/or treatment of gut pathogenesis in animals as well as for maintenance of overall health.

I. Definitions

[0028] “Organic acids,” as used herein, refers to an organic compound with acidic properties. In some non-limiting embodiments, organic acid compounds are selected from the group consisting of lactic acid (2-hydroxypropionic acid), succinic acid, furandicarboxylic acid, fumaric acid, maleic acid, citric acid, glutamic acid, aspartic acid, acrylic acid, oxalic acid, and glucanic acid. Other non-limiting organic acids include formic acid (methanoic acid), acetic acid (ethanoic acid), propionic acid (propanoic acid), butanoic acid (butyric acid), isobutyric acid (2-methylpropanoic acid), valeric acid (pentanoic acid), and isovaleric acid (3 -methylbutanoic acid). Inclusive in this definition of organic acids are also the conjugate bases of organic acids including, for example, lactate, glutamate, fumarate, malate, formate, acetate, propionate, butyrate, isobutyrate, valerate, isovalerate etc.

[0029] As used herein, "microorganism" or “microbe” refers to a bacterium, a fungus, a virus, a protozoan, and other microbes or microscopic organisms.

[0030] As used here in the term “direct fed microbial” refers to a composition for consumption by animals (i.e. as an or as a component of animal feed) that contains viable microorganisms, i.e. microorganisms that are capable of living and reproducing. See, for example, U.S. Pat. No. 8,420,074. A direct fed microbial may comprise one or more (such as any of 1, 2, 3, 4, 5, or 6 or more) of any of the microbial strains described herein.

[0031] A bacterial “strain” as used herein refers to a bacterium which remains genetically unchanged when grown or multiplied. The multiplicity of identical bacteria is included. [0032] By ‘ ‘at least one strain,” is meant a single strain but also mixtures of strains comprising at least two strains of microorganisms. By “a mixture of at least two strains,” is meant a mixture of two, three, four, five, six or even more strains. In some embodiments of a mixture of strains, the proportions can vary from 1% to 99%. When a mixture comprises more than two strains, the strains can be present in substantially equal proportions in the mixture or in different proportions.

[0033] For purposes of this disclosure, a “biologically pure strain” means a strain containing no other bacterial strains in quantities sufficient to interfere with replication of the strain or to be detectable by normal bacteriological techniques. “Isolated,” when used in connection with the organisms and cultures described herein, includes not only a biologically pure strain, but also any culture of organisms which is grown or maintained other than as it is found in nature. In some embodiments, the strains are mutants, variants, or derivatives of strains A1, A2, A3, D1, D2, D3, H1, H2, H3, S1, S1a, S1b, S2, S2a, S2b, and S3 that also provide benefits comparable to that provided by A1, A2, A3, D1, D2, D3, H1, H2, H3, S1, S2, and S3. In some embodiments, the strains are strains having all of the identifying characteristics of strains A1, A2, A3, D1, D2, D3, H1, H2, H3, S1, S2, and S3. Further, each individual strain (A1, A2, A3, D1, D2, D3, H1, H2, H3, S1, S1a, S1b, S2, S2a, S2b, and S3) or any combination of these strains can also provide one or more of the benefits described herein. It will also be clear that addition of other microbial strains, carriers, additives, enzymes, yeast, or the like will also provide one or more benefits or improvement of one or more metrics in an animal and will not constitute a substantially different DFM.

[0034] The term “16S rRNA” or “16S ribosomal RNA” means the rRNA constituting the small subunit of prokaryotic ribosomes. In bacteria, this sequence can be used to identify and characterize operational taxonomic units.

[0035] The term “sequence identity” or “sequence similarity” as used herein, means that two polynucleotide sequences, a candidate sequence and a reference sequence, are identical (i.e. 100% sequence identity) or similar (i.e. on a nucleotide-by-nucleotide basis) over the length of the candidate sequence. In comparing a candidate sequence to a reference sequence, the candidate sequence may comprise additions or deletions (i.e. gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Optimal alignment of sequences for determining sequence identity may be conducted using the any number of publicly available local alignment algorithms known in the art such as ALIGN or Megalign (DNASTAR), or by inspection.

[0036] The term “percent (%) sequence identity” or “percent (%) sequence similarity,” as used herein with respect to a reference sequence is defined as the percentage of nucleotide residues in a candidate sequence that are identical to the residues in the reference polynucleotide sequence after optimal alignment of the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.

[0037] As used herein, “prevent,” “preventing,” “prevention” and grammatical variations thereof refers to a method of partially or completely delaying or precluding the onset or recurrence of a disorder or condition (such as necrotic enteritis) and/or one or more of its attendant symptoms or barring an animal from acquiring or reacquiring a disorder or condition or reducing an animal's risk of acquiring or reacquiring a disorder or condition or one or more of its attendant symptoms.

[0038] As used herein, the term “reducing” in relation to a particular trait, characteristic, feature, biological process, or phenomena refers to a decrease in the particular trait, characteristic, feature, biological process, or phenomena. The trait, characteristic, feature, biological process, or phenomena can be decreased by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or greater than 100%.

[0039] The term “poultry,” as used herein, means domesticated birds kept by humans for their eggs, their meat or their feathers. These birds are most typically members of the superorder Galloanserae, especially the order Galliformes which includes, without limitation, chickens, quails, ducks, geese, emus, ostriches, pheasant, and turkeys.

[0040] As used herein “administer” or “administering” is meant the action of introducing one or more microbial strain, an exogenous feed enzyme and/or a strain and an exogenous feed enzyme to an animal, such as by feeding or by gavage.

[0041] As used herein, “effective amount” means a quantity of DFM and/or exogenous enzymes to improve one or more metrics in an animal. Improvement in one or more metrics of an animal (such as, without limitation, any of increased body weight gain, intestinal health status, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces) can be measured as described herein or by other methods known in the art. An effective amount can be administered to the animal by providing ad libitum access to feed containing the DFM and exogenous enzymes. The DFM and exogenous enzymes can also be administered in one or more doses.

[0042] The term “intestinal health status” refers to the status of the gut wall structure and morphology which can be affected by, for example, infectious agents or a non-infectious cause, such as a suboptimal formulated diet. “Gut wall structure and morphology” or “gut barrier integrity” can refer to, without limitation, epithelial damage and epithelial permeability which is characterized by a shortening of villi, a lengthening of crypts and an infiltration of inflammatory cells (such as, without limitation, CD3+ cells). The latter damage and inflammation markers can also be associated with a “severe” macroscopic appearance of the gut -compared to a “normal” appearance- when evaluated using a scoring system such as the one described by Teirlynck et al. (2011).

[0043] As used herein, the term “feed” is used synonymously herein with “feedstuff.” Feed broadly refers to a material, liquid or solid, that is used for nourishing an animal, and for sustaining normal or accelerated growth of an animal including newborns or young and developing animals. The term includes a compound, preparation, mixture, or composition suitable for intake by an animal (such as, e.g., for poultry such as quail, ducks, turkeys, and chickens). In some embodiments, a feed or feed composition comprises a basal food composition and one or more feed additives or feed additive compositions. The term "feed additive" as used herein refers to components included for purposes of fortifying basic feed with additional components to promote feed intake, treat or prevent disease, or alter metabolism. Feed additives include pre-mixes. In other embodiments, a feed additive refers to a composition that supplements a feed but is not necessarily a component of the feed or food. For example, in one embodiment, the feed additive composition supplements a feed via delivery through a fluid (such as water) that is administered to the animal separately from the feed or food (for example, via a waterline or water distribution system).

[0044] A “premix,” as referred to herein, may be a composition composed of micro- ingredients such as, but not limited to, one or more of vitamins, minerals, chemical preservatives, antibiotics, fermentation products, and other essential ingredients. Premixes are usually compositions suitable for blending into commercial rations. [0045] As used herein, “improving one or more metrics in an animal” refers to improvements on measurements relevant to the growth and/or health of an animal (such as a domesticated bird, for example, a chicken), measured by one or more of the following parameters: average daily weight gain (ADG), overall weight, mortality, feed conversion (which includes both feed:gain and gaimfeed), feed intake, intestinal health status, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces. “An improvement in a metric” or “improved metric” as used herein, refers to an improvement in at least one of the parameters listed under the metrics in an animal definition.

[0046] As used herein, the term "feed conversion ratio" (FCR) refers to the amount of feed fed to an animal to increase the weight of the animal by a specified amount. An improved feed conversion ratio means a lower feed conversion ratio. By "lower feed conversion ratio" or "improved feed conversion ratio" it is meant that the use of a feed additive composition in feed results in a lower amount of feed being required to be fed to an animal to increase the weight of the animal by a specified amount compared to the amount of feed required to increase the weight of the animal by the same amount when the feed does not comprise said feed additive composition.

[0047] The phrase “antibiotic resistance genes” or “antimicrobial resistance (AMR) genes,” as used interchangeably herein, refers to genes that confer resistance to antibiotics, for example by coding for enzymes which destroy it, by coding for surface proteins which prevent it from entering a microorganism, actively exports it, or by being a mutant form of the antibiotic's target so that it can ignore it. Examples of AMR genes may be found on the ARDB — Antibiotic Resistance Genes Database (Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742; gene.https://ardb.cbcb.umd.edu/). Non-limiting examples of AMR genes include, but are not limited to, extended- spectrum beta lactamse (ESBL) genes, the methicillin resistance gene CTX-M-15; the vancomycin resistance genes ndm-1,2,5,6, vanA, vanB, vanC, and vanD, the nucleotidyltransferase InuC, the acetyltransferase vatE, and/or the tetracycline-resistant ribosomal protection genes tetM and tetW. In some embodiments, one or more AMR genes can be associated with a mobile genetic element (such as a transposon) near the gene (such as within any of about 10 kb, 9 kb, 8 kb, 7 kb, 6 kb, 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or closer to the gene, including distances falling in between any of these values). In other embodiments, one or more AMR genes are not associated with a mobile genetic element,, such as a transposon.

[0048] As used herein “mobile genetic element’ is meant to include any type of nucleic acid molecule that is capable of movement within a genome or from one genome to another. For example, these can include, without limitation, transposons or transposable elements (including retrotransposons, DNA transposons, and insertion sequences); plasmids; bacteriophage elements (including Mu; and group II introns).

[0049] Certain ranges are presented herein with numerical values being preceded by the term "about." The term "about" is used herein to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating unrecited number can be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number. For example, in connection with a numerical value, the term “about” refers to a range of - 10% to +10% of the numerical value, unless the term is otherwise specifically defined in context.

[0050] As used herein, the singular terms “a,” “an,” and “the” include the plural reference unless the context clearly indicates otherwise.

[0051] It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements or use of a “negative” limitation.

[0052] It is also noted that the term “consisting essentially of,” as used herein refers to a composition wherein the component(s) after the term is in the presence of other known component(s) in a total amount that is less than 30% by weight of the total composition and do not contribute to or interferes with the actions or activities of the component(s).

[0053] It is further noted that the term "comprising,” as used herein, means including, but not limited to, the component(s) after the term “comprising.” The component(s) after the term “comprising” are required or mandatory, but the composition comprising the component(s) can further include other non-mandatory or optional component(s). [0054] It is also noted that the term “consisting of,” as used herein, means including, and limited to, the component(s) after the term "consisting of.” The component(s) after the term “consisting of’ are therefore required or mandatory, and no other component(s) are present in the composition.

[0055] It is intended that every maximum numerical limitation given throughout this specification includes every lower numerical limitation, as if such lower numerical limitations were expressly written herein. Every minimum numerical limitation given throughout this specification will include every higher numerical limitation, as if such higher numerical limitations were expressly written herein. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.

[0056] Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains.

[0057] Other definitions of terms may appear throughout the specification.

II. Compositions

A. Strains

[0058] Direct fed microbials (DFMs) refer to the feeding of beneficial microbes to animals, such as domestic birds, when they are under periods of stress (disease, ration changes, environmental or production challenges) or as a part of a daily nutritional regimen to prevent disease and facilitate nutrient usage during digestion. Probiotics is another term for this category of feed additives. Probiotics or DFMs have been shown to improve animal performance in controlled studies. In some embodiments, DFMs include both direct fed bacteria and/or yeast-based products and, in particular embodiments, include viable microorganisms. The term "viable microorganism" means a microorganism which is metabolically active or able to differentiate.

[0059] In one embodiment, the DFM may be a spore forming bacterium and hence the term DFM may refer to a composition that is comprised of or contains spores, e.g., bacterial spores. Therefore, in one embodiment the term "viable microorganism" as used herein may include microbial spores, such as endospores or conidia. In another embodiment, the DFM in the feed additive composition according to the present invention is not comprised of or does not contain microbial spores, e.g. endospores or conidia (i.e., the DFM is non-spore forming).

