WO2022221477A1

WO2022221477A1 - Probiotic composition for weaning infants

Info

Publication number: WO2022221477A1
Application number: PCT/US2022/024716
Authority: WO
Inventors: David J. Kyle; Ryan Mitchell
Original assignee: Evolve Biosystems, Inc.
Priority date: 2021-04-13
Filing date: 2022-04-13
Publication date: 2022-10-20
Also published as: EP4322771A1

Abstract

Missing abstract

Description

Probiotic Composition for Weaning Infants FIELD OF THE INVENTION [0001] The inventions described herein relate generally to digestive healthcare, and more particularly, to the feeding of mammals, particularly human infants, who are making a transition from a microbiome driven by a single or limited diet to a variable and less predictable diet. These inventions relate to certain diet circumstances that impact microbiome function and stability especially introducing transitional or complementary foods to human infants comprising new fermentable nutritional components in addition to the human milk oligosaccharides (HMO) with a bacterial consortium that have characteristics that favor the utilization of these transitional glycans. The present inventions provide combinations of foods and commensal bacteria that can protect the mammalian gut from blooms of pathogenic bacteria under the circumstances where the nutrient supply to the mammalian gut is changing either through the course of weaning from human milk to other sources of nutrition, or in individuals whose gut microbiome has been extensively depleted through antibiotic and/or post-chemotherapeutic treatment and is transitioning to a higher diversity adapted/stable microbiome with the introduction of new dietary fiber, or in response to a particular disease condition where changing dietary conditions and the microbiome are advantageous to prevention and/or treatment of said disease. BACKGROUND [0002] The intestinal microbiome is the community of microorganisms that live within the gastrointestinal tract, the majority of which is found in the large intestine or colon. In a healthy individual, most simple dietary carbohydrates are absorbed by the body before they reach the colon. However, many foods contain indigestible carbohydrates (i.e., dietary fiber) that remain generally intact and are poorly absorbed, if at all, during transit through the gut to the colon. The colonic microbiome is thereby rich in bacterial species that can partially consume these fibers and utilize the constituent sugars for energy and metabolism and, in many cases, provide additional benefits to the host (Duar, 2020; Front. Nutr., 14 April 2020, doi.org/10.3389/fnut.2020.00033). In mammalian species, the nursing infant’s intestinal microbiome during breast-feeding is quite different from that of an adult microbiome. The adult gut microbiome generally contains a large variety of microorganisms, each present as a minor portion of the total population. The gut microbiome diversity is proportional to the dietary diversity of the individual and can be diminished with the introduction of antibiotics. Recovery of the gut microbiome after antibiotic therapy is a slow process, leaving open nutritional niches that can allow immediate colonization by opportunistic pathogens, and may not result in a complete recovery of the original pre-antibiotic treatment diversity. Different dietary fibers from plant or animal sources provide a multitude of nutritional niches for different microbiome taxa leading to a gut microbiome of high taxonomic diversity.Human infants have historically (over millennia) had only a single source of nutrition for the first few months of life – human breast milk. Human milk is highly enriched in a soluble fiber (human milk oligosaccharides - HMO) that is indigestible by the infant but can support the growth of certain gut microbiome taxa that are capable of deconstructing and metabolizing these HMOs. Only a few taxa have the capability of utilizing HMO for energy, but among them Bifidobacterium longum subsp infantis is particularly successful in doing so (Underwood, 2015; Pediatric Research, 77(1-2):229-35. (doi: 10.1038/pr.2014.156. Epub 2014 Oct 10). Consequently, the gut microbiome of the breastfed infant can be represented by up to 80-90% by this single taxon if human milk is the major source of nutrition for the infant (Frese SA, 2017; Persistence of supplemented Bifidobacterium longum subsp. infantis EVC001 in breastfed infants. mSphere 2:e00501-17. (doi.org/10.1128/mSphere.00501-17). [0003] Beyond 6 months of age, human milk alone cannot provide enough calories to support adequate growth of the infant. At some stage, even before 6 months of age, infants start to consume other sources of nutrition which may be an infant formula or complementary foods with new sources of glycans coming into the gut ecosystem. Weaning is a highly variable process. These new food sources open new nutritional niches and allow new taxa to colonize or expand their footprint in the infant gut ecosystem, thereby altering composition and functional capacity of the gut microbiome. As in the case of recovery of the gut microbiome after an antibiotic event, there is the possibility of opportunistic pathogens also occupying some of those new nutritional niches, leading to enteric inflammation, discomfort, and serious pathologies for the human host. A controlled transition of the gut microbiome during this recovery or changes in the diversity of dietary inputs feeding the microbiome would be beneficial to the health of that infant or patient. [0004] A major problem in weaning an infant (from breast milk as a sole source of nutrition to complimentary foods where more complex plant or animal-based glycans can dominant the colon) is the potential for bacterial blooms, enteric inflammation, and dysbiosis that occurs in the microbiome during transitional stages, with infection, with disease states, or putting an individual at risk of diseases. Chronic enteric inflammation may lead to systemic inflammation that can affect the health and development of other organ systems including, but not limited to, immune programming, central nervous system development, and pancreatic, hepatic, and cardiac development 'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution,’ Bärbel Stecher, Lisa Maier & Wolf-Dietrich Hardt, Nature Reviews Microbiology 11, 277-284, April 2013). [0005] The inventors have established that when Bifidobacterium longum subsp infantis (B. infantis) is not present in the gut of an exclusively breastfed infant, the infant will exhibit chronic enteric inflammation which can negatively deflect the development of that infant’s immune system (Henrick, 2019, Pediatric Research (2019) 86:749–757). doi.org/10.1038/s41390-019-0533-2. If B. infantis is present at levels of 70-80% of the gut microbiome taxa, there is little or no enteric inflammation. The chronic inflammation is the result of a gut dysbiosis or a loss of key bacteria, such as B. infantis, that contribute specific microbiome function around the use of human milk oligosaccharides from human milk that occur in the absence of B. infantis (Newborn Gut Deficiency, or NGD) where the gut microbiome is dominated by opportunistic pathogens including Enterobacteriaceae, Clostridiaceae, Staphlococcaceae, and Streptococaceae as well as an abundance of mucolytic taxa that erode the newborn’s gut mucous layer, triggering the inflammatory response. In the presence of B. infantis at levels of 70-80% of the total gut microbiome, HMOs are catabolized to the fermentative end products acetate and lactate, which lower the gut pH and prevent the growth of the opportunistic pathogens and mucolytic taxa. This is referred to as colonization resistance. Inventors have further established that it is the presence of these key functions, rather than the taxonomic identity of the organisms themselves, that is critical to the protection of a healthy gut microbiome. SUMMARY OF THE INVENTION [0006] The inventors have discovered that although certain B. infantis strains have all the genes necessary to consume all HMOs in human milk, genes coding for enzymes that can deconstruct other plant- based glycans may be missing. Through analyzing other B. infantis strains, other Bifidobacterium species, and other commensal gut bacteria, the inventors discovered that the genes responsible for the capture and internal or external processing of different glycans were significantly divergent, even between different strains of the same species. Utilizing this new understanding, the inventors assembled an array of functional genes that would be required for the utilization of new dietary glycans that are provided to an infant during the transition from breast feeding to complimentary foods and form the basis for the adult diet. Although many bacterial taxa can deconstruct plant glycans quite efficiently, the Bifidobacterium metabolic process produces acetate and lactate as end products, lowering the intestinal pH and minimizing enteric inflammation in the infant gut. [0007] The inventors have developed rational consortia of bacteria exhibiting a variety of key microbiome functions related to carbohydrate catabolic pathways including those used to breakdown mammalian milk glycans and either plant or animal/meat glycans that would allow the transitional changes in the gut microbiome during the difficult period of weaning where new glycans are introduced to the infant. The inventors also discovered and designed rational consortia of bacteria to repopulate the gut microbiome after having been extensively depleted through antibiotic, post-chemotherapeutic treatment, and/or any other potential cause of gut microbiome depletion including, but not limited to particular disease states or sub-clinical changes leading to gut dysbiosis to facilitate the transition to a higher diversity adapted/stable microbiome with the introduction of new dietary fiber or food stuffs. Rational consortia comprising two of more strains of Bifidobacterium are described that collectively coexist. Such consortia are capable of the conversion of HMOs during the breast milk feeding stage and can further accommodate new glycans introduced during the transition to an infant formula or complementary food at any time up to 3 years of age. Rational consortia comprising at least one strain of bacteria where the rational consortia possess certain key microbiome functions regardless of taxonomic identity are further described. Such rational consortia will similarly be capable of conversion of HMOs and simultaneously accommodate new glycans. [0008] The functional capacity of a microbiome needed for an infant being introduced to new food and diets, or any subject going through an intestinal gut microbiome transition due to illness or specific medical treatments may not be apparent without significant and costly testing that is too slow for clinical utility. Transition periods are inherently destabilizing and may open or close specific nutritional niches making the subject undergoing such a transition vulnerable to blooms of opportunistic pathogens or overt pathogens. Other commensals acquired from the environment may not be suited to confer additional capacity to the microbiome. The microbiome as a result may not respond adequately or optimally to either short or long-term changes in diet or to provide sufficient bacterial metabolites to confer benefit to host. Transitional stability may be enhanced by supplying a composition that delivers