Pharmaceutical compositions for treating infant gastrointestinal diseases

Abstract

Provided herein are pharmaceutical compositions comprising a bacterial population. The bacterial population comprises one bacterial strains or at least two bacterial strains. Such pharmaceutical compositions can be administered to a subject for prevention and / or treatment of dysbiosis and dysbiosis associated conditions and diseases, such as infant gastrointestinal diseases.

Description

Attorney Docket No.: 53206-717601PHARMACEUTICAL COMPOSITIONS FOR TREATING INFANT GASTROINTESTINAL DISEASESCROSS-REFERENCE

[0001] This application claims the benefit of Untied States Patent Application No.63 / 723949, filed November 22, 2024, which is incorporated by reference herein in its entirety.SEQUENCE LISTING

[0002] The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on November 20, 2025, is named 53206-717_601_SL.xml and is 42.796 megabytes in size.BACKGROUND

[0003] Recent developments in the areas of microbiome and genome research provide evidence that the microbiome-host relationships influence human health or disease onset and progression. For example, they been implicated in the inflammatory diseases Necrotizing Enterocolitis (NEC), playing key roles in the etiology of these disorders. The rising incidence of these diseases is concerning and represents a major public health challenge.

[0004] Currently available pharmaceutical compositions, however, can lack effectiveness, scalability, reliability, or stability.BRIEF SUMMARY

[0005] Provided herein are methods of treating or preventing a disease or condition in a subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, and wherein said first growth ratio is at least about 10 % different than said secondAttorney Docket No.: 53206-717601growth ratio.

[0006] In some embodiments, said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, and wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source. In some embodiments, said energy source or said second energy comprises a carbohydrate. In some embodiments, said second energy source comprises glucose. In some embodiments, said energy source comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract. In some embodiments, said energy source comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’-Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin, or a combination thereof. In some embodiments, said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said third growth ratio is at least about 10 % different than said fourth growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, and wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source. In some embodiments, said first growth ratio is at least about 10 % or at least about 25 % higher than said second growth ratio, and wherein said fourth growth ratio is at least about 10 % or at least about 25 % higher than said third growth ratio. In some embodiments, said energyAttorney Docket No.: 53206-717601source comprises LNnT or GlcNAc, and wherein said third energy source comprises galactose. In some embodiments, said composition comprises said bacterial population. In some embodiments, said composition comprises said mixture. In some embodiments, said composition comprises said derivative of said mixture or said bacterial population.

[0007] Provided herein are methods of treating or preventing a disease or condition in a subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein when administered into said subject, said composition: (1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by a control composition; or (2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise (a), (b), (c), or (d).

[0008] In some embodiments, when administered into said subject, said composition inhibits said expression of said intestinal immune response signaling marker by at least about 0.1 % relative to said expression of said intestinal immune response signaling marker inhibited by said control composition. In some embodiments, said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof. In some embodiments, when administered into said subject, said composition increases said level of said first bacterial strain or said second bacterial strain present within said subject by at least about 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition. In some embodiments, wherein when administered into said subject, said composition inhibits a growth of a pathogen in a gastrointestinal tract of said subject by at least about 0.1 % relative to said growth of said pathogen inhibited by said control composition. In some embodiments, wherein said pathogen comprises E. coli, K. pneumoniae, C. perfringens, S. aureus, S. flexneri, or a combination thereof. In someAttorney Docket No.: 53206-717601embodiments, wherein when administered into said subject, said composition increases an epithelial integrity of a gastrointestinal tract of said subject by at least about 0.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject increased by said control composition. In some embodiments, wherein said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, wherein when administered into said subject, said composition induces a difference of a level of microbiota structure present within said subject by at least about 0.1 % relative to said level of said microbiota structure present within said subject induced by said control composition. In some embodiments, wherein said composition comprises said bacterial population, and wherein said control composition does not comprise said bacterial population. In some embodiments, wherein said composition comprises said mixture, and wherein said control composition does not comprise said mixture. In some embodiments, wherein said composition comprises said derivative of said mixture or said bacterial population, and wherein said control composition does not comprise said derivative of said mixture.

[0009] In some embodiments, said bacterial population comprises at least 3 different bacteria species. In some embodiments, said bacterial population comprises at least 4 different bacteria species. In some embodiments, said first bacterial strain and said second bacterial strain comprises Bifidobacterium longum, Bifidobacterium bifidum, o Lactobacillus plantarum. In some embodiments, said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium bifidum, or Lactobacillus plantarum. In some embodiments, said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, ox Bifidobacterium bifidum. In some embodiments, said disease or condition comprises a gastrointestinal disease or condition.

[0010] Provided herein are methods of preventing a disease or condition in a subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein administration of said formulation into said subject is initiated within about 48 hours from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

[0011] Provided herein are methods of treating a disease or condition in a subject in needAttorney Docket No.: 53206-717601thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein administration of said formulation into said subject is initiated within about 30 days from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

[0012] In some embodiments, said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC), infectious gastroenteritis, neonatal cholestasis, pediatric intestinal motility disorders, gastroenteritis, Inflammatory bowel disease (IBD), Irritable bowel syndrome (IBS), or a combination thereof. In some embodiments, said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC). In some embodiments, the subject is an infant. In some embodiments, subject is a preterm infant or a neonate. In some embodiments, said composition further comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract. In some embodiments, the composition further comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’-Fucosyllactose (2’-FL), galactose, fucose, maltodextrin, pectin.