[0060] The strains provided herein include Lactobacillus reuteri strain S1, L. reuteri strain S2, L. reuteri strain S3, L. gallinarum strain H1, L. salivarius strain H2, L. agilis strain H3, L. salivarius strain A1, L. reuteri strain A2, L. reuteri strain A3, L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3, which are also referred to herein as S1, S2, S3, H1, H2, H3, A1, A2, A3, D1, D2, and D3, respectively.

[0061] L. reuteri strain S1, L. reuteri strain S2, L. reuteri strain S3, L. reuteri strain A2, L. gallinarum strain H1, L. salivarius strain H2, and L. agilis strain H3 were deposited on July 24, 2019 at the Westerdijk Fungal Biodiversity Institute (WFDB), Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands and given accession numbers CBS 145921, CBS 145922, CBS 145923, CBS 145924, CBS 145918, CBS 145919, and CBS 145920, respectively. The deposits were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. One or more strain provided herein can be used as a direct-fed microbial (DFM).

[0062] Additional strains provided herein include Lactobacillus reuteri strain SI a, L. reuteri strain S lb, L. reuteri strain S2a, and L. reuteri strain S2b, which are also referred to herein as S1a, S1b, S2a, and S2b, respectively. These strains are derived from L. reuteri strains S1 and S2. As discussed in Example 5, genome analysis of SI and S2 revealed that these strains contained a number of antibiotic resistance markers (AMRs). As AMRs have been implicated in the spread of antibiotic resistance in animal and humans, these AMRs were removed from the genomes of strains S1 and S2. The new strains, now engineered (i.e. are non-naturally occurring) to lack one or more AMRs, were designated L. reuteri strain S1a, L. reuteri strain S1b, L. reuteri strain S2a, and L. reuteri strain S2b.

[0063] L. reuteri strain S1a (ABM01), L. reuteri strain S1b (ABM02), L. reuteri strain S2a (ABM03), and L. reuteri strain S2b (ABM04) were deposited on December 2, 2020 at the Westerdijk Fungal Biodiversity Institute (WFDB), Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands and given accession numbers CBS 147267, CBS 147268, CBS 147269, and CBS 147270, respectively. The deposits were made under the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. One or more strain provided herein can be used as a direct- fed microbial (DFM).

[0064] The DFM strains disclosed herein are primarily found in the genus Lactobacillus. As of March 2020, Lactobacilli comprised 261 species that are extremely diverse phenotypically, ecologically, and genotypically. Given recent advances in whole genome sequencing and comparative genomics, the genus Lactobacillus was recently divided into 25 separate genera with strains belonging to previously designated Lactobacilli species being transferred to new species and/or genera (see Zheng et al., 2020, Int. J. Sy st. Evol.

Microbiol. ,70:2782-2858; Pot et al., Trends in Food Science & Technology 94 (2019) 105- 113; and Koutsoumanis et al., 2020, EFSA Journal, 18(7):6174, the disclosures of each of which are incorporated by reference herein). For purposes of the instant disclosure, the previous classification of Lactobacillus species will continue to be employed. However, in some embodiments Lactobacillus agilis is also classified as as Ligilactobacillus agilis. In other embodiments, Lactobacillus salivarius is also classified as Ligilactobacillus salivarius. In further embodiments, Lactobacillus reuteri is also classified as Limosilactobacillus reuteri.

[0065] DFM compositions can include those that contain one or more strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of Lactobacillus reuterv, and/or L. salivarius. L. reuteri is a gram-positive bacterium that naturally inhabits the gut of mammals and birds. First described in the early 1980s, some strains of L. reuteri are used as probiotics. Some L. reuteri can produce a novel broad- spectrum antibiotic substance known as reuterin.

Lactobacillus salivarius is a probiotic bacteria species that has been found to live in the gastrointestinal tract and exert a range of therapeutic properties including suppression of pathogenic bacteria. The DFM composition can further include those that contain one or more strains (such as any of about 1, 2, 3, 4, 5, 6, 7, or 8 or more strains) of L. agilis, L. crispatus, and/or L. gallinarum.

[0066] The DFM composition can also include only strains of L. reuteri (such as 1, 2, 3, 4, 5, 6, 7, or 8 strains of L. reuteri without any other microbials present). For example, the DFM composition can include one or more of L. reuteri strains S1, S1a, S1b, S2, S2a, S2b and/or S3 or one or more microbe(s) having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of one or more of L. reuteri strain S1, S1a, S1b (SEQ ID NO:7), S2, S2a, S2b (SEQ ID NO:8), and/or S3 (SEQ ID NO:9). In some embodiments, the DFM composition includes only L. reuteri strain S1, S1a, S1b, S2, S2a, S2b or S3. In another embodiment, DFM composition includes L. reuteri strains S1 and S2; L. reuteri strains S1 and S3; L. reuteri strains S2 and S3; or L. reuteri strains S1, S2, and S3. In another embodiment, DFM composition includes L. reuteri strains S1a and S2a; L. reuteri strains S1a and S3; L. reuteri strains S2a and S3; or L. reuteri strains S1a, S2a, and S3. In another embodiment, DFM composition includes L. reuteri strains S1b and S2b; L. reuteri strains S1b and S3; L. reuteri strains S2b and S3; or L. reuteri strains S1b, S2b, and S3. In another embodiment, DFM composition includes L. reuteri strains S1a and S2b; L. reuteri strains S1a and S3; L. reuteri strains S2b and S3; or L. reuteri strains S1a, S2b, and S3. In another embodiment, DFM composition includes L. reuteri strains S1b and S2a; L. reuteri strains S1b and S3; L. reuteri strains S2a and S3; or L. reuteri strains S1b, S2a, and S3. Additionally, when cultured together, one or more L. reuteri strains S1, S1a, S1b, S2, S2a, S2b and/or S3 have one or more physiological or metabolic properties that individually cultured L. reuteri strains lack. These properties can include, without limitation, changes in the amount and/or type of organic acid produced, change in metabolic profile, and/or a change in the composition of media in which the bacteria are cultured together (such as lactate).

[0067] The DFM compositions provided herein can include one or more of L. reuteri strains S1, S1a, S1b, S2, S2a, S2b and/or S3 (i.e. the compositions include the actual bacteria from these strains) and/or one or more culture supernatants derived from the culturing of these strains (individually or in co-culture).

[0068] DFM compositions can additionally include those that contain one or more of L. salivarius microbes, L. gallinarum microbes, L. agilis microbes, and/or L. reuteri microbes.

[0069] The DFM composition can include one or more of L. salivarius strain H2, L. gallinarum strain H1, L. reuteri strain A2, and/or L. agilis strain H3 or one or more microbe(s) having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of one or more of L. salivarius strain H2 (SEQ ID NO: 10), L. gallinarum strain H1 (SEQ ID NO: 11), L. reuteri strain A2 (SEQ ID NO: 12), and/or L. agilis strain H3 (SEQ ID NO:1). In some embodiments, the DFM composition includes only L. salivarius strain H2, L. gallinarum strain H1, L. reuteri strain A2, or L. agilis strain H3. In another embodiment, the DFM composition includes L. salivarius strain H2 and L. gallinarum strain H1; L. salivarius strain H2 and L. reuteri strain A2; L. salivarius strain H2 and L. agilis strain H3; L. gallinarum strain H1 and L. reuteri strain A2; L. gallinarum strain H1 and L. agilis strain H3; L. reuteri strain A2 and L. agilis strain H3; L. salivarius strain H2, L. gallinarum strain H1, and L. reuteri strain A2 ; L. salivarius strain H2, L. reuteri strain A2, and L. agilis strain H3; L. gallinarum strain H1, L. reuteri strain A2, and L. agilis strain H3; L. salivarius strain H2, L. gallinarum strain H1, L. reuteri strain A2, and L. agilis strain H3; L. salivarius strain H2, L. gallinarum strain H1, and L. reuteri strain A2; or L. salivarius strain H2, L. gallinarum strain H1, and L. agilis strain H3. Additionally, when cultured together, one or more L. salivarius strain H2, L. gallinarum strain H1, L. reuteri strain A2, and/or L. agilis strain H3 (such as L. salivarius strain H2, L. gallinarum strain H1, and L. reuteri strain A2; or L. salivarius strain H2, L. gallinarum strain H1, and L. agilis strain H3) have one or more physiological or metabolic properties that individually cultured strains lack. These properties can include, without limitation, changes in the amount and/or type of organic acid production (such as the production of lactic acid).

[0070] The DFM compositions provided herein can include one or more L. salivarius strain H2, L. gallinarum strain H1, L. reuteri strain A2, and/or L. agilis strain H3 (such as L. salivarius strain H2, L. gallinarum strain H1, and L. reuteri strain A2; or L. salivarius strain H2, L. gallinarum strain H1, and L. agilis strain H3) (i.e. the compositions include the actual bacteria from these strains) and/or one or more culture supernatants derived from the culturing of these strains (individually or in co-culture).

[0071] DFM compositions can additionally include those that contain one or more of L. salivarius microbes, L. agilis microbes, and/or L. reuteri microbes.

[0072] The DFM composition can include one or more of L. salivarius strain A1, L. reuteri strain A2, and/or L. agilis strain A3 or one or more microbe(s) having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of one or more of L. salivarius strain Al (SEQ ID NO:9), L. reuteri strain A2 (SEQ ID NO: 10), and/or L. agilis strain A3 (SEQ ID NO: 11). In some embodiments, the DFM composition includes only L. salivarius strain A1, L. reuteri strain A2, or L. agilis strain A3. In another embodiment, the DFM composition includes L. salivarius strain Al and L. reuteri strain A2; L. salivarius strain Al and L. agilis strain A3; L. reuteri strain A2 and L. agilis strain A3; L. salivarius strain A1, L. reuteri strain A2, and L. agilis strain A3. Additionally, when cultured together, one or more L. salivarius strain A1, L. reuteri strain A2, and/or L. agilis strain A3 have one or more physiological or metabolic properties that individually cultured strains lack. These properties can include, without limitation, changes in the amount and/or type of organic acid produced (such as the production of lactic acid) change in metabolic profile, and/or a change in the composition of media in which the bacteria are cultured together.

[0073] The DFM compositions provided herein can include one or more of L. salivarius strain A1, L. reuteri strain A2, and/or L. agilis strain A3 (i.e. the compositions include the actual bacteria from these strains) and/or one or more culture supernatants derived from the culturing of these strains (individually or in co-culture).

[0074] DFM compositions can additionally include those that contain one or more of L. salivarius microbes, L. agilis microbes, and/or L. crispatus microbes.

[0075] The DFM composition can include one or more of L. agilis strain D1, L. salivarius strain D2, and/or L. crispatus strain D3 or one or more microbe(s) having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of one or more of L. agilis strain DI (SEQ ID NO:5), L. salivarius strain D2 (SEQ ID NO:4), and/or L. crispatus strain D3 (SEQ ID NO:6). In some embodiments, the DFM composition includes only L. agilis strain D1, L. salivarius strain D2, or L. crispatus strain D3. In another embodiment, the DFM composition includes L. agilis strain DI and L. salivarius strain D2; L. agilis strain DI and L. crispatus strain D3; L. salivarius strain D2 and L. crispatus strain D3; L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3. Additionally, when cultured together, one or more L. agilis strain D1, L. salivarius strain D2, and/or L. crispatus strain D3 have one or more physiological or metabolic properties that individually cultured strains lack. These properties can include, without limitation, changes in the amount and/or type of organic acid produced (such as the production of lactic acid) change in metabolic profile, and/or a change in the composition of media in which the bacteria are cultured together.

[0076] The DFM compositions provided herein can include one or more L. agilis strain D1,

L. salivarius strain D2, and/or L. crispatus strain D3 i.e. the compositions include the actual bacteria from these strains) and/or one or more culture supernatants derived from the culturing of these strains (individually or in co-culture).

[0077] In some embodiments, one or more of (such as any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11) the strains provided herein including L. reuteri strain SI (CBS 145921), L. reuteri strain S2 (CBS 145922), E. reuteri strain S3 (CBS 145923), E. gallinarum strain H1 (CBS 145918), E. salivarius strain H2 (CBS 145919), E. reuteri strain A2 (CBS 145924), E. agilis strain H3, L. salivarius strain A1, L. agilis strain A3, L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3 further comprise one or more (such as any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) inactivated or deleted AMR genes.

B. Exogenous enzymes

[0078] Supplemental enzymes can be used as additives to animal feed, particularly poultry and swine feeds, as a means to improve nutrient utilization and performance characteristics.

[0079] In one embodiment, the disclosure relates to a composition comprising one or more DFM (such as DFMs containing any of the microbial strains disclosed herein) and one or more exogenous feed enzymes. In another embodiment, the disclosure relates to a composition comprising, consisting of, or consisting essentially of a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and one or more exogenous feed enzymes. In one embodiment, the exogenous feed enzymes include, but are not limited to, xylanase, amylase, phytase, beta-glucanase, and protease. In still another embodiment, the composition comprises a feed additive.