key functions through a combination of 2 or more Bifidobacterium strains that are upregulated or down regulated in response to the subject diet in real-time and to account for inconsistencies in adherence, timing or other factors associated with managing dietary intake in humans. [0009] The instant invention is a rational consortium of bacteria that can be used simultaneously throughout the breast-feeding and weaning stages of a newborn infant’s life to provide for a controlled transition of the gut microbiome, preventing gut disturbances associated with blooms of opportunistic bacteria during the weaning transition. In some embodiments of this invention, the rational consortium of bacteria may comprise, but is not limited to, Bifidobacterium. Such Bifidobacterium may be a B. infantis strain that has a complete complement of HMO processing genes, as well as genes that allow the catabolism of glycans from plant or animal sources that are not HMO. Alternatively, for example, one of the strains may have HMO or glycan processing genes that are complimentary to the missing genes in the other strains, so that both HMO and plant or animal glycans can be maximally processed. BRIEF DESCRIPTION OF TABLES AND FIGURES [0010] Table 1. Describes the minimal types of GH families that are represented in a first member of a multi-strain rational consortium of bacteria (Species 1). [0011] Table 2. Sugar monomer composition associated with glycans found in common complimentary foods fed to infants. The type of GH required may be matched to preference for specific sugar monomer [0012] Table 3. Describes the GH families expected to be observed in a second member of a multi- strain rational consortium (Species /strain 2) [0013] Table 4. Demonstrates the selection of different strains to achieve additive functions for different glycosylhydrolases as a basis for a rational consortium of bacteria. [0014] Table 5. Genome analysis identifying the presence or absence of different glycosyl hydrolases in genomes from various strains (1-109) of Bifidobacterium species including B. longum subsp. infantis (strains 1-9); B. longum subsp. longum (10-29); B. animalis/B.lactis (31-52); B. adolescentis (54- 60); B. dentium (62-64); and B. breve (66-109). [0015] Table 6. The analysis of publicly available genome sequences with the number of genes within any given GH family. Absence of a check mark means not found. [0016] Table 7. Consortium building using GH function for different Bifidobacterium species [0017] Table 8. Consortium building using complementary B. infantis strains for GH functions. [0018] Table 9. Consortium building using complementary B.infantis strains for Carbohydrate binding modules (CBMs) functions. [0019] Figure 1 (A). Change in absolute abundance of B. infantis EVC001 in infant stool based on actual dietary intake of LNT in a formula fed infant in low vs high LNT groups. (B) Change in absolute abundance of B. infantis EVC001 in infant stool based on actual dietary intake of LNT in a formula fed infant by subject (C) Comparison of pH measurements from samples at baseline and during the intervention period by all treatment groups combined; and (D) Comparison of pH measurements from samples at baseline and during the intervention period by individual treatment groups. [0020] Figure 2. (A) Correlation between LNT consumed and pH change (B) Correlation between relative abundance of specific bacterial families and pH change from baseline. [0021] Figure 3. Relative Abundance of Bifidobacterium by 16S (Next Generation Sequencing). Supplementation 1 period was No LNT for Bif alone group, 3 g/L of LNT for Low LNT group, and 6 g/L of LNT for High LNT group. Supplementation 2 period was No LNT for Bif alone group, 8 g/L of LNT for Low LNT group, and 12 g/L of LNT for High LNT group. [0022] Figure 4. Absolute abundance of B. infantis as determined by qPCR (log10 CFU/ug DNA) overall (A) and by subject (B) [0023] Figure 5. (A) Results of bacterial species growth on carbohydrates from the BioMerieux API 50 CH assay. (B) Comparison of bacterial growth on D-xylose for 48 hours. (C) Comparison of bacterial growth on mannose for 48 hours. DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS Definitions [0024] Glycosyl hydrolases (GH) are a wide range of enzymes that have different affinities and abilities to cleave bonds between sugar residues organized into different families. Glycosyl hydrolases are annotated in such databases as CAZY. The GH(#) refer to a family of related enzymes. For example, GH2 refers to enzymes with a beta-galactosidase activity. A list of enzymes classes and examples can be found in at least Tables 1, 3, 4 and 7. [0025] Rational consortium of bacteria means a selected group of microbial (bacterial) strains which have been chosen so that the total complement of bacteria in the consortium provide genes encoding enzymes with a desired combination of features, without regard to whether the genes are in any particular bacterial strain. The selection and delivery of 2 or more species into the consortium in a microbiome can fulfill the same, different, or overlapping functions that represent metabolic pathways related to catabolic or breakdown products of different carbohydrate sources. In particular indigestible carbohydrates that are fermented or broken into smaller subunits by functions of different bacteria with a given consortium. A consortium is made up of different strains that may include one or more species that are selected based on sequencing of individual genomes, metagenomic analysis and known in vitro and or in vivo functions of specific GHs or CBMs. A strain identifier is able to differentiate specific members within a single species based on an understanding of its genotype and/or phenotype to form a basis for its rational selection in a consortium. Bacteria may be transient or persistent members in the microbiome. While in the past microbiomes were defined by certain taxa, they may more accurately be defined by function or capacity of certain metabolic pathways. These pathways may be expressed through increase in relative abundance of certain bacteria, or may be achieved through redundancy – lots of bacteria contributing to the overall expression of particular metabolic pathways giving rise to an overall microbiome function. While the focus is on increasing overall Bifidobacterium functionality, one skilled in the art would recognize that other bacteria outside Bifidobacterium (if containing the necessary GHs) may also be used to achieve to the functional requirements for a particular nutritional or disease state related to the metabolic output derived from the cumulative activities of the rational consortium of bacteria in a given background microbiome. The concept of multi-strain consortium still holds if a bacteria is engineered to achieve the function rationally assigned to 2 or more species who can respond to the nutrient environment with different functional glycosyl hydrolases through the analyses included herein. As such, a recombinant bacteria may deliver the increased functionality that more than one bacteria isolated for such purpose would deliver, thus reducing the number of recombinant organisms needed to improve microbiome function. [0026] Gut microbiome means the community of organisms that reside predominantly in the colon but may include organism that reside in the small intestine and may be determined in stool or biopsy samples. The microbiome may be defined by taxonomic composition and/or functional capacity. Dysbiosis is the lack of certain bacteria, overabundance of potential pathogens, or loss of function. [0027] In accordance with the concept of this invention, the rational consortium of bacterial strains may be present in a variety of compositions, including a medicament or pharmaceutical preparation, a growing culture, a mammalian intestine, the contents of a vial (which may be a storage vial or an inoculum), a nutritional supplement, a food, or other forms. The microbial consortium is “rational” by virtue of the conscious selection of the taxonomic components and/or functions included in the consortium. The composition containing a consortium of bacterial strains may also contain any other components appropriate to the composition, such as macro- or micro-nutrients, buffers, cryoprotectant or other stabilizers, or other excipients, so long as the bacterial components of the composition are limited to the strains of the consortium. In a preferred mode, the bacteria of the consortium are the only living components of this composition. [0028] The microbiome health may be measured by indices of diversity and/or stability by analysis of the bacterial families (composition), or by deep sequencing or metagenomics to assess functional capacity. Low diversity, low relative abundance of key bacteria, or loss of certain bacteria, and overabundance of opportunistic pathogens or pathogens lead to loss of function and dysbiosis. Low diversity may lead to a microbiome ill-suited to manage glycans reaching the colon. A healthy microbiome or a desirable microbiome may simultaneously have high diversity, high stability, and high relative abundance of certain species, such as Bifidobacterium. The relative abundance of members of the microbiome may be controlled by the selectivity of the available nutrients, in particular glycans reaching the colon, or the diversity of the glycans present. [0029] Choice of Species/Strain 1 of the rational consortium of bacteria. The deconstruction of glycans, digestible fiber, and non-digestible fiber as well as the deglycosylation of glycoproteins all require specialized glycoside hydrolase (GH) enzymes that catalyze the hydrolysis of a glycosidic bond between two sugars or between a sugar and an amino acid in the case of a glycopeptide. There are about 170 families of such genes that are generally distinguished by substrate specificity and mechanism of action. An updated list of these GH enzymes can be found at the CAZY Website (CAZY.org). Some of these GH families are further subdivided into sub-families. Polysaccharide lyases (PLs) are also important catabolic enzymes that can release usable glycans to the microbiota in the gut. Forty-one families of PLs are also recognized in the CAZY database. Carbohydrate binding modules (CBMs) are also important for the binding and transport of sugars and oligosaccharides into the cell for internal deconstruction and/or metabolism of the individual sugar moieties. There are 87 families of CBMs reported to date. Bifidobacterium longum subsp infantis (B. infantis) is one sub-species that is efficient in the metabolism of HMO. Within the genome of B. infantis there are 5 unique gene clusters and over 700 genes unique to this species compared to closely related Bifidobacterium longum species. The H1 cluster includes Blon_2331, Blon_2332, Blon_2334, Blon_2336, Blon_2342, Blon_2343, Blon_2344, Blon_2347, Blon_2348, Blon_2350, Blon_2351, Blon_2352, Blon_2354 and Blon_2355. The H2 cluster (fuscosidase pathways/activities) includes Blon_0243, Blon_0244, Blon_0245, Blon_0246, Blon_0247, Blon_0248 and. The H3 cluster (fucosidase related pathways/activities) includes Blon_0423, Blon_0424, Blon_0425, and Blon_0426. The H4 (sialidase related pathways) includes Blon_0641, Blon_0642, Blon_0643, Blon_0644, Blon_0645, Blon_0646, Blon_0647, Blon_0648, Blon_0649, Blon_0650 and Blon_0651. The H5 (lacto-N- pathways/activities include