[0013] Provided herein, are methods. In an aspect, a method comprises (a) providing a plurality of bacterial strains; (b) identifying abacterial strain from said plurality bacterial strains that ranks at top 50 percentile among said plurality bacterial strains in: (i) a score of adherence to an intestinal epithelial cell (IEC), (ii) a score of growth in a culture medium comprising a carbohydrate as an energy source, wherein said carbohydrate is present within an infant gastrointestinal tract, (iii) a score of inhibition of a growth of an infant gastrointestinal pathogen, (iv) a score of inhibition of an immune response signaling pathway of a cell, or (v) any combination of (i)-(iv); and (c) selecting said bacterial strain for generating a composition for treating or preventing a gastrointestinal disease or condition of a subject, wherein said composition comprises abacterial strain of Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae.

[0014] In some embodiments, said plurality bacterial strains is derived from a fecal sample of a human. In some embodiments, said human does not have said gastrointestinal disease or condition. In some embodiments, said human is an adult. In some embodiments, said humanAttomey Docket No.: 53206-717601is an infant. In some embodiments, said bacterial strain ranks at top 10 percentile among said plurality bacterial strains in (i) or (ii). In some embodiments, said bacterial strain ranks at top 10 percentile among said plurality bacterial strains in (i) and (ii). In some embodiments, said carbohydrate comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2'-Fucosyllactose (2'-FL), galactose, fucose, maltodextrin, pectin, or a combination thereof, optionally lactose, galactose, GlnNAc, or LNnT. In some embodiments, said bacterial strain exhibits a growth ratio of about at least about 0.7 between (1) a number of bacterial cells of said bacterial strain within about 48 hours after said bacterial strain is inoculated in said culture medium and (2) a number of bacterial cells of said bacterial strain within about 48 hours after said bacterial strain is inoculated in a culture medium comprising glucose. In some embodiments, said bacterial strain exhibits an adherence value of at least 1x104[colony-forming units (CFU) / 9.5 centimeter square (cmA2) of a surface area of said IEC], optionally of at least 1x107log CFU / cm2of said surface area of said IEC. In some embodiments, said bacterial strain inhibits the growth of said infant gastrointestinal pathogen in vitro by at least 50%, relative to a growth of said infant gastrointestinal pathogen in vitro when inhibited by a control bacteria strain that is not said bacterial strain. In some embodiments, said bacterial strain inhibits said immune response signaling pathway of said cell by at least 50%, relative to an immune response signaling pathway when inhibited by a control bacteria strain that is not said bacterial strain.

[0015] Provided herein are compositions for treating or preventing a disease or condition in a subject in need thereof. In an aspect, a composition for treating or preventing a disease or condition in a subject in need thereof comprises: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, and wherein said first growth ratio is at least about 10 % different than said second growth ratio.

[0016] In some embodiments, said first growth ratio is measured as a ratio between (1) aAttorney Docket No.: 53206-717601number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, and wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source. In some embodiments, said energy source or said second energy comprises a carbohydrate. In some embodiments, said second energy source comprises glucose. In some embodiments, said energy source comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract. In some embodiments, said said energy source comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’-Fucosyllactose (2’-FL), galactose, fucose, maltodextrin, pectin, or a combination thereof. In some embodiments, said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said third growth ratio is at least about 10 % different than said fourth growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, and wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source. In some embodiments, said first growth ratio is at least about 10 % or at least about 25 % higher than said second growth ratio, and wherein said fourth growth ratio is at least about 10 % or at least about 25 % higher than said third growth ratio. In some embodiments, said energy source comprises LNnT or GlcNAc, and wherein said second energy source comprises galactose. In some embodiments, said composition comprises said bacterialAttomey Docket No.: 53206-717601population. In some embodiments, said composition comprises said mixture. In some embodiments, said composition comprises said derivative of said mixture or said bacterial population.

[0017] Provided herein are compositions for treating or preventing a disease or condition in a subject in need thereof. In an aspect, a composition for treating or preventing a disease or condition in a subject in need thereof comprises: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein when administered into said subject, said composition is configured to: (1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by said control composition; or (2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise (a), (b), (c), or (d).

[0018] In some embodiments, when administered into said subject, said composition is configured to inhibit said expression of said intestinal immune response signaling marker by at least about 0.1 % relative to said expression of said intestinal immune response signaling marker inhibited by said control composition. In some embodiments, said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof. In some embodiments, when administered into said subject, said composition is configured to increase said level of said first bacterial strain or said second bacterial strain present within said subject by at least about 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition. In some embodiments, when administered into said subject, wherein said composition is configured to inhibit a growth of a pathogen in a gastrointestinal tract of said subject by at least about 0.1 % relative to said growth of said pathogen inhibited by said control composition. In some embodiments, said pathogen comprises E. cob, K. pneumoniae, C. perfringens, S. aureus, S.flexneri, or a combination thereof. In some embodiments, when administered into said subject, said composition increases an epithelial integrity of said gastrointestinal tract of said subject by at least aboutAttomey Docket No.: 53206-7176010.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject increased by said control composition. In some embodiments, said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, when administered into said subject, said composition induces a difference of a level of microbiota structure present within said subject by at least about 0.1 % relative to said level of said microbiota structure present within said subject induced by said control composition. In some embodiments, said composition comprises said bacterial population, and wherein said control composition does not comprise said bacterial population. In some embodiments, said composition comprises said mixture, and wherein said control composition does not comprise said mixture. In some embodiments, said composition comprises said derivative of said mixture or said bacterial population, and wherein said control composition does not comprise said derivative of said mixture.

[0019] In some embodiments, said bacterial population comprises at least 3 different bacteria species. In some embodiments, said bacterial population comprises at least 4 different bacteria species. In some embodiments, said first bacterial strain and said second bacterial strain comprises Bifidobacterium longum, Bifidobacterium bifidum, o Lactobacillus plantarum. In some embodiments, said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium bifidum, or Lactobacillus plantarum. In some embodiments, said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, ox Bifidobacterium bifidum. In some embodiments, said disease or condition comprises a gastrointestinal disease or condition. In some embodiments, said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC), infectious gastroenteritis, neonatal cholestasis, pediatric intestinal motility disorders, gastroenteritis, Inflammatory bowel disease (IBD), Irritable bowel syndrome (IBS), or a combination thereof. In some embodiments, said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC). In some embodiments, the subject is an infant. In some embodiments, the subject is a preterm infant or a neonate. In some embodiments, the composition further comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract. In some embodiments, the composition further comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto- Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’-Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin.