1. Xylanases

[0080] Xylanase is the name given to a class of enzymes that degrade the linear polysaccharide P-l,4-xylan into xylose, thus breaking down hemicellulose, one of the major components of plant cell walls. Xylanases, e.g., endo-P-xylanases (EC 3.2.1.8) hydrolyze the xylan backbone chain. In one embodiment, provided herein are compositions comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and one or more xylanase.

[0081] In one embodiment, the xylanase may be any commercially available xylanase. Suitably the xylanase may be an endo-l,4-P-d-xylanase (classified as E.G. 3.2.1.8) or a 1 ,4p~ xylosidase (classified as E.G. 3.2.1.37). In one embodiment, the disclosure relates to a DFM in combination with an endoxylanase, e.g. an endo-1,4-P-d-xylanase, and another enzyme. All E.C. enzyme classifications referred to herein relate to the classifications provided in Enzyme Nomenclature — Recommendations (1992) of the nomenclature committee of the International Union of Biochemistry and Molecular Biology — ISBN 0-12-226164-3, which is incorporated herein

[0082] In another embodiment, the xylanase may be a xylanase from Bacillus, Trichodermna, Therinomyces, Aspergillus and Penicillium. In still another embodiment, the xylanase may be the xylanase in Axtra XAP® or Avizyme 1502®, both commercially available products from Danisco A/S. In one embodiment, the xylanase may be a mixture of two or more xylanases. In still another embodiment, the xylanase is an endo-1,4-β-xylanase or a 1 ,4-[3- xylosidase. In yet another embodiment, the xylanase is from an organism selected from the group consisting of: Bacillus, Trichoderma, Thermomyces, Aspergillus, Penicillium, and Humicola. In yet another embodiment, the xylanase may be one or more of the xylanases or one or more of the commercial products recited in Table 1.

Table 1: Representative commercial xylanases

[0083] In one embodiment, the disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and xylanase. In one embodiment, the composition comprises 10-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-550, 550-600, 600-650, 650-700, 700- 750, and greater than 750 xylanase units/g of composition.

[0084] In one embodiment, the composition comprises 500-1000, 1000-1500, 1500-2000, 2000-2500, 2500-3000, 3000-3500, 3500-4000, 4000-4500, 4500-5000, 5000-5500, 5500- 6000, 6000-6500, 6500-7000, 7000-7500, 7500-8000, and greater than 8000 xylanase units/g composition.

[0085] It will be understood that one xylanase unit (XU) is the amount of enzyme that releases 0.5 pmol of reducing sugar equivalents (as xylose by the Dinitrosalicylic acid (DNS) assay-reducing sugar method) from an oat- spelt- xylan substrate per min at pH 5.3 and 50° C. (Bailey, et al., Journal of Biotechnology, Volume 23, (3), May 1992, 257-270).

2. Amylases

[0086] Amylase is a class of enzymes capable of hydrolysing starch to shorter-chain oligosaccharides, such as maltose. The glucose moiety can then be more easily transferred from maltose to a monoglyceride or glycosylmonoglyceride than from the original starch molecule. The term amylase includes a-amylases (E.G. 3.2.1.1), G4-forming amylases (E.G. 3.2.1.60), β-amylases (E.G. 3.2.1.2) and γ-amylases (E.C. 3.2.1.3). Amylases may be of bacterial or fungal origin, or chemically modified or protein engineered mutants. In one embodiment, provided herein are compositions comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and one or more amylase.

[0087] In one embodiment, the amylase may be a mixture of two or more amylases. In another embodiment, the amylase may be an amylase, e.g. an a- amylase, from Bacillus licheniformis and an amylase, e.g. an a-amylase, from Bacillus amyloliquefaciens. In one embodiment, the a-amylase may be the a-amylase in Axtra XAP® or Avizyme 1502®, both commercially available products from Danisco A/S. In yet another embodiment, the amylase may be a pepsin resistant a-amylase, such as a pepsin resistant Trichoderma (such as Trichoderma reesei) alpha amylase. A suitably pepsin resistant a-amylase is taught in UK application number 101 1513.7 (which is incorporated herein by reference) and PCT/IB2011/053018 (which is incorporated herein by reference). [0088] In one embodiment, the amylase for use in the present invention may be one or more of the amylases in one or more of the commercial products recited in Table 2.

Table 2: Representative commercial amylases

[0089] it will be understood that one amylase unit (AU) is the amount of enzyme that releases 1 mmol of glucosidic linkages from a water insoluble cross-linked starch polymer substrate per min at pH 6.5 and 37° C. (this may be referred to herein as the assay for determining 1 AU).

[0090] In one embodiment, disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and amylase. In one embodiment, disclosure relates to a composition comprising a multi-strain DFM, xylanase and amylase. In one embodiment, the composition comprises 10-50, 50-100, 100- 150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750, and greater than 750 amylase units/g composition.

[0091] In one embodiment, the composition comprises 500-1000, 1000-1500, 1500-2000, 2000-2500, 2500-3000, 3000-3500, 3500-4000, 4000-4500, 4500-5000, 5000-5500, 5500- 6000, 6000-6500, 6500-7000, 7000-7500, 7500-8000, 8000-8500, 8500-9000, 9000-9500, 9500-10000, 10000-11000, 11000-12000, 12000-13000, 13000-14000, 14000-15000 and greater than 15000 amylase units/g composition.

3. Proteases

[0092] The term protease as used herein is synonymous with peptidase or proteinase. The protease may be a subtilisin (E.G. 3.4.21.62) or a bacillolysin (E.G. 3.4.24.28) or an alkaline serine protease (E.G. 3.4.21.x) or a keratinase (E.G. 3.4.X.X). In one embodiment, the protease is a subtilisin. Suitable proteases include those of animal, vegetable or microbial origin. Chemically modified or protein engineered mutants are also suitable. The protease may be a serine protease or a metalloprotease, e.g., an alkaline microbial protease or a trypsin-like protease. In one embodiment, provided herein are compositions comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and one or more protease.

[0093] Examples of alkaline proteases are subtilisins, especially those derived from Bacillus sp., e.g., subtilisin Novo, subtilisin Carlsberg, subtilisin 309 (see, e.g., U.S. Pat. No. 6,287,841), subtilisin 147, and subtilisin 168 (see, e.g., WO 89/06279). Examples of trypsin-like proteases are trypsin (e.g., of porcine or bovine origin), and Fusarium proteases (see, e.g., WO 89/06270 and WO 94/25583). Examples of useful proteases also include but are not limited to the variants described in WO 92/19729 and WO 98/20115.

[0094] In another embodiment, the protease may be one or more of the proteases in one or more of the commercial products recited in Table 3.

Table 3: Representative commercial proteases

[0095] In one embodiment, the protease is selected from the group consisting of subtilisin, a bacillolysin, an alkine serine protease, a keratinase, and a Nocardiopsis protease.

[0096] It will be understood that one protease unit (PU) is the amount of enzyme that liberates from the substrate (0.6% casein solution) one microgram of phenolic compound (expressed as tyrosine equivalents) in one minute at pH 7.5 (40 mM Na₂PO₄/lactic acid buffer) and 40° C. This may be referred to as the assay for determining 1 PU.

[0097] In one embodiment, disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and a protease. In another embodiment, disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and a xylanase and a protease. In still another embodiment, the disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and an amylase and a protease. In yet another embodiment, the disclosure relates to a composition comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and a xylanase, an amylase and a protease.

[0098] In one embodiment, the composition comprises 10-50, 50-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-550, 550-600, 600-650, 650- 700, 700-750, and greater than 750 protease units/g composition.

[0099] In one embodiment, the composition comprises 500-1000, 1000-1500, 1500-2000, 2000-2500, 2500-3000, 3000-3500, 3500-4000, 4000-4500, 4500-5000, 5000-5500, 5500- 6000, 6000-6500, 6500-7000, 7000-7500, 7500-8000, 8000-8500, 8500-9000, 9000-9500, 9500-10000, 10000-11000, 11000-12000, 12000-13000, 13000-14000, 14000-15000 and greater than 15000 protease units/g composition.

4. Phytases

[0100] In one embodiment, provided herein are compositions comprising a multi-strain DFM (such as any of the multi-strain DFM compositions disclosed herein) and one or more phytase. The phytase for use in the present invention may be classified a 6-phytase (classified as E.C. 3.1.3.26) or a 3-phytase (classified as E.C. 3.1.3.8). In one embodiment, the phytase for use in the present invention may be one or more of the phytases in one or more of the commercial products below in Table 4:

Table 4: Representative commercial phytases

[0101] In one embodiment the phytase is a Citrobacter phytase derived from e.g. Citrobacter freundii, preferably C. freundii NCIMB 41247 and variants thereof e.g. as disclosed in W02006/038062 (incorporated herein by reference) and W02006/038128 (incorporated herein by reference), Citrobacter braakii YH-15 as disclosed in WO 2004/085638, Citrobacter braakii ATCC 51113 as disclosed in W02006/037328 (incorporated herein by reference), as well as variants thereof e.g. as disclosed in W02007/112739 (incorporated herein by reference) and WO2011/117396 (incorporated herein by reference), Citrobacter amalonaticus, preferably Citrobacter amalonaticus ATCC 25405 or Citrobacter amalonaticus ATCC 25407 as disclosed in W02006037327 (incorporated herein by reference), Citrobacter gillenii, preferably Citrobacter gillenii DSM 13694 as disclosed in W02006037327 (incorporated herein by reference), or Citrobacter intermedins, Citrobacter koseri, Citrobacter murliniae, Citrobacter rodentium, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Citrobacter species polypeptides or variants thereof.

[0102] In some embodiments, the phytase is an E. coli phytase marketed under the name Phyzyme XP™ Danisco A/S. Alternatively, the phytase may be a Buttiauxella phytase, e.g. a Buttiauxella agrestis phytase, for example, the phytase enzymes taught in WO 2006/043178, WO 2008/097619, WO2009/129489, W02008/092901, PCT/US2009/41011 or PCT/IB2010/051804, all of which are incorporated herein by reference.

[0103] In one embodiment, the phytase may be a phytase from Hafnia, e.g. from Hafnia alvei, such as the phytase enzyme(s) taught in US2008263688, which reference is incorporated herein by reference. In one embodiment, the phytase may be a phytase from Aspergillus, e.g. from Apergillus orzyae. In one embodiment, the phytase may be a phytase from Penicillium, e.g. from Penicillium funiculosum.

[0104] Preferably, the phytase is present in the feedstuff in range of about 200 FTU/kg to about 1000 FTU/kg feed, more preferably about 300 FTU/kg feed to about 750 FTU/kg feed, more preferably about 400 FTU/kg feed to about 500 FTU/kg feed. In one embodiment, the phytase is present in the feedstuff at more than about 200 FTU/kg feed, suitably more than about 300 FTU/kg feed, suitably more than about 400 FTU/kg feed. In one embodiment, the phytase is present in the feedstuff at less than about 1000 FTU/kg feed, suitably less than about 750 FTU/kg feed. Preferably, the phytase is present in the feed additive composition in range of about 40 FTU/g to about 40,000 FTU/g composition, more preferably about 80 FTU/g composition to about 20,000 FTU/g composition, and even more preferably about 100 FTU/g composition to about 10,000 FTU/g composition, and even more preferably about 200 FTU/g composition to about 10,000 FTU/g composition. In one embodiment, the phytase is present in the feed additive composition at more than about 40 FTU/g composition, suitably more than about 60 FTU/g composition, suitably more than about 100 FTU/g composition, suitably more than about 150 FTU/g composition, suitably more than about 200 FTU/g composition. In one embodiment, the phytase is present in the feed additive composition at less than about 40,000 FTU/g composition, suitably less than about 20,000 FTU/g composition, suitably less than about 15,000 FTU/g composition, suitably less than about 10,000 FTU/g composition.

[0105] It will be understood that as used herein 1 FTU (phytase unit) is defined as the amount of enzyme required to release 1 pmol of inorganic orthophosphate from a substrate in one minute under the reaction conditions defined in the ISO 2009 phytase assay — A standard assay for determining phytase activity and 1 FTU can be found at International Standard ISO/DIS 30024: 1-17, 2009. In one embodiment, the enzyme is classified using the E.C. classification above, and the E.C. classification designates an enzyme having that activity when tested in the assay taught herein for determining 1 FTU. C. DFM Formulations

[0106] In one embodiment, the DFM (such as any of the multi-strain DFM compositions disclosed herein) and, optionally, exogenous enzymes may be formulated as a liquid, a dry powder or a granule. In one embodiment, the DFMs and exogenous enzymes can be formulated as a single mixture. In another embodiment, the DFMs and the exogenous enzymes can be formulated as separate mixtures. In still another embodiment, separate mixtures of DFMs and the exogenous enzymes can be administered at the same time or at different times. In still another embodiment, separate mixtures of DFMs and the exogenous enzymes can be administered simultaneously or sequentially. In yet another embodiment, a first mixture comprising DFMs can be administered followed by a second mixture comprising exogenous enzymes. In still another embodiment, a first mixture comprising exogenous enzymes can be administered followed by a second mixture comprising DFMs.