Blon_2171, Blon_2172, Blon_2173, Blon_2174, Blon_2175, Blon_2176, and Blon_2177. In particular, the presence of Blon_2177 (gene name: extracellular solute-binding protein, family); Blon_2176 (gene name: binding-protein-dependent transport systems inner membrane component); Blon_2175 (gene name: binding-protein-dependent transport systems inner membrane component) can be used to identify bacteria with a functional H5 gene cluster. List of genes that are associated with HMO consumption in B. infantis as described in Locascio 2010 and Garrido (2013) Microbiology 159: 649-664. The prefix Blon refers to genes in B. longum and B. infantis. In some embodiments, bgl and ngl cluster are present. Bgl is a predicted b-glucoside utilization gene cluster while Ngl is an N-glycan utilization gene cluster. The Bgl gene cluster possesses, but is not limited to, a TetR family transcriptional regulator, an ABC transport system, and three putative glycoside hydrolases PSJQZKPSN H d%NHQHJYTXPKHXL& COL >NQ NLSL JQZXYLW UTXXLXXLX$ IZY PX STY QPRPYLK YT$ HS 345 YWHSXUTWY X^XYLR$ EndoBI-2 and EndoBB-2 (GH85), and genes predicted to be a GH38, a GH5_18, and GH20. [0030] The gene clusters are divided based on the predicted substrate utilized and are made up of CBMs including transporters, regulatory elements, and glycoside hydrolases. The efficient utilization of HMO by B. infantis is related to its ability to capture and transport HMO into the cell, thereby preventing access to other taxa that could externally deconstruct the HMO to provide smaller oligosaccharides that could cross-feed other pathogenic and nonpathogenic species. The inventors have identified glucoside hydrolases from 15 different GH families and 2 families of CBMs that are required for the complete metabolism of HMO and that would be required by Species/Strain 1 of the rational Bifidobacterium consortium for the instant invention. These are included in Table 1. Inventors have further discovered that not all B. infantis strains have all the necessary intact GHs or transporters to import and catabolize all the oligosaccharide structures found in human milk. Therefore, the Glycosyl Hydrolases (GH) listed in Table 1, including GH2, GH3, GH5, GH13, GH18, GH20, GH29, GH32, GH33, GH36, GH42, GH77, GH95, GH112, and GH151 families are the minimum representative genes that would provide for Species/Strain 1 of the rational consortium in the instant invention. Exemplary members of Species/Strain 1 for the rational Bifidobacterium consortium would include but are not limited to select strains of B. infantis, B. longum, B. breve, B. adolescentis, B. dentium, B. bifidum, B. pseudolongum, and B. pseudocatenulatum. Preferred embodiments of Species 1 would be B. infantis and B. breve, and a more preferred embodiment of Species 1 of the rational Bifidobacterium consortium would be B. infantis. A most preferred embodiment of Species 1 of the rational Bifidobacterium consortium would be B. infantis strain containing all the GH and CBMs required to metabolize all HMOs such as, but not limited to strain characteristics represented in the EVC001 genome. [0031] Rational Bifidobacterium Consortium for the transition to complementary food. The transition to complimentary foods for a breastfed infant is generally a long process, with the infant continuing to get substantial nourishment from breast milk during this process. Demand for additional calories for the growing infant by 4-6 months of age requires providing new foods in addition to breast milk, and those new foods represent a new source of glycan such as, but not limited to, those listed in Table 2. The introduction of new fibers and non-digestible glycans to the GI tract represent new nutritional niches that may not be available to the milk-oriented microbiota like B. infantis EVC001. Different GHs and CBMs are required for the deconstruction, uptake, and/or metabolism of these new fibers. In addition to the GHs listed in Table 1 for Species 1, Species 2 in the rational Bifidobacterium consortium of the instant must add capabilities to allow the metabolism of these new glycan sources. The inventors have established that these capabilities can be provided by members of any of 18 additional GH families (GH1, GH4, GH8, GH23, GH25, GH26, GH30, GH31, GH38, GH42, GH44, GH51, GH53, GH58, GH78, GH 85, GH92, GH120, GH121, GH125, GH127, and GH136) and 11 additional CBM families (CBM5, CBM6, CBM13, CBM22, CBM23, CBM25, CBM32, CBM41, CBM46, CBM50, and CBM61) listed in Table 4. Of the combined 33 families of GHs listed in Tables 1 and 3, a preferred embodiment of the instant invention will include 20 or more of the GH family activities being provided by Species 1 and Species 2. In a more preferred embodiment 25 or more of the activities will be provided by Species 1 and Species 2. In a most preferred embodiment, 30 or more of the GH activities and all the CBM activities will be provided by Species 1 and Species 2. [0032] In some embodiments, Species or strain 1 will contain genes that represent at least 5, at least 6, at least, at least 7, at least 8, at least 9 of the GH families and/or CDMs. In some embodiments, Species or strain 2 will contain genes that represent at least 5, at least 6, at least, at least 7 of the GH families and/or CDMs. In some embodiments, the consortium will cover at least, 15%, at least 20%, at least 25%, at least 30% at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60% at least 65%, at least 70%, at least 75%, at least 80%, at least 90%, at least 95% or 100% of GH1, GH4, GH8, GH23, GH25, GH26, GH30, GH31, GH38, GH42, GH44, GH51, GH53, GH58, GH78, GH 85, GH92, GH120, GH121, GH125, GH127, and GH136 CBM5, CBM6, CBM13, CBM22, CBM23, CBM25, CBM32, CBM41, CBM46, CBM50, and CBM61 divided into 2 or more strains. [0033] Another embodiment of the instant invention includes the addition of a third species (Species 3) which in combination with Species 1 and 2 will result in a combined gene pool to encompass all 33 families of GHs in Tables 1 and 3 and all 11 CBMs listed in Table 7 and 9. [0034] An additional embodiment of the instant invention is the use of two strains of the same species to provide the missing functionalities of Strain 1. Such a composition of 2 strains of the same species can be used alone or in combination with a third organism of any different Bifidobacterium species. Further embodiments of the instant invention may include 3 or more species. [0035] Exemplary members of Species 2 and 3 for the rational Bifidobacterium consortium would include but are not limited to select strains of B. infantis, B. longum, B. suis, B. breve, B. adolescentis, B. dentium, B. bifidum, B. pseudolongum and B. pseudocatenulatum. Preferred embodiment of Species 2 would be a second strain of B. infantis, or B. longum, B. dentium B. adolescentis, B. pseudocatenulatum and B. breve. A more preferred embodiment of Species 2 of the rational Bifidobacterium consortium would be B. infantis, and B. breve. A preferred embodiment of a rational 3 -strain composition would be B. infantis, B. breve, and B. longum or B. infantis, B. dentium, and B. adolescentis. In further embodiments of the instant invention may include more than 3 species. [0036] In some embodiments, the rational Bifidobacterium consortium also includes cryoprotectants (including but not limited to milk protein, pea protein, polysaccharides, trehalose, other sugars), stabilizers and excipients (including but not limited to lactose, maltodextrin, FOS, inulin, PDX, GOS, mineral oil, olive oil, sunflower oil, medium chain triglyceride (MCT) oil, mineral oil, super refined petroleum jelly, lanolin, lecithin, fat soluble vitamins, A,D.E and/or K, human milk oligosaccharides (i.e LNT, LNnT. LNFP1, LNFPII), bovine milk oligosaccharides, or plant glycans, human or bovine whey glycoproteins or glycopeptides). In some embodiments, the rational Bifidobacterium consortium is part of a food, such as an infant formula, a meal replacer, a human milk fortifier, donor human milk, a weaning food. The rational Bifidobacterium consortium may be a dry blended powder delivered in a sachet or stickpack or can. The powdered product may be mixed with an oil to form a suspension or paste. Stabilizers may be used to form a gel or liquid product. [0037] Rational Bifidobacterium Consortium for the transition to infant formula. The transition to infant formula as a sole source of nutrition for a breastfed infant or a newborn generally involves the introduction of a narrow range of fiber referred to as “prebiotics” in infant formulas. These prebiotics include galactooligosaccharides (GOS), fructooligosaccharides (FOS), polydextrose (PDX) and the like. These artificial fibers are poorly utilized by the infant, but they make their way to the infant colon, where they are a source of nutrition for the gut microbiome. GOS, FOS and PDX can be consumed by many different taxa, including commensals like Bifidobacterium, as well as opportunistic pathogens such as taxa in the Enterobacteriaceae, Clostridiaceae, Staphlococcaceae, and Streptococaceae, as well as mucolytic taxa that erode the newborn’s gut mucous layer, triggering the inflammatory response. These opportunistic pathogens collectively result in chronic enteric inflammation in the infant gut. The inventors have discovered that B. infantis can utilize such infant formula prebiotics effectively, and increase their presence in the infant gut by several orders of magnitude, decrease gut pH, and reduce the carriage of Enterobacteriaceae. Inventors further discovered that with the addition of an HMO (lacto-N-tetrose; LNT) to the formula-fed infants, at levels for from 4-12 g/l, the effect was enhanced. The inventors therefore concluded that Species 1 of the Rational Bifidobacterium Consortium should be B. infantis, and in a preferred embodiment, the Consortium should be supplemented with and HMO at levels for from 1-20 g/L, more preferably from 2-15 g/l, and most preferably from 5-12 g/L. HMO used in this invention include, but are not limited to: natural or synthetically-produced oligosaccharides including lacto-N-biose, 2'- fucosyllactose, 3-fucosyllactose, lacto-N-tetraose, lacto-N-neotetraose, N-difucosyllactose, lacto-N- fucosylpentaose I, lacto-N-fucosylpentaose II, lacto-N-fucosylpentaose III, lacto-N-fucosylpentaose V, 3'- sialyllactose, 6'-sialyllactose, 3'-sialy-1-3-fucosyllactose, sialyllacto-N-tetraose, N-acetylgalactosamine, and 6'-sialyllactosamine, which can be used in the form of processed human milk or may have been purified to at least 80% before providing to a human. The definition of synthetically produced oligosaccharides in this invention includes those oligosaccharides produced in genetically modified organisms as well as through chemosynthetic processes. [0038] The selective metabolism of GOS, FOS, or PDX in infant formula, and the scavenging of additional glycans from whey proteins in the formula, can be enhanced with a second or third species of Bifidobacterium. In addition to the glycoside hydrolases listed in Table 1 for Species 1, Species 2 in the rational Bifidobacterium consortium adds the capabilities provided by members of any of the 18 additional families of glycosyl hydrolases in Table 3. That is, Species 2 of the rational Bifidobacterium consortium should contain 12 or more, 10 or more, 8 or more, 5 or more, 4 or more, 3 or more, 2 or more, or at least one additional GH from the GH1, GH4, GH8, GH23, GH25, GH26, GH30, GH31, GH38, GH42, GH44, GH51, GH53, GH58, GH78, GH 