[0020] Provided herein are methods of treating or preventing a disease or condition in aAttorney Docket No.: 53206-717601subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation to said subject, wherein said formulation comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein a first growth ratio of said first bacterial strain is at least about 10 % different than a second growth ratio of said second bacterial strain.

[0021] Provided herein are methods of treating or preventing a disease or condition in a subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein when administered into said subject, said composition: (1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by a control composition, or (2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise said first bacterial strain and said second bacterial strain.

[0022] Provided herein are compositions for treating or preventing a disease or condition in a subject in need thereof. In an aspect, a composition for treating or preventing a disease or condition in a subject in need thereof comprises: a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, wherein said first growth ratio is at least about 10 % different than said second growth ratio.

[0023] Provided herein are compositions for treating or preventing a disease or condition in a subject in need thereof. In an aspect, a composition for treating or preventing a disease or condition in a subject in need thereof comprises: a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. orAttorney Docket No.: 53206-717601Vertebrate- Associated ZactoZ>acz7 / aceae, and wherein when administered into said subject, said composition is configured to: (1) inhibit expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by said control composition, or (2) increase a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise first bacterial strain and said second bacterial strain.

[0024] Provided herein are methods of treating or preventing a disease or condition in a subject in need thereof. In an aspect, a method of treating or preventing a disease or condition in a subject in need thereof comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, wherein said first growth ratio is at least about 10 % higher than said second growth ratio, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said fourth growth ratio is at least about 10 % higher than said third growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cellsAttorney Docket No.: 53206-717601of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said energy source comprises LNnT or GlcNAc, wherein said second energy source comprises glucose, and wherein said third energy source comprises galactose.

[0025] Provided herein are compositions for treating or preventing a disease or condition in a subject in need thereof, wherein said composition. In an aspect, a composition for treating or preventing a disease or condition in a subject in need thereof comprises: (a) a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain; (b) a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain; (c) a derivative of said mixture or said bacterial population; or (d) any combination of (a)-(c), wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, wherein said first growth ratio is at least about 10 % higher than said second growth ratio, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said fourth growth ratio is at least about 10 % higher than said thirdAttorney Docket No.: 53206-717601growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said energy source comprises LNnT or GlcNAc, wherein said second energy source comprises glucose, and wherein said third energy source comprises galactose.

[0026] Restoring the microbiome-host homeostasis can help treating these disorders.Effective treatments can comprise administration of live biotherapeutics.

[0027] Provided herein are compositions. In an aspect, a composition comprises: a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein said composition is configured to treat a disease or disease condition at least in part by: (1) inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of said pathogen inhibited by a control composition; (2) inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by said control composition; (3) increasing an epithelial integrity of the gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of said subject increased by said control composition; (4) increasing a level of said first bacterial strain or said second bacterial stain present within said subject by at least 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition; or (5) inducing a difference of a level of microbiota structure present within said subject by at least 0.1 % relative to a level of said microbiota structure present within said subject induced by said control composition; or (6) any combinations thereof, wherein said control composition does not comprise said first bacterial strain and said second bacterial strain. In some embodiments, said composition is configured to inhibit said growth of said pathogen in said gastrointestinal tract of said subject by at least 0.1 % relative to said growth of said pathogen inhibited by said control composition; optionallyAttorney Docket No.: 53206-717601wherein said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, said composition is configured to inhibit said expression of said intestinal immune response signaling marker by at least 0.1 % relative to said expression of said intestinal immune response signaling marker inhibited by said control composition; optionally wherein said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin-lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof. In some embodiments, said composition is configured to increase said epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject increased by said control composition; optionally wherein said gastrointestinal tract comprises ileum or distal ileum; further optionally wherein said epithelial integrity of said gastrointestinal tract of said subject is measured by hematoxylin and eosin staining of said gastrointestinal tract. In some embodiments, said composition is configured to increase said level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition. In some embodiments, said composition is configured to induce said difference of said level of microbiota structure present within said subject by at least 0.1 % relative to said level of said microbiota structure present within said subject induced by said control composition; optionally wherein said level of microbiota structure present within said subject is measured by Bray-Curtis dissimilarity.