[0107] The dry powder or granules may be prepared by means known to those skilled in the art, such as, in top-spray fluid bed coater, in a buttom spray Wurster or by drum granulation (e.g. High sheer granulation), extrusion, pan coating or in a microingredients mixer.

[0108] In another embodiment, the DFM and/or the enzyme(s) may be coated, for example encapsulated. Suitably the DFM and enzymes may be formulated within the same coating or encapsulated within the same capsule. Alternatively, one or more of the enzymes may be formulated within the same coating or encapsulated within the same capsule while the DFM can be formulated in a separate coating from the enzymes.

[0109] In some embodiments, such as where the DFM is capable of producing endospores, the DFM may be provided without any coating. In such circumstances, the DFM endospores may be simply admixed with one or more enzymes. In the latter case, the enzymes may be coated, e.g. encapsulated, for instance one or more or all of the enzymes may be coated, e.g. encapsulated. The enzymes may be encapsulated as mixtures (i.e. comprising one or more, two or more, three or more or all) of enzymes or they may be encapsulated separately, e.g. as single enzymes. In one preferred embodiment, all enzymes may be coated, e.g. encapsulated, together. In one embodiment, the coating protects the enzymes from heat and may be considered a thermoprotectant.

[0110] In another embodiment, the DFMs and exogenous feed enzymes may be mixed with feed or administered in the drinking water, such as via a waterline. In one embodiment, the dosage range for inclusion into water is about 1x10³ CFU/animal/day to about

1x10¹⁵ CFU/animal/day, for example, about 1x10³ CFU/animal/day, 1x10⁴ CFU/animal/day,

1x10⁵ CFU/animal/day, 1x10⁶ CFU/animal/day, 1x10⁷ CFU/animal/day,

1x10⁸ CFU/animal/day, 1x10⁹ CFU/animal/day 1x10¹⁰ CFU/animal/day,

1x10¹¹ CFU/animal/day, 1x10¹² CFU/animal/day, 1x10¹³ CFU/animal/day,

1x10¹⁴ CFU/animal/day, or 1x10¹⁵ CFU/animal/day, inclusive of all dosages falling in between these values.

D. Feed Additive Compositions

[0111] In one embodiment, provided herein are feed additive compositions comprising one or more DFMs (such as any of the multi-strain DFMs disclosed herein) and, optionally, one or more exogenous feed enzymes. In one embodiment, the feed additive composition can be formulated in any suitable way to ensure that the formulation comprises viable DFMs and, optionally, active enzymes.

[0112] In one embodiment, the feed additive composition may be used in the form of solid or liquid preparations or alternatives thereof. Examples of solid preparations include powders, pastes, boluses, capsules, ovules, pills, pellets, tablets, dusts, and granules which may be wettable, spray-dried or freeze-dried. Examples of liquid preparations include, but are not limited to, aqueous, organic or aqueous-organic solutions, suspensions and emulsions.

[0113] In another embodiment, the feed additive composition can be used in a solid form. In one embodiment, the solid form is a pelleted form. In solid form, the feed additive composition may also contain one or more of: excipients such as microcrystalline cellulose, lactose, sodium citrate, calcium carbonate, dibasic calcium phosphate and glycine; disintegrants such as starch (preferably corn, potato or tapioca starch), sodium starch glycollate, croscarmellose sodium and certain complex silicates; granulation binders such as polyvinylpyrrolidone, hydroxypropylmethylcellulose (HPMC), hydroxypropylcellulose (HPC), sucrose, gelatin and acacia; lubricating agents such as magnesium stearate, stearic acid, glyceryl behenate and talc may be included.

[0114] Examples of nutritionally acceptable carriers for use in preparing the forms include, for example, water, salt solutions, alcohol, silicone, waxes, petroleum jelly, vegetable oils, polyethylene glycols, propylene glycol, liposomes, sugars, gelatin, lactose, amylose, magnesium stearate, talc, surfactants, silicic acid, viscous paraffin, perfume oil, fatty acid monoglycerides and diglycerides, petroethral fatty acid esters, hydroxymethyl- cellulose, polyvinylpyrrolidone, and the like.

[0115] In one embodiment, the feed additive composition is formulated to a dry powder or granules as described in WO2007/044968 (referred to as TPT granules) or WO 1997/016076 or WO 1992/012645 (each of which is incorporated herein by reference).

[0116] In one embodiment, the feed additive composition may be formulated to a granule feed composition comprising: an active agent comprising one or more DFM (such as any of the multi-strain DFM compositions disclosed herein) and, optionally, one or more exogenous feed enzyme and at least one coating. In one embodiment, the active agent of the granule retains activity after processing. In one embodiment, the active agent of the granule retains an activity level after processing selected from the group consisting of: 50-60% activity, 60-70% activity, 70-80% activity, 80-85% activity, 85-90% activity, and 90-95% activity.

[0117] In another embodiment, the granule may contain one coating. The coating may comprise a moisture hydrating material that constitutes at least 55% w/w of the granule. In another embodiment, the granule may contain two coatings. The two coatings may be a moisture hydrating coating and a moisture barrier coating. In some embodiments, the moisture hydrating coating may be from 25% to 60% w/w of the granule and the moisture barrier coating may be from 2% to 15% w/w of the granule. The moisture hydrating coating may be selected from inorganic salts, sucrose, starch, and maltodextrin and the moisture barrier coating may be selected from polymers, gums, whey and starch.

[0118] In yet another embodiment, the granule may be produced using a feed pelleting process and the feed pretreatment process may be conducted between 70° C. and 95° C. for up to several minutes, such as between 85° C. and 95° C. In another embodiment, the granule may be produced using a steam-heated pelleting process that may be conducted between 85° C. and 95° C. for up to several minutes.

[0119] In one embodiment, the granule may have a moisture barrier coating selected from polymers and gums and the moisture hydrating material may be an inorganic salt. The moisture hydrating coating may be between 25% and 45% w/w of the granule and the moisture barrier coating may be between 2% and 20% w/w of the granule.

[0120] In one embodiment, the active agent retains activity after conditions selected from one or more of: (a) a feed pelleting process; (b) a steam-heated feed pretreatment process; (c) storage; (d) storage as an ingredient in an unpelleted mixture; and (e) storage as an ingredient in a feed base mix or a feed premix comprising at least one compound selected from trace minerals, organic acids, reducing sugars, vitamins, choline chloride, and compounds which result in an acidic or a basic feed base mix or feed premix.

[0121] In some embodiments, the DFM (e.g. DFM endospores, for example) may be diluted using a diluent, such as starch powder, lime stone or the like. In one embodiment, the DFM and the enzymes may be in a liquid formulation suitable for consumption preferably such liquid consumption contains one or more of the following: a buffer, salt, sorbitol and/or glycerol. In another embodiment, the feed additive composition may be formulated by applying, e.g. spraying, the enzyme(s) onto a carrier substrate, such as ground wheat for example.

[0122] In one embodiment, the feed additive composition may be formulated as a premix. By way of example only, the premix may comprise one or more feed components, such as one or more minerals and/or one or more vitamins.

[0123] In one embodiment, the DFM and exogenous feed enzymes may be formulated with at least one physiologically acceptable carrier selected from at least one of maltodextrin, limestone (calcium carbonate), cyclodextrin, wheat or a wheat component, sucrose, starch, Na2SO4, Talc, PVA, sorbitol, benzoate, sorbiate, glycerol, sucrose, propylene glycol, 1,3- propane diol, glucose, parabens, sodium chloride, citrate, acetate, phosphate, calcium, metabisulfite, formate and mixtures thereof.

[0124] In another embodiment, the feed additive composition can be delivered as an aqueous suspension and/or an elixir. The feed additive composition may be combined with various sweetening or flavoring agents, coloring matter or dyes, with emulsifying and/or suspending agents and with diluents such as water, propylene glycol and glycerin, and combinations thereof. The feed additive composition may also be delivered as an aqueous suspension through a waterline.

E. Feedstuffs

[0125] In another embodiment, provided herein are feed additive compositions containing any of the multi-strain DFM compositions disclosed herein that may be used as a feed or in the preparation of a feed. The feed may be in the form of a solution or as a solid depending on the use and/or the mode of application and/or the mode of administration. When used as a feed or in the preparation of a feed, such as functional feed, the feed additive composition may be used in conjunction with one or more of the following: a nutritionally acceptable carrier, a nutritionally acceptable diluent, a nutritionally acceptable excipient, a nutritionally acceptable adjuvant, a nutritionally active ingredient.

[0126] In one embodiment, the feed additive composition disclosed herein is admixed with a feed component to form a feedstuff. In one embodiment, the feed may be a fodder, or a premix thereof, a compound feed, or a premix thereof. In one embodiment, the feed additive composition disclosed herein may be admixed with a compound feed, a compound feed component or a premix of a compound feed or to a fodder, a fodder component, or a premix of a fodder.

[0127] In one embodiment, fodder may be obtained from one or more of the plants selected from: alfalfa (lucerne), barley, birdsfoot trefoil, brassicas, Chau moellier, kale, rapeseed (canola), rutabaga (swede), turnip, clover, alsike clover, red clover, subterranean clover, white clover, grass, false oat grass, fescue, Bermuda grass, brome, heath grass, meadow grasses (from naturally mixed grassland swards, orchard grass, rye grass, Timothy- grass, corn (maize), millet, oats, sorghum, soybeans, trees (pollard tree shoots for tree-hay), wheat, and legumes.

[0128] Compound feeds can be complete feeds that provide all the daily required nutrients, concentrates that provide a part of the ration (protein, energy) or supplements that only provide additional micronutrients, such as minerals and vitamins. The main ingredients used in compound feed are the feed grains, which include com, soybeans, sorghum, oats, and barley.

[0129] A “premix,” as referred to herein, may be a composition composed of micro- ingredients such as vitamins, minerals, chemical preservatives, antibiotics, fermentation products, and other essential ingredients. Premixes are usually compositions suitable for blending into commercial rations.

[0130] In one embodiment, a feedstuff as disclosed herein may comprise one or more feed materials selected from the group comprising cereals, such as small grains (e.g., wheat, barley, rye, oats and combinations thereof) and/or large grains such as maize or sorghum; by products from cereals, such as com gluten meal, Distillers Dried Grain Solubles (DDGS), wheat bran, wheat middlings, wheat shorts, rice bran, rice hulls, oat hulls, palm kernel, and citrus pulp; protein obtained from sources such as soya, sunflower, peanut, lupin, peas, fava beans, cotton, canola, fish meal, dried plasma protein, meat and bone meal, potato protein, whey, copra, sesame; oils and fats obtained from vegetable and animal sources; and minerals and vitamins. [0131] In yet another embodiment, a feedstuff may comprise at least one high fiber feed material and/or at least one by-product of the at least one high fiber feed material to provide a high fiber feedstuff. Examples of high fiber feed materials include: wheat, barley, rye, oats, by products from cereals, such as com gluten meal, Distillers Dried Grain Solubles (DDGS), wheat bran, wheat middlings, wheat shorts, rice bran, rice hulls, oat hulls, palm kernel, and citrus pulp. Some protein sources may also be regarded as high fiber: protein obtained from sources such as sunflower, lupin, fava beans and cotton

[0132] In still another embodiment, the feed may be one or more of the following: a compound feed and premix, including pellets, nuts or (cattle) cake; a crop or crop residue: com, soybeans, sorghum, oats, barley, com stover, copra, straw, chaff, sugar beet waste; fish meal; freshly cut grass and other forage plants; meat and bone meal; molasses; oil cake and press cake; oligosaccharides; conserved forage plants: hay and silage; seaweed; seeds and grains, either whole or prepared by crushing, milling etc.; sprouted grains and legumes; yeast extract.

[0133] In one embodiment, the feed additive composition of disclosed herein is admixed with the product (e.g. feedstuff). Alternatively, the feed additive composition may be included in the emulsion or raw ingredients of a feedstuff. In another embodiment, the feed additive composition is made available on or to the surface of a product to be affected/treated. In still another embodiment, the feed additive compositions disclosed herein may be applied, interspersed, coated and/or impregnated to a product (e.g. feedstuff or raw ingredients of a feedstuff) with a controlled amount of DFM and, optionally, enzymes.

[0134] In yet another embodiment, the DFM and optional enzymes may be used simultaneously (e.g. when they are in admixture together or even when they are delivered by different routes) or sequentially (e.g. they may be delivered by different routes).