85, GH92, GH120, GH121, GH125, GH127, or GH136 families of glucoside hydrolases. Exemplary members of Species 2 for the rational Bifidobacterium consortium would include but are not limited to select strains of B. infantis, B. longum, B. breve, B. adolescentis, B. dentium, B. bifidum, B. pseudolongum and B. pseudocatenulatum. Preferred embodiment of Species 2 would be B. infantis, B. longum, B. dentium and B. breve. A more preferred embodiment of Species 2 of the rational Bifidobacterium consortium would be B. infantis, B. dentium and B. breve. Another preferred embodiment of Species 2 of the rational Bifidobacterium consortium would be B. infantis and B. dentium. [0039] Rational Bifidobacterium Consortium for repopulation of the Gut Microbiome. The transition to contemporary foods for a non-infant human whose microbiome has been severely affected through chronic dysbiosis and the use of antibiotics to treat a variety of illnesses can be a problematic process, as open ecological and nutritional niches can be quickly occupied by opportunistic pathogens. As in the weaning infant transitioning to complementary foods, different glycoside hydrolases are required for the deconstruction of available dietary fibers. In such a situation, it is important to quickly supplement the individual with fiber that will provide a selective growth medium for a keystone commensal bacterium that does not significantly erode the gut mucous layer and further, provides colonization resistance against opportunistic pathogens. This can be provided by Species 1 of the rational Bifidobacterium consortium where that Species 1 is B. infantis, and preferably, B. infantis strain EVC001 in conjunction with a specific fiber such as an HMO at a daily dose of up to 50 g/d. Preferably the HMO dose is between 10 and 40 g/d, more preferably between 15 and 25 g/d. [0040] Glycans for use in the compositions of this invention are typically MMO (oligosaccharides found in any mammalian milk including, but not limited to human, bovine, goat) and may be free oligosaccharides, or glycans bound to protein or lipid, or the same glycans released from the protein or lipid. The fiber providing selective growth medium of the instant invention can be HMO selected from, but not limited to, natural or synthetically-produced oligosaccharides including lacto-N-biose (LNB), N-acetyl lactosamine, lacto-N-triose, lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), fucosyllactose (FL), lacto-N-fucopentaose (LNFP), lactodifucotetraose, (LDFT) sialyllactose (SL), disialyllacto- N-tetraose (DSLNT), 2'-fucosyllactose (2FL), 3'-sialyllactosamine (3SLN), 3'-fucosyllactose (3FL), 3'-sialyl-3-fucosyllactose(3S3FL), 3'-sialyllactose (3SL), 6'-sialyllactosamine (6SLN), 6'-sialyllactose (6SL), difucosyllactose (DFL), lacto-N-fucopentaose I (LNFPI), lacto-N-fucopentaose II (LNFPII), lacto- N-fucopentaose III (LNFPIII), lacto-N-fucopentaose V (LNFPV), sialyllacto-N-tetraose (SLNT), their derivatives, or combinations thereof. Other glycans include but are not limited to trifucosyllacto-N- hexaose (TFLNH), LnNH, lacto-N-hexaose (LNH), lacto-N-fucopentaose III (LNFPIII), monofucosy lated lacto-N -Hexose III (MFLNHIII), Monofucosylmonosialyllacto-N-hexose (MFMSLNH) which preferably have been purified to at least 50% purity before providing to a human. As the fiber providing selective growth, the medium may also include galactooligosaccharides (GOS) or fructooligosaccharides (FOS) that are enriched in DP-4 and DP-5 polymers as described in U.S. Pat. No. 8,425,930 (incorporated here by reference in its entirety) as these structures also provide differential growth of B. infantis. [0041] “Mammalian milk oligosaccharide” (MMO) or glycan is defined here as any oligosaccharide that exists naturally in any mammalian milk whether it is in its free form or bound to a protein or lipid. MMO and glycans encompass synthetic structures as well as those extracted or purified from sources other than mammalian milk so long as the compound mimics that found in mammalian milk in structure and/or function. That is, while MMOs may be sourced from mammalian milk, they need not be for the purposes of this invention. Sources of MMO may include colostrum products from various animals including, but not limited to cows, goats and other commercial sources of colostrum. It may include MMO enriched from whey permeate; milk products that are modified through processes such as skimming, protein separation, pasteurization, retort sterilization may also be a source of MMO. MMO includes human milk oligosaccharides. [0042] “Human milk oligosaccharide” (HMO) is defined here as any oligosaccharide which exists in human milk. HMO includes synthetic structures, as well as those extracted or purified from sources other than human milk, so long as the compound mimics that found in human milk in structure and/or function. That is, while HMOs may be sourced from human milk, they need not be for the purposes of this invention. [0043] In addition to Strain 1, the rational Bifidobacterium consortium of the instant invention provided to an individual in the need thereof including but not limited to such an individual with a depleted gut microbiome as the result of an antibiotic treatment or any other chemotherapy, may also include a second or third Species of the rational Bifidobacterium consortium, which adds the capabilities provided by members of any of the 18 additional families of glycosyl hydrolases in Table 3. That is, Species 2 of this rational Bifidobacterium consortium should contain 12 or more, 10 or more, 8 or more, 5 or more, 4 or more, 3 or more, 2 or more, or at least one additional GH from the GH1, GH4, GH8, GH23, GH25, GH26, GH30, GH31, GH38, GH42, GH44, GH51, GH53, GH58, GH78, GH 85, GH92, GH120, GH121, GH125, GH127, or GH136 families of glucoside hydrolases. Exemplary members of Species 2 for the rational Bifidobacterium consortium would include but are not limited to select strains of B. infantis, B. longum, B. breve, B. adolescentis, B. dentium, B. bifidum, B. pseudolongum and B. pseudocatenulatum. Preferred embodiment of Species 2 would be B. infantis, B. longum, B. dentium and B. breve. A more preferred embodiment of Species 2 of the rational Bifidobacterium consortium would be B. infantis, B. dentium and B. breve. A most preferred embodiment of Species 2 of the rational Bifidobacterium consortium would be B. infantis and B. dentium. [0044] Compositions comprising a Rational Bifidobacterium Consortium. The rational consortium of Bifidobacterium strains described above will typically be included in a composition adapted to the uses described herein. In some embodiments, the rational Bifidobacterium consortium is part of a food, such as an infant formula, a meal replacer, a human milk fortifier, donor milk, a weaning food. Compositions according to this invention may also include cryoprotectants, stabilizers and other excipients. The rational Bifidobacterium consortium may be a dry blended powder delivered in a sachet or stickpack or can. The powdered product may be mixed with an oil to form a suspension or paste. Stabilizers may be used to form a gel or liquid product. Compositions comprising a rational consortium according to this invention generally offer an improvement over the combinations of microbes disclosed in WO2017/156548 and WO2017156550, incorporated herein by reference, and the multistrain consortia of this invention may be used in any of the methods disclosed in those publications. [0045] A rational Bifidobacterium consortium comprises at least 0.1 million, at least 1 million, at least 10 million, at least 100 million, at least 1 billion, at least 4, billion, at least 8 billion, at least 18 billion or at least 50 billion colony forming units (CFU). In certain embodiments, the desired range may be 0.1 million through to 1 trillion CFU/gram, CFU/serving or CFU/unit dose or CFU/per day. More preferred embodiments include 0.1-1 million, 1 million-100 million, 100 million -1 billion, 1 billion-100 billion, and more than 100 billion CFU daily intake. A composition intended for the prophylactic or treatment of gut dysbiois related to a disease risk or a disease state may be administered in single or multiple units per day to reach desired daily intake. The administration may be part of a dietary regime for at least 1 day, at least 3 days, at least 5 days, at least 10 days, at least 2 weeks, at least 4 weeks, at least 3 months, at least 6 months, at least 1 year or more than 1 year. A treatment modality may use different animal glycans, plant glycans or mammalian glycans in different ratios and/or different times than the bacteria. [0046] In one embodiment of the instant invention any two bacteria containing bacteria with desired carbohydrate catabolic functions from but not limited to GH and CBM. The bacteria may be combined in a ratio of from 100:1 to 100:1 based on live colony-forming unit (cfu) measurements. In some embodiments, two Bifidobacterium strains may be combined in a ratio of from 100:1 to 100:1 based on live colony-forming unit (cfu) measurements. [0047] The rationale consortium may also comprise Lactobacillus and/or Akkermansia species to provide additional microbiome function. The Lactobacillus may be from species, such as L. acidophilus, L. antri, L. brevis, L. casei, L. coleohominis, L. crispatus, L. curvatus, L. fermentum, L. gasseri, L. johnsonii, L. mucosae, L. pentosus, L. plantarum, L. reuteri, L. rhamnosus, L. sakei, L. salivarius L. paracasei, L. kisonensis., L. paralimentarius, L. perolens, L. apis, L. ghanensis, L. dextrinicus, L. shenzenensis, or L. harbinensis. Lactobacillus species have recently been reclassified and one skilled in the art understands the species named herein may have new names but are the same organisms [International Scientific Association for Probiotics and Prebiotics. New names for important probiotic Lactobacillus species.2020 Apr 12 [cited 20 April 2020]. In: ISAPP Science Blog [Internet]. Sacramento: ISAPP 2020. [about 2 screens]. Available from: isappscience.org/new-names-for-important-probiotic-lactobacillus-species/.] [0048] A rational Bifidobacterium consortium will typically be selected to affect the microbiome of a mammalian subject (usually human), and the subject’s microbiome may be monitored for one or more of the following characteristics: 1) a microbiome that is at least 40%, 50%, 60%. 70%, 80% or 90% Bifidobacterium species; 2) at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, or at least 90% of any B. infantis species; 3) at least 30%, 40%, 50%, 60%, 70%, 80% or 90%, of an H5 positive B. infantis, such as but not limited to B. infantis EVC001; 4) produces indole lactate (ILA), 5) reduced enteric inflammation; 6) pH less than 5.8, less than 5.5, less than 5.0; 7) overall production of acetate:lactate in ratio approaching 3:2; 8) acetate concentrations of at least 15 umol/g feces, at least 20 umol/g feces, at least 25 umol/g feces, at least 30 umol/g feces, at least 35 umol/g feces, at least 40 umol/g feces, at least 45 umol/g feces, at least 50 umol/g feces or at least 55 umol/g feces or lactate concentrations of at least 2 umol/g feces, at least 3 umol/g feces, at least 5 umol/g feces, at least 10 umol/g feces, at least, 15 umol/g feces, 20 umol/g feces, at least 25 umol/g feces, at least 30 umol/g feces, at least 35 umol/g feces. Units may also be expressed as umol/ml. See WO 2018/006080, incorporated herein by reference.