[0028] Provided herein are compositions. In an aspect, a composition comprises: a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein when said first bacterial strain is cultured with (1) said second bacterial strain or (2) a cultured medium of said second bacterial strain: (a) said first bacterial strain inhibits a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of said pathogen in said gastrointestinal tract of said subject when inhibited by a control bacterial strain comprising said first bacterial strain not cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, respectively; (b) said first bacterial strain inhibits expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of said intestinal immune response signaling marker when inhibited by said control bacterial strain, respectively; (c) said first bacterial strain increases a level of said first bacterial strain or said second bacteria strain present within said subject by at least 0.1 %Attorney Docket No.: 53206-717601relative to a level of said first bacterial strain or said second bacterial strain present within said subject when increased by said control bacterial strain, respectively; (d) said first bacterial strain increases an epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of said gastrointestinal tract of said subject when increased by said control bacterial strain, respectively; (e) said first bacterial strain induces a difference of a level of microbiota structure present within said subject by at least 0.1 % relative to a level of said microbiota structure present within said subject when induced by said control bacterial strain, respectively; (f) a cultured medium of said first bacterial strain inhibits a growth of said pathogen in said gastrointestinal tract of said subject by at least 0.1 % relative to a growth of said pathogen in said gastrointestinal tract of said subject when inhibited by a cultured medium of said control bacterial strain, respectively; (g) said cultured medium of said first bacterial strain inhibits said expression of said intestinal immune response signaling marker by at least 0.1 % relative to said expression of said intestinal immune response signaling marker when inhibited by said cultured medium of said control bacterial strain, respectively; (h) said cultured medium of said first bacterial strain increases a level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject when increased by said cultured medium of said control bacterial strain, respectively; (i) said cultured medium of said first bacterial strain increases an epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of said gastrointestinal tract of said subject when increased by said cultured medium of said control bacterial strain, respectively; or (j) said cultured medium of said first bacterial strain induces a difference of a level of microbiota structure present within said subject by at least 0.1 % relative to a level of said microbiota structure present within said subject when induced by said cultured medium of said control bacterial strain, respectively; or (k) any combinations thereof. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said first bacterial strain inhibits said growth of said pathogen in said gastrointestinal tract of said subject by at least 0.1 % relative to said growth of said pathogen in said gastrointestinal tract of said subject when inhibited by said control bacterial strain comprising said first bacterial strain not cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, respectively; optionally wherein said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium ofAttorney Docket No.: 53206-717601said second bacterial strain, said first bacterial strain inhibits said expression of said intestinal immune response signaling marker by at least 0.1 % relative to said expression of said intestinal immune response signaling marker when inhibited by said control bacterial strain, respectively; optionally said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or said combination thereof. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said first bacterial strain increases an epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of said gastrointestinal tract of said subject when increased by said control bacterial strain, respectively; optionally wherein said gastrointestinal tract comprises ileum or distal ileum; further optionally wherein said epithelial integrity of said gastrointestinal tract of said subject is measured by hematoxylin and eosin staining of said gastrointestinal tract. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said first bacterial strain increases said level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject when increased by said control bacterial strain, respectively. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said first bacterial strain induces said difference of said level of microbiota structure present within said subject by at least 0.1 % relative to said level of said microbiota structure present within said subject when induced by said control bacterial strain, respectively; optionally wherein said level of microbiota structure present within said subject is measured by Bray-Curtis dissimilarity. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said cultured medium of first bacterial strain inhibits said growth of said pathogen in said gastrointestinal tract of said subject by at least 0.1 % relative to said growth of said pathogen in said gastrointestinal tract of said subject when inhibited by said cultured medium of said control bacterial strain comprising said first bacterial strain not cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, respectively; optionally wherein said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said cultured medium of said first bacterial strain inhibits saidAttorney Docket No.: 53206-717601expression of said intestinal immune response signaling marker by at least 0.1 % relative to said expression of said intestinal immune response signaling marker when inhibited by said cultured medium of said control bacterial strain, respectively; optionally wherein said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin-lb (IL1B), or Lipocalin-2 (Lcn2), or said combination thereof. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said cultured medium of said first bacterial strain increases said epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject when increased by said cultured medium of said control bacterial strain, respectively; optionally wherein said gastrointestinal tract comprises ileum or distal ileum; further optionally wherein said epithelial integrity of said gastrointestinal tract of said subject is measured by hematoxylin and eosin staining of said gastrointestinal tract. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said cultured medium of said first bacterial strain increases said level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject when increased by said cultured medium of said control bacterial strain, respectively. In some embodiments, when said first bacterial strain is cultured with (1) said second bacterial strain or (2) said cultured medium of said second bacterial strain, said cultured medium of said first bacterial strain induces said difference of said level of microbiota structure present within said subject by at least 0.1 % relative to said level of said microbiota structure present within said subject when induced said cultured medium of by said control bacterial strain, respectively; optionally wherein said level of microbiota structure present within said subject is measured by Bray-Curtis dissimilarity.

[0029] Provided herein are compositions. In an aspect, a composition comprises: a cultured medium or derivative thereof of a bacterial population comprising (1) a first bacterial strain and (2) a second bacterial strain or a supernatant thereof, wherein said second bacterial strain is different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, wherein said cultured medium or derivative thereof is configured to: (a) inhibit a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of said pathogen in said gastrointestinal tract of said subject when inhibited by a control cultured medium or derivative thereof of a control bacterial population; (b) inhibit expression of anAttorney Docket No.: 53206-717601intestinal immune response signaling marker by at least 0.1 % relative to expression of said intestinal immune response signaling marker when inhibited by said control cultured medium or derivative thereof of said control bacterial population; (c) increase a level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject when increased by said control cultured medium or derivative thereof of said control bacterial population; (d) increase an epithelial integrity of the gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of said subject when increased by said control cultured medium or derivative thereof of said control bacterial population; or (e) induces a difference of a level of microbiota structure present within said subject by at least 0.1 % relative to a level of said microbiota structure present within said subject when induced by said control cultured medium or derivative thereof of said control bacterial population; or (f) any combinations thereof, wherein said control bacterial population does not comprise (1) said first bacterial strain and (2) said second bacterial strain or said supernatant thereof. In some embodiments, said cultured medium or derivative thereof is configured to inhibit said growth of said pathogen in said gastrointestinal tract of said subject by at least 0.1 % relative to said growth of said pathogen in said gastrointestinal tract of said subject when inhibited by said control cultured medium or derivative thereof of said control bacterial population; optionally wherein said gastrointestinal tract comprises ileum or distal ileum. In some embodiments, said cultured medium or derivative thereof is configured to inhibit said expression of said intestinal immune response signaling marker by at least 0.1 % relative to said expression of said intestinal immune response signaling marker when inhibited by said control cultured medium or derivative thereof of said control bacterial population; optionally wherein said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof. In some embodiments, said cultured medium or derivative thereof is configured to increase said level of said first bacterial strain or said second bacterial strain present within said subject by at least 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject when increased by said control cultured medium or derivative thereof of said control bacterial population. In some embodiments, said cultured medium or derivative thereof is configured to increase an epithelial integrity of said gastrointestinal tract of said subject by at least 0.1 % relative to an epithelial integrity of said gastrointestinal tract of said subject when increased by said control cultured medium or derivative thereof of said control bacterial population;Attorney Docket No.: 53206-717601optionally wherein said gastrointestinal tract comprises ileum or distal ileum; further optionally wherein said epithelial integrity of said gastrointestinal tract of said subject is measured by hematoxylin and eosin staining of said gastrointestinal tract. In some embodiments, said cultured medium or derivative thereof is configured to induce said difference of said level of microbiota structure present within said subject by at least 0.1 % relative to said level of said microbiota structure present within said subject when induced by said control cultured medium or derivative thereof of said control bacterial population; optionally wherein said level of microbiota structure present within said subject is measured by Bray-Curtis dissimilarity.