[0135] In one embodiment, the DFM and optional enzymes are applied to the feedstuff simultaneously. In yet another embodiment, the DFM and optional enzymes are admixed prior to being delivered to a feedstuff or to a raw ingredient of a feedstuff.

[0136] In one embodiment, the DFMs in the feed additive compositions disclosed herein can be added in suitable concentrations including but not limited to concentrations in the final feed product that offer a daily dose of from about 2x10³ CFU to about 2x10¹¹ CFU, from about 2x10⁶ to about 1x10¹⁰, and from about 3.75x10⁷ CFU to about 1x10¹⁰ CFU.

III. Methods A. Methods for Improving, Performance Metrics in an Animal

[0137] Further provided herein are methods for increasing performance metrics of an animal. In another embodiment, the disclosure relates to methods of increasing performance metrics of a bird. In still another embodiment, the disclosure relates to methods of increasing performance metrics of poultry, including but not limited to broilers, chickens and turkeys.

[0138] In yet another embodiment, the disclosure relates to a method comprising administering to an animal a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and, optionally, exogenous feed enzymes. In still another embodiment, the disclosure relates to a method comprising administering to an animal an effective amount of a composition comprising DFMs and optional exogenous feed enzymes to increase performance of the animal. This effective amount can be administered to the animal in one or more doses. In one embodiment, the animal is poultry. In still another embodiment, the animal is a broiler.

[0139] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optionally exogenous feed enzymes to increase average daily feed intake. In some embodiments, the average daily feed intake increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0140] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to increase average daily weight gain. In some embodiments, the average daily weight gain increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0141] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to increase total weight gain. In some embodiments, total weight gain increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0142] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to increase feed conversion, which can be measured by either feed:gain or gaimfeed. In some embodiments, feed conversion increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi- strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0143] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to increase feed efficiency. In some embodiments, feed efficiency increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0144] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to decrease mortality. In some embodiments, mortality decreases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0145] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to decrease feed conversion ratio (FCR). In some embodiments, FCR decreases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0146] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to increase gut barrier integrity. In some embodiments, gut barrier integrity increases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 105%, or 110%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. “Gut barrier integrity” can refer to, without limitation, epithelial damage and epithelial permeability which is characterized by a shortening of villi, a lengthening of crypts and an infiltration of inflammatory cells (such as, without limitation, CD3+ cells). The latter damage and inflammation markers can also be associated with a “severe” macroscopic appearance of the gut - compared to a “normal” appearance - when evaluated using a scoring system such as the one described by Teirlynck et al. (2011). In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff. [0147] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to decrease or prevent pathogen infection (such as, without limitation, infection by Clostridium perfringens, Campylobacter jejuni, a Salmonela sp., and/or Escherichia coli). In some embodiments, pathogen infection decreases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0148] In another embodiment, the disclosure relates to a method comprising administering to an animal (such as a domesticated bird, for example, a chicken) an effective amount of a composition comprising DFMs (such as any of the multi-strain DFMs disclosed herein) and optional exogenous feed enzymes to decrease or prevent pathogen shedding in the feces (such as, without limitation, shedding of Clostridium perfringens, Campylobacter jejuni, a Salmonela sp., and/or Escherichia coli). In some embodiments, pathogen shedding in the feces decreases by any of about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, inclusive of all values falling in between these percentages, relative to animals who are not administered one or more of the multi-strain DFM compositions disclosed herein. In some embodiments, the composition is a feed additive composition. In other embodiments, the composition is a feed or feedstuff.

[0149] In still another embodiment, the DFM composition (such as a feed or feed additive composition) administered to the animal (such as a domesticated bird, for example, a chicken) is a multi-strain DFM comprising one or more of L. reuteri strain SI (CBS 145921), or a strain having all of the identifying characteristics of L. reuteri strain S1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain SI (SEQ ID NO:7); L. reuteri strain S1a (CBS 147267), or a strain having all of the identifying characteristics of L. reuteri strain S1a, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S1a (SEQ ID NO:7); L. reuteri strain S1b (CBS 147268), or a strain having all of the identifying characteristics of L. reuteri strain S1b, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S1b (SEQ ID NO:7); L. reuteri strain S2 (CBS 145922), or a strain having all of the identifying characteristics of L. reuteri strain S2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2 (SEQ ID NO:8); L. reuteri strain S2a (CBS 147269), or a strain having all of the identifying characteristics of L. reuteri strain S2a, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2a (SEQ ID NO:8); L. reuteri strain S2b (CBS 147270), or a strain having all of the identifying characteristics of L. reuteri strain S2b, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2b (SEQ ID NO:8); and/or L. reuteri strain S3 (CBS 145923), or a strain having all of the identifying characteristics of L. reuteri strain S3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S3 (SEQ ID NO:9). In another embodiment, the DFM composition includes L. reuteri strains S1 and S2; L. reuteri strains S1a and S2; L. reuteri strains S1b and S2; L. reuteri strains S1 and S2a; L. reuteri strains S1 and S2b; L. reuteri strains S1a and S2a; L. reuteri strains S1a and S2b; L. reuteri strains S1b and S2a; L. reuteri strains S1b and S2b; L. reuteri strains S1 and S3; L. reuteri strains S1a and S3; L. reuteri strains S1b and S3; L. reuteri strains S2 and S3; L. reuteri strains S2a and S3; L. reuteri strains S2b and S3; L. reuteri strains S1, S2, and S3; L. reuteri strains S1a, S2, and S3; L. reuteri strains S1b, S2, and S3; L. reuteri strains S1, S2a, and S3; L. reuteri strains S1, S2b, and S3; L. reuteri strains S1a, S2a, and S3; L. reuteri strains S1a, S2b, and S3; L. reuteri strains S1b, S2a, and S3; or L. reuteri strains S1b, S2b, and S3. In some embodiments, the one or more (such as 1, 2, 3, 4, 5, 6, or 7) L. reuteri strain(s) is (are) administered to an animal at a rate of at least 1x10⁴ CFU/animal/day. For poultry, according to one non-limiting embodiment, the one or more L. reuteri strain(s) can be fed at about 1x 10⁵ CFU/g feed to about 1x10¹⁰ CFU/g feed. In at least some embodiments, the one or more L. reuteri strains is (are) fed at about

1x10⁵ CFU/bird/day or about 1x10⁸ CFU/bird/day.

[0150] In still another embodiment, the DFM composition (such as a feed or feed additive composition) administered to the animal (such as a domesticated bird, for example, a chicken) is a multi- strain DFM comprising one or more of L. gallinarum, strain H1 (CBS 145918), or a strain having all of the identifying characteristics L. gallinarum, strain H1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. gallinarum, strain H1 (SEQ ID NO: 11); L. salivarius strain H2 (CBS 145919), or a strain having all of the identifying characteristics of L. salivarius strain H2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain H2 (SEQ ID NO: 10); L. agilis strain H3, or a strain having all of the identifying characteristics of L. agilis strain H3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain H3 (SEQ ID NO;1); and/or L. reuteri strain A2 (CBS 145924), or a strain having all of the identifying characteristics of L. reuteri strain A2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain A2 (SEQ ID NO: 12). In some embodiments, the DFM composition includes only L. gallinarum, strain H1, L. salivarius strain H2, L. agilis strain H3, or L. reuteri strain A2. In another embodiment, the DFM composition includes L. gallinarum, strain H1 and L. salivarius strain H2; L. reuteri strain A2 and L. agilis strain H3; L. gallinarum, strain H1 and L. reuteri strain A2; L. salivarius strain H2 and L. agilis strain H3; L. salivarius strain H2 and L. reuteri strain A2; L. agilis strain H3 and L. reuteri strain A2; L. gallinarum, strain H1, L. salivarius strain H2, and L. agilis strain H3; L. gallinarum, strain H1, L. agilis strain H3, and L. reuteri strain A2; L. salivarius strain H2, L. agilis strain H3, and L. reuteri strain A2; L. gallinarum, strain H1, L. salivarius strain H2, L. agilis strain H3, and L. reuteri strain A2; L. gallinarum, strain H1, L. salivarius strain H2, and L. agilis strain H3; or L. gallinarum, strain H1, L. salivarius strain H2, and L. reuteri strain A2. In some embodiments, L. reuteri strain A2 produces reuterin (3- hydroxypropionaldehyde). In other embodiments, L. reuteri strain A2 does not produce reuterin (3 -hydroxypropionaldehyde). In some embodiments, the one or more H1, H2, H3, and/or A2 strain(s) (such as H1, H2, and H3; or H1, H2, and A2) is (are) administered to an animal at a rate of at least 1x10⁴ CFU/animal/day. For poultry, according to one non-limiting embodiment, the one or more H1, H2, H3, and/or A2 strain(s) (such as H1, H2, and H3; or H1, H2, and A2) can be fed at about 1x10⁵ CFU/g feed to about 1x10¹⁰ CFU/g feed. In at least some embodiments, the one or more H1, H2, H3, and/or A2 strain(s) (such as H1, H2, and H3; or H1, H2, and A2) strains is (are) fed at about 1x10⁵ CFU/bird/day or about

1x10⁸ CFU/bird/day.

[0151] In still another embodiment, the DFM composition (such as a feed or feed additive composition) administered to the animal (such as a domesticated bird, for example, a chicken) is a multi- strain DFM comprising one or more of L. salivarius strain A1, or a strain having all of the identifying characteristics L. salivarius strain A1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain Al (SEQ ID NO:2); L. reuteri strain A2 (CBS 145924), or a strain having all of the identifying characteristics of L. reuteri strain A2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain A2 (SEQ ID NO: 12); and/or L. agilis strain A3, or a strain having all of the identifying characteristics of L. agilis strain A3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain A3 (SEQ ID NO:3). In some embodiments, L. reuteri strain A2 produces reuterin (3- hydroxypropionaldehyde). In other embodiments, L. reuteri strain A2 does not produce reuterin (3 -hydroxypropionaldehyde). In some embodiments, the DFM composition includes only L. salivarius strain A1, L. reuteri strain A2, or L. agilis strain A3. In another embodiment, the DFM composition includes L. salivarius strain Al and L. reuteri strain A2; L. salivarius strain Al and L. agilis strain A3; L. reuteri strain A2 and L. agilis strain A3; or L. salivarius strain A1, L. reuteri strain A2, and L. agilis strain A3. In some embodiments, the one or more A1, A2 and/or A3 strain(s) is (are) administered to an animal at a rate of at least 1x10⁴ CFU/animal/day. For poultry, according to one non-limiting embodiment, the one or more A1, A2 and/or A3 strain(s) can be fed at about 1x10⁵ CFU/g feed to about

1x10¹⁰ CFU/g feed. In at least some embodiments, the one or more A1, A2 and/or A3 strains is (are) fed at about 1x10⁵ CFU/bird/day or about 1x10⁸ CFU/bird/day.

[0152] In still another embodiment, the DFM composition (such as a feed or feed additive composition) administered to the animal (such as a domesticated bird, for example, a chicken) is a multi- strain DFM comprising one or more of L. agilis strain D1, or a strain having all of the identifying characteristics L. agilis strain D1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain DI (SEQ ID NO:5); L. salivarius strain D2, or a strain having all of the identifying characteristics of L. salivarius strain D2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain D2 (SEQ ID NO:4); and/or L. crispatus strain D3, or a strain having all of the identifying characteristics of L. crispatus strain D3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. crispatus strain D3 (SEQ ID NO:6). In some embodiments, the DFM composition includes only L. agilis strain D1, L. salivarius strain D2, or L. crispatus strain D3. In another embodiment, the DFM composition includes L. agilis strain DI and L. salivarius strain D2; L. agilis strain DI and L. crispatus strain D3; L. salivarius strain D2 and L. crispatus strain D3; or L. agilis strain D1, L. salivarius strain D2, and L. agilis strain A3. In some embodiments, the one or more D1, D2 and/or D3 strain(s) is (are) administered to an animal at a rate of at least

1x10⁴ CFU/animal/day. For poultry, according to one non-limiting embodiment, the one or more D1, D2 and/or D3 strain(s) can be fed at about 1x10⁵ CFU/g feed to about

1x10¹⁰ CFU/g feed. In at least some embodiments, the one or more D1, D2 and/or D3 strains is (are) fed at about 1x10⁵ CFU/bird/day or about 1x10⁸ CFU/bird/day.

[0153] The DFM compositions provided herein can be administered, for example, as a strain-containing culture solution, a strain-containing supernatant, or a bacterial product of a culture solution. Administration of a composition comprising a DFM and optional exogenous feed enzymes provided herein to an animal can increase the performance of the animal. In one embodiment, administration of a DFM provided herein to an animal can increase the average daily feed intake (ADFI), average daily gain (ADG), or feed efficiency (gaimfeed; G:F) (collectively, “performance metrics”). One or more than one of these performance metrics may be improved.