[0049] Dietary support for increasing functional GH capacity of the microbiome to generate and/or maintain a particular threshold of metabolically active live bacteria to a subject/host in need of such bacteria. The production of certain threshold of bacterial or host metabolites to demonstrate microbiome function resulting from metabolic activity linked to carbohydrate catabolism. See WO 2019/055718, incorporated herein by reference.

[0050] Examples of excipients and other components that increase functionality of the formulation include different types of ingredients and applications, such as but not limited to oils including but not limited to MCT, Olive, Sunflower, Rice Bran, Mineral, docosahexaenoic acid (DHA) or arachidonic acid (ARA)-containing oils; fat soluble vitamins, such as but not limited to Vitamins: D3 (powder and liquid), E (Alpha tocopherol), K (K1 or K2), Vitamin A or its precursors or derivatives; and oligosaccharide-based ingredients such as but not limited to FOS, GOS, Lactose, 2-FL, LNT, LNnT, LNFP1, 3SL, 6SL, Maltodextrin, Microcrystalline cellulose. Formulations may include unguents, such as lanolin, super refined petroleum jelly, Anhydrous Milk Fat (AMF). Other: TOPCITHIN SF (sunflower lecithin), Lacprodan milk fat globule membrane (MFGM) or any derivative of MGFM, and/or amino acids such as tryptophan, whey protein, or whey peptides that may or may not be glycosylated.

[0051] Gut dysbiosis associated autoimmune and allergic disease refers to any allergy or autoimmune disorder that can be reasonably traced to gut dysbiosis. Such diseases may include, but are not limited to, rheumatoid arthritis, psoriasis, celiac disease, inflammatory bowel diseases (Crohn’s, ulcerative colitis,) IBS, Type 1 diabetes mellitus, atopic dermatitis, asthma, and food allergies or development of oral intolerance to known common food allergens including specific allergenic proteins from milk, egg, soy, shellfish, fish, tree nuts, peanuts, or sesame. In some embodiments, the mammal is a human who may suffer from inflammation that can be an acute, chronic disease of autoimmune origin or otherwise, such as, but not limited to, necrotizing enterocolitis, diaper rash, colic, late onset sepsis, inflammatory bowel disease, irritable bowel syndrome (IBS), colitis, gut pathogen overgrowth (e.g., C. difficile), hospital acquired infections, asthma, wheeze, allergic responses, Type I Diabetes, Type II diabetes, celiac disease, crohn’s, disease, ulcerative colitis, multiple sclerosis, psoriasis, and atopic dermatitis.