[0030] Provided herein are methods of preventing a gastrointestinal disease or condition in a subject in need thereof. In an aspect, a method of preventing a gastrointestinal disease or condition in a subject in need thereof comprises administering a formulation comprising a composition as described herein to said subject.

[0031] Provided herein are methods of treating a gastrointestinal disease or condition in a subject in need thereof. In an aspect, a method of treating a gastrointestinal disease or condition in a subject in need thereof comprises administering a formulation comprising a composition as described herein to said subject.

[0032] Provided herein are methods of preventing a gastrointestinal disease or condition in a subject in need thereof. In an aspect, a method of preventing a gastrointestinal disease or condition in a subject in need thereof comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, and wherein administration of said formulation into said subject is initiated within about 48 hours from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

[0033] Provided herein are methods of treating a gastrointestinal disease or condition in a subject in need thereof. In an aspect, a method of treating a gastrointestinal disease or condition in a subject in need thereof comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, and wherein administrationAttorney Docket No.: 53206-717601of said formulation into said subject is initiated within about 30 days from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

[0034] Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.INCORPORATION BY REFERENCE

[0035] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. To the extentBRIEF DESCRIPTION OF THE DRAWINGS

[0036] The features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and the disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which:

[0037] FIG. 1 shows that the growth curve of the L. crispatus and L. jensenii colonies, species in the Lactobacilli genus on MRS plates over the course of 32 hours (L. crispatus) and 20 hours (L. jensenii).

[0038] FIG. 2 shows a schematic of the Direct Carbohydrate Utilization Screen method for monitoring the growth of Bifidobacteria and Lactobacilli cultures in various carbohydrate-rich mediums. The data analysis method for visualizing the growth rates is also shown.

[0039] FIG. 3 shows the layout of the 96-well plate used for the Direct Carbohydrate Utilization Screen method.

[0040] FIG. 4 shows an example of the growth ratio to glucose for each bacterial strain of interest in each carbohydrate stock solution media as a clustermap.

[0041] FIG. 5 shows an example of a principal coordinates analysis visualizing the AUC ratio of each strain of interest cultured in each carbohydrate stock solution media.Attorney Docket No.: 53206-717601

[0042] FIG. 6 shows an example of the predicted Carbohydrate Utilization Screen AUC results for Lactobacillus strains.

[0043] FIG. 7 shows the method for executing Bifidobacteria screening, a technique to isolate and identify Bz / ztfobacterial strains via DNA sequencing.

[0044] FIGs. 8A-8B show an example of the optical density measurement results for Bifidobacteria DNA. FIG. 8A shows an example of measurement data for the Qubit and Nanodrop, creating an identification profile for the Bz / ztfobacterial strain. FIG. 8B shows an example of the assay results, creating a visual indication for identification of the Bz ztfobacterial strain.

[0045] FIGs. 9A-9G show examples of the nanopore sequencing measurement results for Bifidobacteria DNA, including the length of the DNA and the quality of the DNA. FIG. 9A shows an example of the nanodrop measurement data including examples of the average genome size for each strain of interest. FIG. 9B shows an example of the nanodrop measurement and analysis data including completeness and contamination measurements for various strains of interest. FIG. 9C shows an example of the average data for various strains of interest including completeness, contamination, and genome size averages. FIG. 9D shows an example of the nanodrop measurement and analysis data including the assembly error per million base pairs and the consensus quality score (QV). FIG. 9E shows an example of the gene number data plotted for each species of interest. FIG. 9F shows an example of the gene length data plotted for each species of interest. FIG. 9G shows an example of nanodrop data analyzed for various strains of interest, including polished average gene length ratios.

[0046] FIGs. 10A-10D show the method for membrane integrity screening using a monolayer of Caco-2 cells as an in vitro model for epithelial tissue. FIG. 10A shows the general method for membrane integrity screening. FIG. 10B shows an example of the microscopy visualization of the monolayer of Caco-2 cells in room air and a CO2 incubator.FIG. 10C diagrams a 24-well plate setup in which groups consisting of 4 wells per group were subject to different treatments. FIG. 10D shows an example of the data involving measurement of TNFa induced membrane permeability over a number of hours.

[0047] FIGs. 11A-11B show examples of the results of the TEER membrane permeability analysis. FIG. 11A shows an example of TEER and FD4 fluorescence results for samples treated with various levels of fFNy and / or IFNg treatment over the span of 4 hours for TEER and 48 hours for FD4 results. FIG. 11B shows examples of TEER and FD4 fluorescence results for individual plates over a period of 4 hours for TEER and 24 hours for FD4 results.Attorney Docket No.: 53206-717601

[0048] FIGs. 12A-12D show examples of the results of TEER membrane permeability analysis in room air incubation and alternatively CO2 incubation, as well as with and without the addition of HCO3. FIG. 12A shows examples of TEER results measured with the room air incubation condition with HCO3 as well as without HCO3 for a span of 4 hours posttreatment. FIG. 12B shows examples of TEER results measured with the room air incubation condition with HCO3 as well as without HCO3 for a span of 24 hours post-treatment. FIG. 12C shows examples of TEER results measured with the CO2 incubation condition with HCO3 as well as without HCO3 for a span of 4 hours post-treatment. FIG. 12D shows examples of TEER results measured with the CO2 incubation condition with HCO3 as well as without HCO3 for a span of 24 hours post-treatment.