[0154] The composition comprising DFMs and exogenous feed enzymes may be administered to the animal in one of many ways. For example, the composition can be administered in a solid form as a veterinary pharmaceutical, may be distributed in an excipient, preferably water (such as through a waterline), and directly fed to the animal, may be physically mixed with feed material in a dry form, or the composition may be formed into a solution and thereafter sprayed onto feed material. The method of administration of the compositions disclosed herein to the animal is considered to be within the skill of the artisan.

[0155] When used in combination with a feed material, the feed material can include com, soybean meal, byproducts like distillers dried grains with solubles (DDGS), and vitamin/mineral supplement. Other feed materials can also be used.

[0156] Thus, in at least some embodiments, the effective amount of the composition comprising DFMs and optional exogenous feed enzymes is administered to an animal by supplementing a feed intended for the animal. As used herein, “supplementing,” refers to the action of incorporating the effective amount of bacteria provided herein directly into the feed intended for the animal. Thus, the animal, when feeding, ingests the bacteria provided herein.

B. Methods for Preparing a Feed Additive Composition

[0157] Also provided herein are methods for preparing a feed additive composition comprising combining two or more of the DFMs disclosed herein. In some embodiments, the method includes combining two or more (such as any of 2, 3, 4, 5, 6, or 7) of L. reuteri strain SI (CBS 145921), or a strain having all of the identifying characteristics of L. reuteri strain S1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain SI (SEQ ID NO:7); L. reuteri strain S1a (CBS 147267), or a strain having all of the identifying characteristics of L. reuteri strain S1a, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S1a (SEQ ID N0:7); L. reuteri strain S1b (CBS 147268), or a strain having all of the identifying characteristics of L. reuteri strain S1b, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S1b (SEQ ID NO:7); L. reuteri strain S2 (CBS 145922), or a strain having all of the identifying characteristics of L. reuteri strain S2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2 (SEQ ID NO:8); L. reuteri strain S2a (CBS 147269), or a strain having all of the identifying characteristics of L. reuteri strain S2a, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2a (SEQ ID NO:8); L. reuteri strain S2b (CBS 147270), or a strain having all of the identifying characteristics of L. reuteri strain S2b, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S2b (SEQ ID NO:8); L. reuteri strain S3 (CBS 145923), or a strain having all of the identifying characteristics of L. reuteri strain S3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain S3 (SEQ ID NO:9). In another embodiment, L. reuteri strains S1 and S2 are combined; L. reuteri strains S1a and S2 are combined; L. reuteri strains S1b and S2 are combined; L. reuteri strains S1 and S2a are combined; L. reuteri strains S1 and S2b are combined; L. reuteri strains S1a and S2a are combined; L. reuteri strains S1a and S2b are combined; L. reuteri strains S lb and S2a are combined; L. reuteri strains S lb and S2b are combined; L. reuteri strains S1 and S3 are combined; L. reuteri strains S1a and S3 are combined; L. reuteri strains S1b and S3 are combined; L. reuteri strains S2 and S3 are combined; L. reuteri strains S2a and S3 are combined; L. reuteri strains S2b and S3 are combined L. reuteri strains S1, S2, and S3 are combined; L. reuteri strains S1a, S2, and S3 are combined; L. reuteri strains S1b, S2, and S3 are combined; L. reuteri strains S1, S2a, and S3 are combined; L. reuteri strains S1, S2b, and S3 are combined; L. reuteri strains S1a, S2a, and S3 are combined; L. reuteri strains S1a, S2b, and S3 are combined; L. reuteri strains S1b, S2a, and S3 are combined; or L. reuteri strains S1b, S2b, and S3 are combined. [0158] In yet further embodiments, the method includes combining two or more (such as any of 2, 3, or 4) of L. gallinarum strain H1 (CBS 145918), or a strain having all of the identifying characteristics L. gallinarum strain H1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. gallinarum strain H1 (SEQ ID NO: 11); L. salivarius strain H2 (CBS 145919), or a strain having all of the identifying characteristics of L. salivarius strain H2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain H2 (SEQ ID NO: 10); L. agilis strain H3, or a strain having all of the identifying characteristics of L. agilis strain H3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain H3 (SEQ ID NO:1); and/or L. reuteri strain A2 (CBS 145924), or a strain having all of the identifying characteristics of L. reuteri strain A2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain A2 (SEQ ID NO: 12). In another embodiment, L. gallinarum strain H1 and L. salivarius strain H2 are combined; L. gallinarum strain H1 and L. agilis strain H3 are combined; L. gallinarum strain H1 and L. reuteri strain A2 are combined; L. salivarius strain H2 and L. agilis strain H3 are combined; L. salivarius strain H2 and L. reuteri strain A2 are combined; L. agilis strain H3 and L. reuteri strain A2 are combined; L. gallinarum strain H1, L. salivarius strain H2, and L. agilis strain H3 are combined; L. gallinarum strain H1, L. agilis strain H3, and L. reuteri strain A2 are combined; L. salivarius strain H2, L. agilis strain H3, and L. reuteri strain A2 are combined; L. gallinarum strain H1, L. salivarius strain H2, L. agilis strain H3, and L. reuteri strain A2 are combined; L. gallinarum strain H1, L. salivarius strain H2, and L. agilis strain H3 are combined; or L. gallinarum strain H1, L. salivarius strain H2, and L. reuteri strain A2 are combined.

[0159] In additional embodiments, the method includes combining two or more (such as any of 2 or 3) of L. salivarius strain A1, or a strain having all of the identifying characteristics L. salivarius strain A1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain Al (SEQ ID NO:2); L. reuteri strain A2 (CBS 145924), or a strain having all of the identifying characteristics of L. reuteri strain A2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. reuteri strain A2 (SEQ ID NO: 12); and/or L. agilis strain A3, or a strain having all of the identifying characteristics of L. agilis strain A3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain A3 (SEQ ID NO:3). In another embodiment, L. salivarius strain Al and L. reuteri strain A2 are combined; L. salivarius strain Al and L. agilis strain A3 are combined; L. reuteri strain A2 and L. agilis strain A3 are combined; or L. salivarius strain A1, L. reuteri strain A2, and L. agilis strain A3 are combined.

[0160] In further embodiments, the method includes combining two or more (such as any of 2 or 3) of L. agilis strain D1, or a strain having all of the identifying characteristics L. agilis strain D1, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. agilis strain DI (SEQ ID NO:5); L. salivarius strain D2, or a strain having all of the identifying characteristics of L. salivarius strain D2, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. salivarius strain D2 (SEQ ID NO:4); and/or L. crispatus strain D3, or a strain having all of the identifying characteristics of L. crispatus strain D3, or a microbe having a 16S ribosomal RNA sequence displaying at least about 97.0% sequence similarity (such as any of about 97%, 97.5%, 98%, 98.5%, 99%, 99.5%, or 100% sequence similarity) to a 16S ribosomal RNA sequence of L. crispatus strain D3 (SEQ ID NO:6). In another embodiment, L. agilis strain DI and L. salivarius strain D2 are combined; L. agilis strain DI and L. crispatus strain D3 are combined; L. salivarius strain D2 and L. crispatus strain D3 are combined; or L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3 are combined.

[0161] Additionally, the methods for preparing a feed additive composition can further include combining the feed additive composition with one or more of the exogenous enzymes disclosed herein (for example, one or more of a phytase, a protease, an amylase, a xylanase or a beta-glucanase). The method can additionally include a further step of packaging the feed additive composition for storage or transport.

C. Methods for removing antimicrobial resistance (AMR} genes

[0162] Bacteria have evolved to overcome a wide range of antibiotics, and resistance mechanisms against most of the conventional antibiotics have been identified in some bacteria. Accelerated development of newer antibiotics is being overrun by the pace of bacterial resistance. In the USA, for example, over 70% of hospital- acquired infections involve bacteria resistant to at least one antibiotic, and in Japan over 50% of the clinical isolates of Staphylococcus aureus are multidrug-resistant. Thus, removal of antimicrobial resistance (AMR) genes from probiotic s/DFMs used for the prevention of intestinal inflammation and in the maintenance of intestinal homeostasis can in some instances be desirable.

[0163] AMR genes carried by a variety of bacteria are known in the art and the sequences of antibiotic resistance genes in any particular bacteria can be determined if desired. In certain non-limiting embodiments, the present disclosure includes CRISPR systems which can be used to remove antibiotic resistance genes. In some embodiments, the resistance gene confers resistance to a narrow- spectrum beta-lactam antibiotic of the penicillin class of antibiotics. In other embodiments, the resistance gene confers resistance to methicillin (e.g., methicillin or oxacillin), or flucloxacillin, or dicloxacillin, or some or all of these antibiotics.

[0164] Examples of AMR genes include, but are not limited to, fosfomycin resistance genefosB, tetracycline resistance gene tetM or tetW, kanamycin nucleotidyltransferase aadD, bifunctional aminoglycoside modifying enzyme genes aacA-aphD, chloramphenicol acetyltransferase cat, mupirocin-resistance gene ileS2, vancomycin resistance genes vanX, vanR, vanH, vraE, vraD, methicillin resistance factors femA, fmtA, mecf streptomycin adenylyltransferase spc1, spc2, anti, ant2, spectinomycin adenylyltransferase ant(9), aminoglycoside nucleotidyltransferase spd, aadA2, nucleotidyltransferase InuA, InuB, InuC, acetyltransferase vatE,,and any other resistance gene. In some embodiments, the AMRs are associated with one or more mobile genetic elements (such as a transposon) than can be located near the AMR gene (such as within any of about 10 kb, 9 kb, 8 kb, 7 kb, 6 kb, 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or closer to the AMR gene, including distances falling in between any of these values).

[0165] AMRs can be identified or assayed qualitatively and/or quantitatively by any number of methods known in the art. For example, DNA can be extracted from microbial samples and assessed for the presence of antibiotic resistance genes using, e.g., PCR, quantitative PCR (qPCR), including multiplex quantitative PCR (qPCR). The microbial DNA array assay may test for a plurality of antibiotic resistance genes and facilitate testing for highly prevalent bacterial antibiotic resistance genes in a single reaction with both resistance gene identification (present vs absent) and quantitative profiling (expression relative to an internal standard). Other methods for identifying AMRs include, without limitation, whole genome sequencing via use of short-read sequencing technology (Illumina) and/or long -read sequencing technology platforms such as Oxford Nanopore Technology or PacBio or via the techniques used and discussed in Example 5. Once identified, AMR genes can be removed or inactivated using any number of standard molecular tools available in the art such as recombineering (Zhang et al., 2018, J Bacterial 200; Ozcam et al., 2019, Appl Environ Microbiol 85, the disclosures of which are incorporated by reference herein), or CRISPR based methods (Oh & Van Pijkeren, 2014, Nucleic Acids Res 42:el31; U.S. Patent Application Publication No. 2017/0260546, the disclosures of which are incorporated by reference herein ), or through the loss of plasmids carrying AMR genes (Rosander et al., 2008, Appl Environ Microbiol IN. 6032-6040, incorporated by reference herein).

[0166] In some embodiments, one or more of (such as any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11) the strains provided herein including L. reuteri strain SI (CBS 145921), L. reuteri strain S2 (CBS 145922), L. reuteri strain S3 (CBS 145923), L. gallinarum strain H1 (CBS 145918), L. salivarius strain H2 (CBS 145919), L. reuteri strain A2 (CBS 145924), L. agilis strain H3, L. salivarius strain A1, L. agilis strain A3, L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3 further comprise one or more (such as any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) inactivated or deleted AMR genes.

IV. Kits

[0167] Further provided herein are kits containing one or more of the DFMs (such as one or more of the multi-strain DFMs) disclosed herein. The kits can include one or more of (such as any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11) the strains provided herein including L. reuteri strain SI (CBS 145921), L. reuteri strain S1a (CBS 147267); L. reuteri strain S1b (CBS 147268); L. reuteri strain S2 (CBS 145922), L. reuteri strain S2a (CBS 147269); L. reuteri strain S2b (CBS 147270); L. reuteri strain S3 (CBS 145923), L. gallinarum strain H1 (CBS 145918), L. salivarius strain H2 (CBS 145919), L. reuteri strain A2 (CBS 145924), L. agilis strain H3, L. salivarius strain A1, L. agilis strain A3, L. agilis strain D1, L. salivarius strain D2, and L. crispatus strain D3 along with instructions for proper storage, maintenance, and use for administering to an animal to improve one or more performance metrics. In one embodiment, the kit can include strains S1, S1a, S1b, S2, S2a, S2b, and/or S3. In another embodiment, the kit can include strains H1, H2, H3, and/or A2 (such as H1, H2, and H3; or H1, H2, and A2). In a further embodiment, the kit can include strains A1, A2, and/or A3. In yet a further embodiment, the kit can include strains D1, D2, and/or D3. The kits can additionally include one or more of the exogenous enzymes disclosed herein (for example, one or more of a phytase, a protease, an amylase, a xylanase or a beta-glucanase).