[0052] Any of the compositions may be tailored or targeted to specific age groups, such as a preterm infant who may be bom with a gestational age of less than 33 weeks, the preterm babies may be an extremely low weight (ELBW), very low birth weight (VLBW), or low birth weight (LBW), a term infant (0-3 months), an infant 3-6 months, an infant (6-12 months), a weaning infant (4-12 months), a weaned infant (12 months to 2 years) and toddler (1-3 years), child (3-16 years), an adult (16-70 yr), or an older or geriatric adult (70-100+ yr).

[0053] The subject may be hospitalized or in an outpatient treatment or part of a wellness regime.

EXAMPLES

Example 1. Preparation of a rational bacterial consortium for a breast-fed and/or weaning infant.

[0054] A first Bifidobacterium strain of a multi-strain composition of Bifidobacterium is chosen for its ability to efficiently capture and internally consume HMO structures in breast milk from either secreter, or non-secretor mothers. Such a strain shall include functional genes for GH18, GH20, GH25, GH29, GH33, GH38, GH95, GH112, GH125, GH129, and GH151 glucoside hydrolases as well as carbohydrate binding modules CBM48 and CBM50 (Table 1 and Table 6).

[0055] Table 4 and 5, 6, 7 and 8 provide summaries of the genetic capacities (presence of genes) within single strains to illustrate a strategy and examples for combining strain functions together to achieve more complete coverage of GH functions than any one strain can provide. Increasing abundance and diversity of certain GH functions may improve overall microbiome function. Table 6 provides GH presence in accessible NCBI genomes. Table 8 provides examples of different strain combinations to increase GH abundance. Table 9 provides examples to combine different strains to increase the CBM capacity or function in the rational consortium of bacteria.

[0056] B. longum subsp infantis ATCC 15697 (type strain) meets these requirements and is obtained from the American Type Culture Collection (ATCC) (Washington DC, USA). Other similar strains that also meet that meet these minimum criteria can be used as a First Bifidobacterium Strain. A seed culture of this organism is added to a sterile MRS growth medium comprising 2% lactose and a mammalian milk oligosaccharide such as lacto-N-tetrose (LNT) at a concentration of 10 g/L. The culture was then incubated for 24-48 hr at 37C, under strictly anaerobic conditions, harvested by centrifugation, mixed with a cryopreservative of trehalose plus milk, pea or bean protein and freeze dried, or used directly without preservation. The final dry product is a bacterial mass with a count of about 300 B CFU/g.

[0057] GH1 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for b-glucosidase and b-galactosidase activity of the GH1 family of glycoside hydrolases. Specific strains including, but not limited to B. breve (215W44a), B. adolescentis (ATCC 15703), B. dentium ATCC27534), and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0058] GH8 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for chitosanase, cellulase, licheninase, endo- 1 ,4-P-xylanasc and reducing-end-xylose releasing exo-oligoxylanase activities of the GH8 family of glycoside hydrolases. Specific strains including, but not limited to B. adolescentis (ATCC 15703), B. longum (JDM301) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0059] GH26 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for endo and exo β-l ,4-mannanases, β-1 ,3: 1 ,4-glucanase [2] and β-l,3-xylanase activities, of the GH26 family of glycoside hydrolases. Specific strains including, but not limited to, B. dentium (ATCC27534), and B. pseudocatenulatum (DSM 20438) meet this requirement and is obtained from commercial culture collections.

[0060] GH27 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for GHs with α-galactosidase activity of the GH27 family of glycoside hydrolases. Specific strains including, but not limited to B. infantis (JCM11660, KCTC5934 or 157F), B. longum (JDM301), B. dentium (ATCC27534) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0061] GH30 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for and infant. Such a strain shall include functional genes for b-glucosylceramidase, β-I,6-glucanase, and b-xylosidase (GH30 family). Specific strains including, but not limited to B. infantis (JCM11660, KCTC5934 or 157F), B. longum (JDM301), B. dentium (ATCC27534) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0062] GH31 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for β α-glucosidases, α-xylosidases, isomaltosyltransferases, and maltase/glucoamylase (GH31 family). Specific strains including, but not limited to B. infantis ( JCM11660 , KCTC5934 or 157F), B. longum (JDM301), B. dentium (ATCC27534), B. breve (215W44A) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0063] GH38 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for α-1,2- α-1,3- and /or α-l,6-mannosidases (GH38 family). Specific strains including, but not limited to B. longum (YS108R), B. breve (215W44A) and B. adolescentis (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0064] GH53 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for β-l ,4-galactosidase (GH53 family). Specific strains including, but not limited to B. infantis (Bi26, JCM11347, JCM11660, KCTC5934, JCM7009, or 157F), B. longum (YS108R), B. dentium (ATCC27534), and B. breve (215W44A) meet this requirement and are obtained from commercial culture collections.

[0065] GH78 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for α-L-rhamnosidases (GH78 family). Specific strains including, but not limited to B. infantis (JCM11660), B. longum (YS108R), B. breve (215W44A) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0066] GH85 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for Endo-b-N -acetyl glucosaminidascs (GH85 family). Specific strains including, but not limited to B. infantis (BTl and JCM11660), B. longum (YS108R), and B. breve (215W44A) meet this requirement and are obtained from commercial culture collections.

[0067] GH120 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for b-xylosidase activity (GH120 family). Specific strains including, but not limited to B. infantis ( BT1 , KCTC5934 and 257F), B. longum (YS108R), B. adolescentis (DSM 20438) and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0068] GH121 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for b-L-arabinobiosidases activity (GH121 family). Specific strains including, but not limited to B. infantis (KCTC5934 and 257F), B. longum ( BBMN68 '), B. dentium (ATCC27534), and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0069] GH127 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for b-L-arabinofuranosidase activity, (GH127 family). Specific strains including, but not limited to B. infantis (JCMl 1347, KCTC5934 and 257F), B. longum (JDM341), B. breve (215W44a), B. dentium (ATCC27534), and B. pseudocatenulatum (DSM 20438) meet this requirement and are obtained from commercial culture collections.

[0070] GH136 Family. A second and/or third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is chosen for its ability to efficiently utilize for energy animal or plant glycan structures commonly found in vegetables or meat that are considered valuable complementary feeds for an infant. Such a strain shall include functional genes for lacto-A-biosidase andIacto-N-1etraosidaseactivity(GH136 family). Specific strains including, but not limited to B. infantis (JCMl 1347), and B. longum ( BBMN68 ')) meet this requirement and are obtained from commercial culture collections.

[0071] A seed culture of the second and third Bifidobacterium strain of a multistrain consortium of Bifidobacterium is added to a MRS growth medium comprising 2% lactose, incubated for 24 hr at 37C, under strictly anaerobic conditions, harvested by centrifugation, mixed with a cryopreservative of trehalose plus milk, pea or bean proteins and freeze dried. The final dry product is a bacterial mass with a count of about 130 B CFU/g.

Example 2. Preparation of probiotic and prebiotic compositions for weaning infants.

[0072] Bacterial growth media are prepared wherein the primary carbon source for growth is either

HMO extracted from breast milk, a mixture of fibers extracted from at least 5 of the complementary foods in Table 2, or a 1 : 1 blend of the HMO and fiber mixtures. HMO and fiber mixtures are present in the growth media at a concentration of 10 g/L. To each of the above media is added approximately starting cultures are standardized to an OD600 of 1.0 (or a specified CFU count is added), and a 1:1 mixture of a two-strain composition will be prepared, or of a three-strain composition and the cultures are allowed to grow at 37C under anerobic conditions for 24-48 hr. Growth kinetics are monitored and growth rates for selected, rationally-designed Bifidobacterium cultures with two strains in the HMO/fiber mixtures provide superior performance to any single culture. Various combinations of organisms will be tested to determine functional phenotype on different fiber mixtures.

Example 3. Method of reducing gut distress during weaning.

[0073] A rationally-designed consortium of Bifidobacterium cultures is prepared that includes a strain specifically targeting the exclusively breast fed phase of infant growth (Strain 1 ; B. infantis EVC001 : Bifidobacterium longum subsp. infantis EVCOOl as deposited under ATCC Accession No. PTA-125180), and a second strain specifically targeting the utilization of GOS, FOS, and/or natural fibers from complementary infant foods. These two cultures are provided to an infant at a dose of from 1-10 B CFU/day from 5 days post-partum through the first year of life. Initially the gut of the exclusively breastfed infant is dominated by B. infantis EVCOOl. However as soon as that infant is weaned to infant formula the B. infantis EVCOOl is replaced in part by the second strain of Bifidobacterium that can effectively use the infant formula prebiotics. If the baby transitions directly to complementary feeds without the use of infant formula, the B. infantis EVC001 will still be replaced in part by the second strain of Bifidobacterium which will become more competitive as the percentage of calories from complementary food increases and that from breast milk decreases. This maintenance of high levels of Bifidobacterium in the gut of the infant helps to preserve the initial colonization resistance set up by the B. infantis EVCOOl and thereby keep gut pH and inflammation at a low level resulting in less distress for the infant. The best results are achieved when two strains of B. infantis are used such as B. infantis EVCOOl and B. infantis JCM11660.