[0049] FIGs. 13A-13F show the pathogen growth inhibition assay plate layout and examples of the spectrophotometry data results. FIG. 13A shows the layout of the 96-well plate for the in vitro growth inhibition assay. FIG. 13B shows an example of the cluster map data analysis for the OD600 measurements of various pathogenic strains of interest and various bacterial strains of interest. FIG. 13C shows examples of the OD600 curve of cultured pathogenic E. coli is in media with metabolites of the bacterial strains of interest, for example L. rhamnousus ST34, A. mucinphila ST7, and F prausnitzii ST38 (Fp ST38). FIG. 13D shows examples of the OD600 curve of cultured pathogenic E. coli in media with metabolites of the Bifidobacterium strains of interest, for example B. longum ST59, B. breve ST56, B. longum infantis ST19, B. stercoris ST24, B. dentium ST40, B. stercoris ST101, B. longum ST27, B. bifidum 1 ST50, and 7^. breve 2 ST30. FIG. 13E shows examples of the OD600 curve for growth of cultured pathogenic K. pneumoniae in media with metabolites of the bacterial strains of interest, for example L. rhamnousus ST34. FIG. 13F shows examples of the OD600 curve for growth of cultured pathogenic K. pneumoniae in media with metabolites of the Bifidobacterium strains of interest.

[0050] FIG. 14 shows the OD600 curve for dose-dependent inhibition of E. coli growth.

[0051] FIGs. 15A-15J show the plate setup and examples of results of the SEAP detection assay in detecting inflammatory transcription factor NFKB in RAW-Dual cells after treatment with potential therapeutic strains. FIG. 15A shows an example of the 96-well plate setup for the SEAP assay. FIG. 15B shows examples of SEAP test results at various MOIs. FIG. 15C shows examples of SEAP test results for various metabolite factors of the bacterial strains of interest, for example^, munciniphila ST7 and B. bifidum ST80. FIG. 15D shows examples of NFKB SEAP activity results from the metabolites of various Bifidobacterium strains of interest. FIG. 15E shows examples of basal NFKB SEAP activity results, as well as examplesAttorney Docket No.: 53206-717601of results from the metabolites of various other species of interest, for example Blautia and Roseburia. FIG. 15F shows examples ofNFKB SEAP activity results for various metabolite factors of the bacterial strains of interest on A", coli cell growth. FIG. 15G shows examples of NFKB SEAP activity results at various supernatant dilution factors for various pathogens of interest including E. coli. FIG. 15H shows examples ofNFKB SEAP activity results at various supernatant dilution factors deriving from various bacterial strains of interest including B. bifidum ST80. FIG. 151 shows examples ofNFKB SEAP activity results at various supernatant dilution factors deriving from various bacterial strains of interest including B. longum EV27. FIG. 15J shows examples ofNFKB SEAP activity results at various supernatant dilution factors deriving from various bacterial strains of interest including Fp ST38.

[0052] FIGs. 16A-16H show examples of the results of LUC testing in detecting inflammatory transcription factor IRF in RAW-Dual cells after treatment with potential therapeutic strains. FIG. 16A shows examples of LUC test result data for IRF LUC activity at various concentrations of lipopolysaccharides (LPS). FIG. 16B shows examples of LUC test result data for various MOIs. FIG. 16C shows examples of the results of LUC testing for metabolite factors of the bacterial strains of interest, for example A. munciniphila ST7 and B. bifidum ST80 at various dilutions. FIG. 16D shows examples of the results of LUC testing for IRF LUC activity at various dilution factors for the metabolites of various strains of interest, including B. longum EV27. FIG. 16E shows examples of the results of LUC testing for IRF LUC activity at various dilution factors for the metabolites of various strains of interest, including B. theta ST8. FIG. 16F shows examples of the results of LUC testing for IRF LUC activity at various dilution factors for the metabolites of various strains of interest, including Fp ST38. FIG. 16G shows examples of the results of LUC testing for IRF LUC activity for various metabolites of the strains of interest when interacting with pathogens of interest, for example E. coli. FIG. 16H shows examples of the results of LUC testing for IRF LUC activity for the metabolites of various strains of interest at various LPS concentrations.

[0053] FIG. 17 depicts a cartoon schematic of an exemplary strain selection method as described herein.

[0054] FIG. 18 depicts an exemplary clustermap of vaginally relevant carbohydrate utilization screening results of the exemplary bacterial strains described herein, depicting the growth ratio between the carbohydrate (listed on y-axis) and glucose.

[0055] FIG. 19 depicts an exemplary clustermap of BV pathogen biofilm inhibition results represented by the Biofilm Remaining Ratio.Attorney Docket No.: 53206-717601

[0056] FIG. 20 depicts a cartoon schematic of an exemplary method for identify a therapeutic consortium.

[0057] FIG. 21 depicts an exemplary clustermap of NEC pathogen growth inhibition results represented by the Pathogen Growth Ratio (area under the growth curve of treated culture / area under the curve of a media control).

[0058] FIG. 22A shows the profile of example bacterial population A.

[0059] FIG. 22B shows the study design to evaluate the therapeutic potential of example bacterial population A using a murine model of NEC.

[0060] FIG. 23A shows qPCR results for inflammatory cytokines in the ileum: example bacterial population A suppresses the expression of inflammatory markers in the Ileum.

[0061] FIG. 23B shows qPCR results for inflammatory cytokines in the ileum: example bacterial population A suppressed the expression of the inflammatory marker Lcn2, but not TNF-a.