[0168] The invention can be further understood by reference to the following examples, which are provided by way of illustration and are not meant to be limiting.

EXAMPLES

Example 1 : Materials and Methods

[0169] In the following examples, various methods and assays were used as set forth below for ease in reading. Any deviations from the protocols provided below are indicated in the relevant sections.

[0170] Isolation of Lactobacillus strains from chicken intestinal tracts: GIT samples dissected in the field were transferred into anaerobic transport media as quickly as possible. Strain isolation started once intestinal samples arrived at the lab. Ceca, ileum, jejunum or duodenum samples were dissected using sterile technique inside an anaerobic chamber. The digesta was discarded and mucosal-bound material was scraped using a loop. This material was then transferred into sterile media or buffer and serially diluted. Serial dilutions ranging from 10^-1 to 10^-6 were plated onto petri dishes or omni plates of various media types using plating beads. These plates were then incubated anaerobically until colonies became visible. De Man, Rogosa and Sharpe agar (MRS) or Brain heart infusion medium (BHI) was used for isolation.

[0171] Once colonies were visible on an agar plate, colonies were picked in the anaerobic chamber to liquid media in a 96 deep well plate. Some plates were initially picked into a small volume of liquid media (i.e.200 μl) and then media added to 800 pl 1-4 days later to increase growth. Colony picking could be done at multiple time points for the same plate. For example, large colonies were picked on day 2, and then very small colonies or new colonies were picked at day 5. [0172] Analysis of the microbial composition of mucosa region of the small intestines by 16S sequencing and netB qPCR: To evaluate the microbial composition of the small intestines, chicken swabs of the mucosa region of the small intestines was analyzed by 16S sequencing. Chicken gastro intestinal tract (GIT) is removed and separated into four sections: duodenum, jejunum, ileum and ceca. Each section is squeezed to remove the digesta contents and then cut longitudinally to expose the inner surface. Each section inner surface is swabbed with a FLOQSwab (Copan Mfgr, Murrieta, CA). The swab is added directly to a well of a 96 well Qiagen MagAttract PowerSoil kit (Qiagen, Hilden, Germany). The swabs were processed for bacterial DNA isolation as per the manufacturer’s instructions using the KingFisher Flex automation platform. Isolated metagenomic DNA is then ready for NGS sample preparation

[0173] Metagenomic DNA purified from chicken GIT swabs was prepared for 16S community sequencing as follows: DNA is diluted 1:5 by adding 20μl of molecular biology grade water to 5μl of purified DNA at 0.1 - 10ng/pl. Then 2μl of the diluted DNA was added to a PCR reaction along with 25ul of ABI Universal TaqMan Reaction mix without UNG (ThermoFisher #4326614), 0.1μl each PCR primers at 100uM and 24.8μl of Molecular Biology Grade water for a total volume of 50ul. The PCR primers were the Illumina-V4- 515F-RJ:

TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTGCCAGCMGCCGCGGTAA and Illumina-V4-806R-RJ:

GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGACTACHVGGGTWTCTAAT were used. The PCR reactions were: 10min at 95°C followed by 35 cycles of 95°C 15sec + 55°C 30sec + 72°C for 2min. Amplified reactions were purified using Ampure XP Magnetic Beads (Beckman Coulter A63881) as per manufacturer’s instructions using the Agilent Bravo Automated Robotic Workstation. 2pl of each amplicon pool was then indexed in a second PCR reaction using the same conditions as above with Illumina XT Index Primers (Illumina XT v2.0 #FC- 131-2001-2004) for 15 cycles. Indexed amplicons are then pooled and purified with AmPure XP Magnetic Beads on the Agilent Bravo Automated Robotic Workstation. Pooled, indexed amplicons were quantitated using the Kapa Illumina Library Quantification Kit (KAPA #KK4835) as per manufacturer’s instructions. Purified, quantitated, indexed, pools were loaded on the Illumina MiSeq at a final concentration of 8pM along with 15% Illumina PhiX (Illumina FC-110-3001). Sequencing was run for 2 x 250 Paired End cycles. [0174] The 16S Amplicon data from Illumina Miseq sequencing were analyzed. Paired-end reads were first merged by Flash (Mogoc et al., Bioinformatics . 2011;27:2957-63). The forward and reverse primers were removed from the merged reads, and reads with overall quality score less than 20 were discarded by RDP Initial Process tool (Fish et al., Front Microbiol. 2013;4:291). This step also removes reads originated from chicken mitochondria due to their length shorter than 200 bp. In the next step reads were assigned to bacterial and archaeal taxonomy by RDP Classifier (Wang et al., Appl Environ Microbiol. 73( 16):5261- 5267). The reads passed the above quality processing steps were clustered at 98% by CD- HIT (Li & Godzik, Bioinformatics, 2006; 22:1658-9) to obtain Operational Taxonomic Units (OTU). The representative sequence from each OTU was assigned to the closest species by RDP pairwise alignment tool (Fish et al., Front Microbiol. 2013; 4:291) against a vetted 16S reference database containing mostly 16S genes from type strains and public genomes. The relative abundance of an OTU in a sample was the fraction of reads assigned to that OTU. An OTU was assigned to a species if it has at least 98% identity to that species in the reference database. The average abundance of a species in a consortium in small intestine was calculated as the average relative abundance of that species from DUO, JEJ and ILL samples of each treatment.

[0175] The same DNA preparations were also quantified for netB gene using qPCR. NetB is an important virulence factor for C. perfringens. Each assay was run using 1.5μl of DNA along with 10μl of TaqMan Universal Master Mix, 0.2pl of 10OuM Forward and Reverse Primers, 0.05μl of TaqMan Probe, and 9.55μl Molecular Biology Grade water. The qPCR reaction conditions were as follows: 10min at 95°C + 40 cycles of 95°C 15sec + 60°C 60sec on the ABI Quant Studio qPCR instrument. Sample data was quantified using genomic DNA from a netB positive C. perfringens. Primer and probe sequences used are in Table 5 below.

Table 5: qPCR Primers and Probes

[0176] Binding assay to characterize the capability of Lactobacillus isolates to attach to mucin and collagen: The major component of the mucus membrane in the small intestines is mucin and the ability to bind to mucin was used to evaluate their ability to adhere to GI track. The binding assay was carried out with 96 wells in a sterile non-TC treated polystyrene plate. The initial step was the coating of the plate with mucin (type II or type III porcine mucin, Sigma). The mucin solution (1%) was prepared by stirring for a few hours till a homogenous suspension was obtained. The solution was autoclaved before use. 120 pl of mucin solution was added to each 96 well and the plate was incubated at 4°C overnight. Right before use, the unbound mucin was removed and rinsed twice with 125 pl molecular biology grade water.

[0177] For binding assay, fresh overnight cultures grown in MRS medium at 37 or 40°C were used. The cultures were first collected by centrifugation and washed once with 1x PBS medium. 100 pL culture at 1 OD (600 nm) was added into each well in the washed mucin coated plate and the plate was incubated in the 37°C anaerobic chamber or anaerobic jar for 2 hours. After incubation, the plate was washed with 100 pL 1X PBS twice and the attached cells in each well was stained by adding 100 μl of 0.1% solution of crystal violet (1% stock solution from Sigma) diluted in water. The plate was allowed to sit for 5 to 10 min at room temperature. The unbound dye was removed and each well was washed three times with 100 pl 1X PBS. To measure the dye bound to the attached cells, 100 μl of 1X PBS was used to re-suspend the bound cells by pipetting up and down. Alternatively, 100 μl of ethanol was used to dissolve the dye. After 20 min, the dye intensity was measured at 570 or 590 nm.

The reading reflected the number of attached cells.

[0178] A similar procedure was used to evaluate the ability of Lactobacillus strains to bind the Biocoat collagen IV plates from Coming. It has been reported that collagen binding is one of the important virulence factors for C. perfringens (Vet Microbiol. 2015 Nov

18; 180:299-303). One of the potential beneficial properties of DFM can be the competitive binding of this extracellular matrix.

[0179] Antimicrobial assay to characterize Lactobacillus isolates for antimicrobial activity against C. perfringens’. Microplate based antimicrobial assay was performed using supernatants of Lactobacillus isolates from chicken GIT samples. Isolates were inoculated in MRS liquid medium and grew at 37°C for 2 to 3 days anaerobically. Cultures were centrifuged at 4500 rpm for 5 min and supernatants were collected in Costar 96 well plate and filtered. 20 or 25μl supernatant was used for assay.

[0180] The target pathogen C. perfringens from a fresh plate was inoculated in BHI medium at 37°C and grew overnight anaerobically. C. perfringens culture was diluted into an OD (600 nm) of 0.1 with BHI medium. 175 or 180 pL diluted C. perfringens culture was added to each well containing 20 or 25μl supernatant to a final volume of 200 pl. For the control, 20 or 25μl of MRS medium was used. The assay plate was incubated under anaerobic conditions at 37°C for 18 hours and then OD (600 nm) was measured. The amount of the growth relative to the control was used to measure the antimicrobial activity. Alternatively, the growth was monitored continuously using a microtiter reader.

[0181] Animal model for necrotic enteritis caused by C. perfringens’. A challenged diseased model for broiler chicken has been used extensively {Front Microbiol. 2016, 7:1416; J Anim Sci Biotechnol. 2018, 9:25; Poult Sci. 2018, Nov 18). In this experiment, chickens at day 9 were first challenged with live 1 x Eimeria vaccine (ADVENT® coccidiosis vaccine, Huvepharma, Inc., Lincoln, NE 68528). Seventeen (17) birds were in each of the experimental and control groups. The vaccine was diluted in water and each chicken received 1ml orally. At day 11, each chicken received 1 ml of pathogen cocktail orally. The pathogen cocktail consisted of five Clostridium perfringens strains isolated from diseased tissues. All strains contained the netB and tpel genes based on the genome analysis. These strains were grown individually in cooked meat medium (Sigma) overnight and the fresh cultures were mixed in equal volume in a glove box to make up the cocktail. The cocktail was used the same day to induce necrotic enteritis.

[0182] With this disease model, Lactobacillus isolates were evaluated for their efficacy against C. perfringens infection. Lactobacillus strains were grown in MRS medium under anaerobic conditions. Fresh cultures were mixed in equal volume and the mixed cell suspension for each consortium was aliquoted into serum bottles. The serum bottles were stored at 80°C and thawed before use. The Lactobacillus consortia were fed to each chicken daily by gavage starting at day 1. At day 15, chicken intestines were collected for histopathology analysis and the mucosa samples were used for DNA isolation as described supra. Example 2: Binding and Antimicrobial properties of Lactobacillus strains isolated from Chicken small intestines

[0183] Table 6 summarized the in vitro assay results of Lactobacillus strains for their antimicrobial ability and their ability to bind to either mucin or collagen as described per the methods of Example 1. While the activities were strain-dependent, the supernatants from L. salivarious isolates had high antimicrobial activity. Those from L. reuteri had lower antimicrobial activity, but quite a few had excellent ability to bind to collagen.

Table 6: Results of in vitro assays of Lactobacillus strains

Example 3: Animal model for necrotic enteritis caused by C. perfringens

[0184] DFM candidates were evaluated for their efficacy against C. perfringens infection in an animal model. For animal study, the lactobacillus strains were grouped as consortia based on their phylogenetic diversity and representation of a broad spectrum of in vitro assay results. The consortia and their strain composition are listed in Table 7. These strains were grown in MRS medium under anaerobic conditions and the fresh culture were mixed in equal volume inside the glovebox to make up a specific consortium for the animal trial. The mixed cell suspension for each consortium was aliquoted into serum bottles under anaerobic conditions inside a glove box. The serum bottles were stored at 80°C and thawed before use. Each consortium was fed to chicken daily by gavage starting at day 1. At day 15, chicken intestines were collected for histopathology analysis and the mucosa samples were used for DNA isolation as described in Example 1.

Table 7: List of Lactobacillus strains used for animal study

[0185] The abundance of C. perfringens based on 16S analysis using samples from day 15 as described in Example 1 is summarized in Table 8. In the control group (disease model) where no Lactobacillus strains were used, necrotic enteritis in the small intestines was observed. Consistent with this result, there was abundance of C. perfringens as quantified based on 16S analysis and netB qPCR. Chicken feed with consortia E and C, showed similar high abundance of C. perfringens as the chicken in the control group. Chicken from these two groups suffered from necrotic enteritis. This suggests that these two consortia did not show efficacy against the expansion of the pathogen in the animal trial. On the other hand, the abundance of C. perfringens was much lower in consortia A, D, H, and S.