Example 4. In vitro evaluation of growth on different glycan structures by species.

[0074] In vitro functional assays. Evaluating synergistic and/or competitive growth of B. infantis

JCM11660 and EVCOOl on specific combinations of glycans are determined by serial subculture over a 72-hour period. Three parallel cultures of each strain were initiated by transferring single colonies into 10 ml MRS medium (Difco BD, Franklin Lakes, NJ). To initiate experiments, 16-hour cultures of each strain were standardized to an OD600 of 1.0. Strains were co-inoculated as a 100-fold dilution in 10 mL of MRS media containing 20g/L of combinations of LNT, LNnT, 2’-FL or a combination of all three HMO; 15g/L of combinations of LNT, LnNT, 2FL’ with 5 g/L of GOS; or 10 g/L HMO combination with 10g/L GOS; or 5 g/L HMO with 15 g/L GOS or 20 g/L GOS. In a second set of experiments, the ratio of HMO: plant glycan will be varied from exclusively HMO to exclusively plant glycan. Serial passages are performed every 24 hours by diluting the culture 1:100 so that 0.1 mL of the medium with bacteria was transferred into a 10 mL of fresh medium containing same HMO. At each transfer, the cultures were first mixed by vortexing for 30 seconds. All incubations were performed at 37°C inside anaerobic chamber maintained at 5 % ¾, 5 % CO2, and 90 % N2 (Coy Laboratory Products, Grass Lake, MI). 1.0 mL samples collected from the inoculum and at the end of each incubation period (24, 48 and 72 hours). Growth curves are generated. After each cycle, cells from each well are spun down and pellets frozen at -80 °C. Genomic DNA is extracted from the cell pellets. DNA extraction is performed using a KingFisher flex purification system (ThermoFisher Scientific, Waltham, MA), with reagents from the ZymoBIOMICS 96 MagBead DNA kit (Zymo Research, Irvine, CA). Standard curves are used for absolute quantification of each strain using genomic DNA extracted from previously quantified cultures. Quantitative PCR was performed on a QuanStudio3 (ThermoFisher Scientific, Waltham, MA). The reaction mixture consisted of 0.5 μL of each primer (10 mM each), 5 pL of PerfeCTa Multiplex qPCR ToughMix (QuantaBio, Beverly, MA), 11.5 pL of water and 5 pL of template DNA. The PCR conditions included 1 cycle of initial denaturation at 95°C for 3 min, followed by 40 cycles at 95°C for 15 seconds and 60°C for 1 min. The relative amounts of individual strains are expected to vary based on the amount of HMO vs GOS in the growth media.

[0075] Glycoprofiling. Bacterial cultures in mMRS medium containing were collected at 6 and 30 hours of growth representing mid-log phase and late stationary phase. Bacterial cells were removed by centrifugation at 10,000 x g for 2 minutes. Supernatant was collected and diluted 10,000-fold. Dilutions were filtered through a 0.22 pm cellulose acetate membrane (VWR International, Radnor, PA) and 25 pL of these supernatants were injected into a High-Performance Anion-Exchange Chromatograph Coupled with Pulsed Amperometric Detection instrument (HPAE-PAD ICS-5000, Thermo Scientific, Sunnyvale, CA) according to methods from [43] with some modifications. Briefly, chromatographic separation was carried out on a CarboPac PA1 analytical column (4 x 250 mm, Dionex) and CarboPac PA1 guard column (4 x 50 mm, Dionex) with an isocratic gradient: 0-30 min 73.5% A, 25% B, 1.5% C, at 1.0 mL/min flow rate, where solvent A was deionized water, solvent B 100 mM NaOH and solvent C was 500 mM NaOAc in 100 mM NaOH. HMO were quantified using calibration curves generated using reference standards of LNT, LNnT (Dextra, Reading, UK) and 2’-FL (Carbosynth,St. Gallen Switzerland), ranging in concentration from 0.00025 to 0.005 mg/mL. All samples were analyzed in triplicate.

Example 5. In vivo demonstration of addition of B. infantis EVCOOl to formula feeding infants receiving variable amounts of LNT.

[0076] A single-center, prospective, randomized, open label study of an infant probiotic {B. infantis EVCOOl) and a prebiotic supplement (LNT) in exclusively formula-fed infants was conducted with the following groups: Group 1: 8 x 10⁹ CFU B. infantis + LNT (3 g/L then 8 g/L); Group 2: 8 x 10⁹ CFU B. infantis + LNT (6 g/L then 12 g/L); and Group 3: 8 x 10⁹ CFU B. infantis alone

[0077] Each infant was given a once-daily oral feeding of B. infantis EVCOOl (8.0 x 10⁹ CFU) mixed with infant formula for 28 consecutive days. Two out of three of the treatment groups (Group 1 & Group 2) also received two dose-escalated concentrations of the prebiotic supplement (LNT) mixed with each feeding of infant formula: Group 1 received a concentration of 3 g/L for 2 weeks followed by 8 g/L for the next 2 weeks. Group 2 received a concentration of 6 g/L for 2 weeks followed by 12 g/L for the next 2 weeks. Infants consuming the LNT crossed over to the higher dose without a washout period.

[0078] The absolute abundance of B. infantis was analyzed by LNT consumed by group (Figure 1A) and by subject (Figure IB). Stool pH was analyzed for collected samples, indicating an overall significant reduction in stool pH from Baseline to Day 19 for Evivo (with and without LNT), but no statistical differences between treatment groups were observed (see Figure 1C and D). However, a statistically significant negative correlation between LNT consumed and pH change was identified (see Figure 2A). the change in pH from baseline was also analyzed by bacterial family (Figure 2B).

[0079] Relative abundance of B. infantis was analyzed by 16s sequencing (Figure 3) and by qPCR (Figure 4).

Example 6. In vitro growth evaluation of different bacterial species on various glycan structures.

[0080] In vitro API 50 CH carbohydrate assay. Initial screening for bacterial growth on specific carbohydrates and their derivatives was conducted using the API 50 CH assay (BioMerieux, Marcy-l'Etoile, France). To initiate experiments, 48-hour bacterial colonies were transferred to 1ml sterile 0.9% saline using a swab and resuspended by vortexing. Bacteria screened included B. infantis EVCOOl, 2D9, andNLS, B. breve 7051 - 1 a and 41408, B. bifidum 41410, B. dentium 7015, and B. pseudocatenulatum ATCC 27919 (Figure 5). Drops of the bacterial suspension were transferred to 5ml of sterile 0.9% saline to reach 2 McFarland turbidity, recording the number of drops required. Ampules of API CHB/E media (BioMerieux, Marcy-l'Etoile, France) were inoculated by transferring twice the number of drops that was required to reach 2 MacFarland turbidity of the bacterial suspension. API 50 CH wells were filled with inoculated API media and the strips were incubated for 48-hours at 37C inside an anaerobic chamber (Coy Laboratory Products, Grass Lake, MI). The color of the wells was recorded at 24- and 48-hours as a measure for when the carbon source was metabolized. A yellow color signifies an acidification of the media due to carbon metabolism and was recorded as positive for metabolism (Figure 5).

[0081] In vitro functional growth assays. Evaluating growth of bacteria on specific combinations of glycans as determined by 48-hour growth curves (Figure 5). Tested strains included B. infantis EVCOOl, 2D9, and NLS, B. bifidum 41410, and a B. dentium. To begin, 16-hour cultures of each strain grown in 3 ml of MRS medium (Difco BD, Franklin Lakes, NJ) were standardized to an OD600 of 0.5. Strains were inoculated as a 20-fold dilution into a 96-well plate containing 200ul per well of modified MRS media containing lg/L of D-xylose or mannose. All incubations were performed at 37C inside an anaerobic chamber maintained at 5 % H2, 5 % C02, and 90 % N2 (Coy Laboratory Products, Grass Lake, MI). 48-hour growth curves were monitored by optical density OD600 using a Epoch2 spectrophotometer (Biotek, Winooski, VT) placed inside the anaerobic chamber, holding at 37C. Two biological replicates were conducted per strain.