[0062] FIG. 24 shows the hematoxylin and eosin (H& E) staining of the distal ileum: example bacterial population A preserves intestinal epithelial cell architecture.

[0063] FIG. 25 shows that example bacterial population A strains displace NEC pathogens in the distal ileum of NEC mice.

[0064] FIG. 26 shows that Microbial community structures in healthy mice, mice with NEC, and mice treated with example bacterial population A are significantly different.

[0065] FIG. 27A shows that example bacterial population A strains are significantly increased ceca of treated mice, while NEC pathobionts are significantly reduced.

[0066] FIG. 27B shows that example bacterial population A strains are significantly increased Ilea of treated mice, while NEC pathobionts are significantly reduced (Family level comparison).

[0067] FIG. 27C shows that example bacterial population A strains displace NEC pathogens in the distal ileum of mice

[0068] FIG. 27D shows that example bacterial population A strains are significantly increased ceca of treated mice, while NEC pathobionts are significantly reduced (Family level comparison).

[0069] FIG. 28A shows that example bacterial population A therapeutic candidate strains are significantly elevated in the ilea of treated mice fed formula.

[0070] FIG. 28B shows that example bacterial population A therapeutic candidate strains are significantly elevated in the ceca of treated mice fed formula.Attorney Docket No.: 53206-717601

[0071] FIG. 29 shows that microbiome profiles from clinical studies were analyzed to identify bacterial species consistently and significantly associated with healthy outcomes or protection from disease onset or recurrence.

[0072] FIG. 30 shows that metabolic products from example candidate strains can inhibit the growth ofE. coli up to 75% more than comparator strains.

[0073] FIG. 31 shows the specificity and directionality of the metabolic cross-feeding between the example strains.

[0074] FIG. 32 shows that metabolic products from non-limiting example candidate strains inhibit the growth of E. coli up to 75% more than comparator strains. Black dashed line across the top represents the growth of E. coli in the control media. Red dashed line represents a 50% reduction in the growth of E. coli (such strains can be selected as strains for generating the bacterial population as described herein). Multiple candidate Bifidobacterium strains can inhibit the growth of E. coli greater than that of the competitor B. longum EV27. All candidate Lactobacillus strains inhibit the growth of E. coli greater than that of the competitor L. reuteri BG49.

[0075] FIG. 33 shows that no example candidate strains or comparators inhibited LPS-stimulated TLR4 alone by more than 18%.

[0076] FIG. 34 shows that example human milk oligosaccharide (HMO) consuming strains can cross-feed additional therapeutic candidates and enhance their growth.

[0077] FIG. 35 shows that cross-fed combinations of example candidate strains can inhibit TLR4 activation up to 90%, while single strain comparators are ineffective.

[0078] FIG. 36A shows the growth of various example bacteria in culture medium comprising milk filtered whey liquid (FWL).

[0079] FIG. 36B shows the NEC pathogen inhibition ability of various example bacteria cultured in culture medium comprising milk filtered whey liquid (FWL).

[0080] FIG. 37 shows an example schematic for generating filtered whey liquid (FWL).

[0081] FIG. 38A shows the ability to adhere to an intestinal epithelial cell of a first set of example bacteria. FIG. 38B shows the growth profiles of the first set of example bacteria in various selected carbohydrates. FIG. 38C shows the growth of two example bacteria of the first set of example bacteria in the culture medium comprising FWL. FIG. 38D shows the NEC pathogen inhibition ability of two example bacteria of the first set of example bacteria that been cultured in the culture medium comprising FWL.Attorney Docket No.: 53206-717601

[0082] FIG. 39A shows the ability to adhere to an intestinal epithelial cell of a second set of example bacteria. FIG. 39B shows the growth profiles of two example bacteria of the second set of example bacteria in the culture medium comprising FWL. FIG. 39C shows the NEC pathogen inhibition ability of two example bacteria of the second set of example bacteria that been cultured in the culture medium comprising FWL.

[0083] FIG. 40 shows cross-feeding of various pairs of example bacteria.DETAILED DESCRIPTIONMicrobial Dysbiosis and Diseases

[0084] Microbial dysbiosis, the imbalance of microbiome / microbiota (the group or community of microbes or microorganism residing within a subject), can cause or be associated in various diseases and disease / pathological conditions. In some cases, while the microbial dysbiosis may not cause the diseases or disease conditions, it can affect the development and / or progression of the symptoms of the diseases and disease / pathological conditions. In some cases, restoring the microbial dysbiosis can treat / prevent the diseases or disease conditions and improve / alleviate the development / progression of the symptoms of the diseases or disease conditions. One way to restore the microbial dysbiosis can comprise administration of microbes to a subject or patient.

[0085] A microbial dysbiosis-associated disease can comprise gastrointestinal diseases that affect gastrointestinal tract, such as infant gastrointestinal diseases or disease conditions. Necrotizing enterocolitis (NEC) is an infant gastrointestinal disease or disease condition that affects about 100,000 infants annually in the U. S. NEC is one of the leading causes of illness and death among preterm infants, amounting to 1 billion dollars in annual costs. The health care costs average >$300,000 / infant when surgical management is required. This number continues to go up as the viability of earlier and earlier preterm births increases. About 5-12% of preterm infants (i.e., born before the 37 weeks of pregnancy) can develop NEC. About 40-50% of infants with NEC die from the disease. NEC usually occurs before the newborn leaves the hospital. There are no FDA-approved treatments for NEC

[0086] NEC can result from intestinal inflammation in preterm infants. NEC is a gastrointestinal disease or disease condition characterized by inflammation, ischemia, and tissue necrosis. Infants with NEC display impaired epithelial barrier integrity with decreased mucus; decreased intracellular junction integrity (such as tight junction); increased intestinal permeability; reduced peristaltic movement; and impaired epithelial cell regeneration;Attorney Docket No.: 53206-717601decreased immunoglobulin A, feeding intolerance, lethargy, temperature instability, abdominal distention, blood in stools, diarrhea, vomiting, and signs of sepsis; and / or altered microbiota, leading to inflamed intestine (inflamed wall with gas bubbles). In many cases it is diagnosed by the radiographic observation of Pneumatosis Intestinalis (bubbles caused by reaction to bacteria) presence of fixed or dilated intestinal loops, and edema / swelling. While the exact cause of NEC is not well understood, it is well appreciated that there are some characteristics that been well described in premature babies that suffer from NEC.