Histopathology indicated no sign of necrotic enteritis. This result suggests these four consortia had efficacy in the prevention of C. perfringens infection. From this animal study, it is clear that the efficacy against C. perfringens infection depended on the specific composition of the consortium since both consortia C and E had some of the same Lactobacillus species as consortia in A, D, H, and S

Table 8: Results of animal trials

Example 4: Large scale animal trial to assess improved mortality benefits of consortium

[0186] In February 2020, four commercial broiler chicken houses located in the United States were each stocked with approximately 56,000 birds (approximately 224,000 total birds were used in this study). Necrotic enteritis affecting large-scale chicken production in the U.S. is typically most prevalent during the months of November through April.

[0187] Each house was divided into two halves; 50% of the birds were supplemented with the Direct Fed Microbial (DFM; a combination of 3 L. reuteri strains S1, S2, and S3), the remaining 50% of each house were used as unsupplemented controls. Each half of the house received water via a different waterline. All birds were fed a typical U.S. com/soy based pelleted feed ad libitum.

[0188] Birds were placed on Day 1 and slaughtered on Day 52. The DFM was supplemented into the waterline via the medicator at a dose of 1.2 x 10⁸ CFU/bird/day on days 17, 18, 19, 20 and 21 of production for three out of 4 houses and day 17 only for one house (day 17 onwards coincides with the highest rate of necrotic enteritis outbreaks typically observed in the field during this time of the year).

[0189] Flock mortality data for each of the houses was collected and is shown in FIG. 1. Control birds exhibited a combined mortality rate of approximately 11% whereas birds receiving DFM supplementation exhibited mortality rates of 6.9% (i.e. a 61.5% total reduction in mortality over the course of the study).

[0190] Survival probability analysis was conducted, and production cost savings were calculated on a per million bird bases. To calculate the cost savings delivered by the DFM supplementation, the following parameters were taken into consideration: weekly mortality, weekly feed consumption, feed cost ($0.11 per lb), chick cost ($0.34 USD per chick), and approximate condemnations. In this study, DFM supplementation and the associated reduction in mortality resulted in avoided losses of approximately $5769 USD or savings of $51,514 USD per million birds.

Example 5: Identification and removal of antimicrobial resistance (AMR) genes

[0191] This Example demonstrates the identification and removal of antimicrobial resistance (AMR) genes from consortia members. AMR genes, particularly those associated with mobile genetic elements, are of concern because they can in some instances be transferred among different bacterial cells, thereby promoting antibiotic resistance. To prevent the spread of these AMR markers and to comply with regulatory requirements, it may be beneficial to remove them from strains used as DFMs in livestock.

[0192] The strains from the different consortia were sequenced using a combination of the short-read sequencing technology of Illumina and long-read sequencing technology platforms such as Oxford Nanopore Technology or PacBio. The reads from a strain were processed using standard trimming procedures and assembled into a sequence using standard tools such as SPAdes (Bankevich et al,. 2012, J Comput Biol 19:455-477), Unicycler (Wick et al., 2017, PLoS Comput Biol 13:e1005595), and Pilon (Walker et al., 2014, PLoS One 9:el 12963). The sequence was subsequently annotated using prokka (Seemann, 2014, Bioinformatics 30:2068- 2069) or PATRIC (Wattam et al. 2018, Methods Mol Biol 1704:79-101). Antimicrobial resistance (AMR) genes were identified using CARD (Alcock et al., 2020, Nucleic Acids Res 48:D517-D525), the Comprehensive Antibiotic Resistance Database, and PARTIC (Davis et al., 2016, Sci Rep 6:27930). Any AMR genes identified by these databases were subsequently inspected for mobile genetic elements within the surrounding 10kb.

[0193] Strain S3 was found to be free of AMR genes, while SI and S2 both had two different AMR genes associated with mobile genetic elements: InuC, a transposon-mediated nucleotidyltransferase, and vatE, a transposon-mediated acetyltransferase. Both genes are next to a transposase. The AMR gene and transposase were found to be flanked by a set of indirect and direct repeats (Achard et al., 2005, Antimicrob Agents Chemother 49:2716- 2719). Four copies of InuC spread throughout the genome and one copy of vatE were identified in S1, while one copy of either gene was found in S2. This strain S2 also contained a tetW gene that was not associated with any mobile genetic elements within the surrounding 10kb of the gene.

[0194] Positions of the genes in S 1 were identified based on the PacBio hybrid sequence of InuC (470,273 forward, 995,196 reverse, 1,149,997 forward, 1,775,176 forward) and vatE (1,439,964) and in S2 based on the ONT hybrid sequence of InuC (161,023 forward), vatE (457,661 forward) and tetW (818,067 reverse).

[0195] These genes and their associated transposases were removed using standard molecular tools such as recombineering (Zhang et al., 2018, J Bacterial 200; Ozcam et al., 2019, Appl Environ Microbiol 85) or CRISPR based methods (Oh & Van Pijkeren, 2014, Nucleic Acids Res 42:el31).

[0196] New L. reuteri strains lacking the AMR genes were designated S1a, S1b, S2a, and S2b. FIG. 2 shows deletions in strain S1a verses the parent SI strain, with four InuC AMR genes deleted and one vatE gene deleted. FIG. 3 shows deletions in strain S2b compared to the parent S2 strain, with one InuC AMR and one vatE gene deleted.

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Claims

67 CLAIMS We claim:

1. A biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267.

2. A biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147268.

3. A biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147269.

4. A biologically pure strain of Lactobacillus reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147270.

5. A feed additive composition comprising a direct fed microbial (DFM) comprising one or more biologically pure strains of Lactobacillus reuteri selected from the group consisting of (a) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; and (d) a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270.

6. The feed additive composition of claim 5, further comprising a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923. 68

7. The feed additive composition of claim 6, comprising a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at WFDB under number CBS 147267; a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and a biologically pure strain of L. reuteri displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923.

8. The feed additive composition of any one of claims 1-7, wherein the feed additive composition comprises one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); and/or (d) L. reuteri strain S2a (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147270).

9. The feed additive composition of claim 8, further comprising L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 (CBS 145923).

10. The feed additive composition of any one of claims 5-9, wherein the composition produces one or more organic acids selected from the group consisting of lactate, butyrate, isobutyrate, propionate, acetate, isovalerate, and valerate.

11. The feed additive composition of any one of claims 5-10, further comprising one or more enzymes.

12. The feed additive composition of claim 11, wherein the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase, and a beta-glucanase.

13. The feed additive composition of any one of claims 5-12, further comprising one or more essential oils. 69

14. The feed additive composition of any one of claims 5-13, wherein each strain is present at a concentration of at least about 1 x 10³ CFU/g feed additive composition to at least about 1 x 10¹⁵ CFU/g feed additive composition.

15. The feed additive composition of any one of claims 5-14, wherein the composition inhibits at least one pathogen selected from avian pathogenic Salmonella sp.. Escherichia coll, Clostridium perfringens and Enterobacteriaceae in a gastrointestinal tract of a bird having ingested an effective amount of said direct fed microbial composition.

16. The feed additive composition of any one of claims 5-15, wherein the composition is formulated for delivery to an animal via waterline.

17. A bacterial consortium comprising one or more of (a) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; (d) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and/or (e) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923.

18. The consortium of claim 24, comprising one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); (d) L. reuteri strain S2b (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2b (CBS 147270);(e) L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 70

(CBS 145923) either (A) alone; or (B) in combination with a culture supernatant derived from one or more of these strains.

19. The consortium of claim 17 or claim 18, wherein a) the 16S ribosomal RNA sequence of L. reuteri strain S1a and S1b comprises the nucleotide sequence of SEQ ID NO:7; (b) the 16S ribosomal RNA sequence of L. reuteri strain S2a and S2b comprises the nucleotide sequence of SEQ ID NO:8; and (c) the 16S ribosomal RNA sequence of L. reuteri strain S3 comprises the nucleotide sequence of SEQ ID NO:9.

20. The bacterial consortium of any one of claims 17-19, wherein the consortium produces one or more organic acids selected from the group consisting of lactate, butyrate, isobutyrate, propionate, acetate, isovalerate, and valerate.

21. The bacterial consortium of any one of claims 17-20, wherein each strain is present at a concentration of at least about 1 x 10³ CFU/animal/day to at least about 1 x 10¹⁵ CFU/animal/day in the consortium.

22. The bacterial consortium of any one of claims 17-21, herein the consortium inhibits at least one pathogen selected from avian pathogenic Salmonella sp., Escherichia coll, Clostridium perfringens and Enterobacteriaceae in a gastrointestinal tract of a bird having ingested an effective amount of said direct fed microbial composition.

23. A premix comprising the feed additive composition of any one of claims 5-16 or the bacterial consortium of any one of claims 17-22 and at least one mineral and/or at least one vitamin.

24. A feed comprising the feed additive compositions of any one of claims 5-16 or the bacterial consortium of any one of claims 17-22 or the premix of claim 23.

25. A kit comprising a)(i) the feed additive composition of any one of claims 5-16; (ii) the bacterial consortium of any one of claims 17-22; or (iii) the premix of claim 23; and b) written instructions for administration to an animal.

26. The kit of claim 25, further comprising one or more enzymes.

27. The kit of claim 26, wherein the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase and a beta-glucanase. 71

28. A method for improving one or more metrics in an animal selected from the group consisting of increased body weight gain, intestinal health status, decreased feed conversion ratio (FCR), improved gut barrier integrity, reduced mortality, reduced pathogen infection, and reduced pathogen shedding in feces comprising administering an effective amount of the feed additive composition of any one of claims 5-16, the bacterial consortium of any one of claims 17-22, the premix of claim 23, or the feed of claim 24 to the animal, thereby improving the one or more metrics in the animal.

29. The method of claim 28, wherein the feed additive composition increases one or more of the lactate, acetate, isobutyrate, butyrate, isovalerate, and/or valerate content of the gastrointestinal tract of the animal.

30. The method of claim 27 or claim 28, wherein the pathogen is one or more of Clostridium perfringens, Campylobacter jejuni, Enterobacteriaceae, a Salmonela sp., and/or Escherichia coli.

31. The method of any one of claims 28-30, wherein the method further treats, prevents, or decreases incidence of necrotic enteritis.

32. The method of any one of claims 28-31, wherein the animal is a domesticated bird.

33. The method of claim 32, wherein the domesticated bird is selected from the group consisting of chickens, turkeys, ducks, geese, quail, emus, ostriches, and pheasant.

34. The method of claim 33, wherein the chicken is a broiler or a layer.

35. The method of any one of claims 28-33, wherein the feed additive composition, the bacterial consortium, or the premix is administered by waterline.

36. A method for preparing a feed additive composition or a bacterial consortium comprising combining one or more of (a) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1a deposited at Westerdijk Fungal Biodiversity Institute (WFDB) under number CBS 147267; (b) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S1b deposited at WFDB under number CBS 147268; (c) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal 72

RNA sequence of a L. reuteri strain S2a deposited at WFDB under number CBS 147269; (d) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S2b deposited at WFDB under number CBS 147270; and/or (e) a bacterial strain having a 16S ribosomal RNA sequence displaying at least 97.0% sequence similarity to a 16S ribosomal RNA sequence of a L. reuteri strain S3 deposited at WFDB under number CBS 145923.

37. The method of claim 49, wherein the composition or consortium comprises one or more of (a) L. reuteri strain S1a (CBS 147267) or a live strain having all of the identifying characteristics of L. reuteri strain S1a (CBS 147267); (b) L. reuteri strain S1b (CBS 147268) or a live strain having all of the identifying characteristics of L. reuteri strain S1b (CBS 147268); (c) L. reuteri strain S2a (CBS 147269) or a live strain having all of the identifying characteristics of L. reuteri strain S2a (CBS 147269); (d) L. reuteri strain S2b (CBS 147270) or a live strain having all of the identifying characteristics of L. reuteri strain S2b (CBS 147270);(e) L. reuteri strain S3 (CBS 145923) or a live strain having all of the identifying characteristics of L. reuteri strain S3 (CBS 145923) either (A) alone; or (B) in combination with a culture supernatant derived from one or more of these strains.

38. The method of claim 36 or claim 37, further comprising combining one or more enzyme(s) with the feed additive composition.

39. The method of claim 38, wherein the one or more enzymes are selected from the group consisting of a phytase, a protease, an amylase, a xylanase and a beta-glucanase.

40. The method of any one of claims 36-39, wherein (a) at least about 1 x 10³ CFU/g feed additive composition to at least about 1 x 10¹⁵ CFU/g feed additive composition is combined to form the feed additive composition; or (b) at least about 1 x 10³ CFU/animal/day bacterial consortium to at least about 1 x 10¹⁵ CFU/animal/day is combined to form the bacterial consortium.

41. The method of any one of claims 36-40, further comprising packaging the feed additive composition.

42. A method for preparing a premix comprising combining the feed additive composition of any one of claims 5-16 with at least one mineral and/or at least one vitamin.

43. The method of claim 42, further comprising packaging the premix.