[0082] Carbohydrate metabolism results were recorded (Figure 5), providing in vitro data that metabolism is differential across Bifidobacterium species and strains. As one example, D-xylose was metabolized by B. inf antis NLS but not B. inf antis strains EVCOOl or 2D9. Second, mannose appeared to be metabolized at varying degrees according to the API 50 CH assay which served as a preliminary screen. Therefore, individual growth curves were warranted to further investigate complementary metabolism differences.

[0083] Insofar as the description above and the accompanying figures disclose any additional subject matter that is not within the scope of the claims below, the inventions are not dedicated to the public and the right to file one or more applications to claim such additional inventions is reserved.

_ _ es b

Table 1

B

C h

L

R

V

A

B

S

C

P

C

S

P

F

A b

B

P

Pear X X X X X X

Papaya X X X X X X

Watermelon X X X X X X

Meats X X X X X X

Fish X X X X X X

Cheese /Dairy X X X X X X X

Table 2

GH146 V V V

GH151

GH154

NCI

Table 5 d G G G G G G G (

()ehj GH151 GH154 /$e Table 5, continued

()egj ()ehj GH151 GH154 " /$e " " " " " " " " " " " " " " " " " " " " "

()egj ()ehj GH151 GH154 " " /$e " " " " " " " " " " " " " " " " " "

B. pseudocatenulatum LH659 " " " " " " B. pseudocatenulatum LH34 ^{" " " " " "} B. pseudocatenulatum LH662 " " " " " " B. pseudocatenulatum LH663 " " " " " "

$#.hj " " $#.hl " " " " " " " $#. id " " " $#.im " $#.je " "

()fj GH35 GH39 GH50 GH59 GH94 ()ehj /$e

Claims

Claims: 1. A composition comprising a rational consortium of bacteria collectively having pathways for 2 or more distinct carbohydrate catabolic functions, wherein such carbohydrate catabolic pathways provide microbiome function comprising a) transport and/or metabolism of mammalian milk glycans; and b) transport and/or metabolism of animal or plant-based glycans to a subject in need.

2. A composition of claim 1, wherein the pathways for distinct carbohydrate catabolic functions includes genes encoding for or related to carbohydrate binding molecules (CBM) or glycosyl hydrolases (GH).

3. A composition of claim 2, wherein one or more glycosyl hydrolase (GH) gene is selected from the group consisting of GH2, GH3, GH5, GH13, GH18, GH20, GH29, GH32, GH33, GH36, GH42, GH43, GH77, GH95, GH112, and GH151.

4. The composition of claim 3, wherein the rational consortium of bacteria collectively possesses genes required to transport and metabolize over 90% of the human milk oligosaccharides provided in human milk.

5. A composition of claim 4, wherein at least one strain present in the rational consortium of bacteria possesses a gene or genes with homologous function to human milk oligosaccharide cluster 5 (H5 gene cluster; lacto-N-biose transport and metabolism).

6. A composition of claim 2, wherein one or more glycosyl hydrolase (GH) genes is selected from the group consisting of activities found in the transport and/or metabolism pathways of xylose, mannose, fucose, and/or arabinose.

7. A composition of claim 6, where in the GH is selected from the group comprising GH1, GH8, GH26, GH27, GH29, GH30, GH31, GH38, GH43, GH53, GH78, GH85, GH120, GH121, GH127, GH136.

8. A composition of claim 1, wherein the profile of carbohydrate catabolic functions includes both an intact H5 cluster and genes related to the transport of mannose oligosaccharides.

9. A composition of claim 1, wherein the profile of carbohydrate catabolic functions includes both an intact H5 cluster and genes related to the transport of xylose oligosaccharides

10. A composition of claim 7, wherein the GH functions are found in one or more bacterial species, subspecies, or strain that are different from the bacteria having GH functions found in claim 3.

11. A composition of claim 2, wherein the glycosyl hydrolase includes at least one functional gene for endoglycosidases selected from GH20 or GH18.

12. A composition of claim 11, wherein such endoglycosidases from GH20 or GH18 are homologous to those found in Bifidobacterium infantis or Bifidobacterium bifidum.

13. A composition of claim 12, wherein the endoglycosidase is homologous to EndoBi-1, EndoBi-2, EndoBi-3, or EndoBB-2.

14. A composition of claim 2, wherein at least one gene related to carbohydrate binding molecules (CBM) is selected from the group comprising CBM5, CBM6, CBM13, CBM22, CBM23, CBM25, CBM32, CBM41, CBM46, CBM59, and CBM61.

15. A composition of claim 14 wherein the rational consortium of bacteria includes at least 55% of the carbohydrate binding molecule genes listed in claim 14.

16. A composition of claim 2, wherein the carbohydrate catabolic functions include the Bgl and Ngl gene clusters.

17. A composition of claim 1, wherein the rational consortium of bacteria comprises a preparation of two or more recombinant organisms.

18. A composition of claim 1, wherein the two or more distinct carbohydrate catabolic functions normally expressed in at least two organisms are expressed in a single recombinant organism.

19. A composition of claim 1, wherein the rational consortium of bacteria comprises a preparation of two or more naturally occurring organisms.

20. A composition of claim 1, wherein the rational consortium of bacteria comprises a preparation of at least one recombinant and at least one naturally occurring organism.

21. A composition of claim 1, wherein the rational consortium of bacteria comprises at least Bifidobacterium longum subsp. infantis (B.infantis).

22. The composition of claim 1, wherein the rational consortium of bacteria comprises B. infantis and at least one of B.breve, B. longum, B. dentium, B. adolescentis, B. pseudocatenulatum, and B. pseudolongum.

23. The composition of claim 1, wherein the rational consortium of bacteria comprises at least a B. infantis strain and a B. breve strain.

24. A composition of claim 1, wherein the rational consortium of bacteria comprises three or more bacterial strains from the Bifidobacterium genus, at least one of which is B. infantis.

25. A composition of claim 20, wherein the rational consortium of bacteria comprises three or more bacterial strains, wherein each of B. infantis, B. breve, and B. dentium are present.

26. A composition of any preceding claim wherein the rational consortium of bacteria is provided in a powder form, as a suspension, in an edible oil, as an emulsion, as a paste, or in a liquid form.

27. A composition of any preceding claim further comprising at least one mammalian milk glycan.

28. The composition of claim 27, wherein the source of mammalian milk glycans are from a group consisting of mammalian milk oligosaccharides, glycoproteins, glycopeptides, or glycans released from glycoproteins and glycopeptides, glycolipids or milk fat globule membrane.

29. A composition of claim 28, wherein the glycan is from human, bovine, goat, or sheep.

30. A composition of claim 29, wherein the human glycan is a human milk oligosaccharide selected from the group comprising 2FL, 3FL, 3SL, 6SL, LNT, LNnT, LNFP1, LNFPII.

31. A medicament comprising the composition of any preceding claim.

32. A method for remodeling a gut microbiome, comprising administration of the medicament of claim 31.

33. A method of claim 32, wherein the medicament is administered contemporaneously with human milk, and/or infant formula diet.

34. A method of claim 32 comprising the additional contemporaneous administration of glycans of plant or animal origin.

35. A method of claim 34, wherein such glycans are administered within 24 hours of the medicament.

36. A method of claim 32 wherein such medicament is administered to a subject to reduce or prevent dysbiosis.

37. A method of claim 36 wherein the subject is at a higher risk for dysbiosis, or the dysbiosis has been caused by, antibiotic treatment, chemotherapy, surgery, or other medical intervention.

38. A method of claim 36, wherein a subject is administered a medicament to reduce dysbiosis wherein such underlying dysbiosis is associated with a disease condition.

39. The method of claim 38, wherein the disease condition is selected from the group comprising autoimmune and allergic diseases.

40. A method of claim 32, wherein the desired range may be 0.1 million through to 1 trillion CFU/gram, CFU/serving or CFU/unit dose or CFU/per day, optionally desired ranges include 0.1-1 million, 1 million-100 million, 100 million -1 billion, 1 billion-100 billion, or more than 100 billion CFU daily intake.

41. A method of claim 32, where in the administration may be part of a dietary regime for at least 1 day, at least 3 days, at least 5 days, at least 10 days, at least 2 weeks, at least 4 weeks, at least 3 months, at least 6 months, at least 1 year or more than 1 year.

42. A method of increasing functional GH capacity of the microbiome to generate and/or maintain a particular threshold of metabolically active live bacteria to a subject/host in need of such bacteria.

43. A method of claim 42, where in the metabolically active bacteria provide desirable amount of metabolites. [*incorporate E18 by reference] 44. A method of claim 42, wherein the metabolically active live bacteria is a population comprising Bifidobacterium. 45. A method of claim 42, wherein the threshold is the colonization and/or persistence of bacteria as measured in stool by relative abundance of GH capacity and/or reduction of pathogenic or potentially pathogenic bacteria.