[0087] In infants with NEC, opportunistic pathogens can displace healthy microbiota and dominate the gut of preterm infants. Additionally, preterm birth can negatively impact gut microbiota development. Multiple opportunistic pathogens in the hospital setting can colonize the preterm infant gut, including E.coli, K. pneumoniae, E. clocae, Salmonella, and E.faecalis. Colonization by these bacteria can contribute to inflammation, infection, antibiotic resistance, and sepsis in preterm infants with no protective gut microbiota. These preterm infant colonizing pathogens can also contain antimicrobial resistance genes, rendering treatments with antibiotics ineffective. Additionally, NEC can be characterized by a breakdown of epithelial barrier integrity in the gastrointestinal tract.

[0088] NEC can be driven by a pathogenic microbiome. Opportunistic bacterial pathogens can colonize the intestinal tract in preterm infants. In these infants, beneficial bacteria found in the full-term infant gut are absent. Pathogens can drive the activation of immune response (such as innate immune responses including those regulated by TLR4), resulting in secretion of inflammatory cytokines and drives Thl7 polarization. Uncontrolled intestinal inflammation can increase intestinal epithelial permeability, leading to a cycle of inflammation, infection, and necrosis.

[0089] Currently available therapeutics can lack efficiency, efficacy, and / or applicability to wide population of patients. Currently available therapeutics can be ineffective for not sufficient to inhibit growth or biofilm by the pathogen, thereby unable to prevent engraftment of the pathogens. Currently available therapeutics can be inefficient for not facilitating the engraftment of the infant gastrointestinal tract by healthy microbiota. For example, currently available therapeutics (such as when comprising a microbe for facilitating the engraftment of the microbe to the vagina or gastrointestinal (GI) tract) may not sufficiently adhere to the vaginal or intestinal epithelial cells. Currently available therapeutics may not sufficiently increase barrier integrity. Additionally, these currently available therapeutics may not sufficiently utilize vaginal or a carbohydrate present within an infant gastrointestinal tract (also referred infant gastrointestinally relevant carbohydrates) (for example, as a nutrientAttorney Docket No.: 53206-717601source), rendering them insufficient to proliferate within these organs / tissues and unable to reduce the engraftment by the pathogen microbes. A nutrient source, as used herein, refers to a substance that is metabolized by a microbe or microorganism. In addition, current available therapeutics may not be sufficient to reduce inflammation that contributes to the diseases as described herein, thereby unable to reduce or improve the symptoms associated with the diseases. While antibiotics can be effective in inhibiting or eliminating pathogens in some cases of NEC, it also inhibits and eliminates healthy microbiota, which in turn can prevent the engraftment of the infant gastrointestinal tract by healthy microbiota and increase the risk of the tissue being engrafted by pathogens or losing the healthy microbiota. In other cases, the uses of antibiotics lack effectiveness, due to the antimicrobial resistance acquired by some of the pathogens (such as in NEC). The heterogeneity (such as genetic, epigenetic, environmental, and / microbiome differences) can present difficulty to design therapeutics that can treat or prevent NEC. Currently available therapeutics are also incapable of preventing the disease, for the same reasons as described herein.

[0090] In addition to observational human studies and animal studies, it is understood that microbial interventions can be beneficial or even protective in preterm infants at risk for NEC. There are now examples of the protective supplementation with bacteria as probiotics and live biotherapeutics has been used in attempts to beneficially manipulate the preterm infant gut microbiota. One example here shows the abundance of a human milk oligosaccharide (HMO) (2’-fucosyllactose ) in stool of preterm infants with a live bacterial intervention is reduced to levels typically observed in full term infants with a healthy microbiota, while the abundance of a key SCFA - acetate is increased - in the infants receiving the intervention. Impressively, a recent retrospective analysis found the supplementation of preterm infants with a bacterial intervention was capable of providing complete protection from NEC-related deaths / mortality compared to preterm infants with no microbiome-based intervention.

[0091] Recent studies have shown that the gut microbiota composition in preterm infants differs from full-term infants in that it is dominated by opportunistic pathogens that are not dominant in the gut microbiota of full term, healthy infants. Many at-risk preterm infants spend their first weeks or even months in a hospital setting, and are administered antibiotics as standard of care. While antibiotics can be life-saving, they encourage the colonization of antibiotic resistant microbes from the hospital setting - these hospital acquired microbes tend to be opportunistic pathogens with antibiotic resistance. Many of these hospital acquired microbes contain antibiotic resistance are known pathogens that characterize the NECAttorney Docket No.: 53206-717601microbiota. For example, E. coli, Klebsiella are common gram negative enterobacteria that colonize the preterm infant gut.

[0092] Provided herein, are compositions for treating diseases or disease conditions associated with microbial dysbiosis and methods of using the compositions for treating the diseases or disease conditions. The compositions can comprise a bacteria or a plurality of bacteria. Also provided herein are methods for identify the bacteria or the plurality of bacteria. For example, the method may comprise a systematic strain-level selection of active ingredient microbes / bacteria. In some cases, the bacterial described herein can: (1) strongly adhere to human intestinal epithelial cells; (2) utilize nutrients available in breast milk or milk formula, including human milk oligosaccharide (HMO)s; (3) produce metabolites that directly reduce pathogen growth and biofilm formation; and / or (4) block activation of the receptor TLR4 to reduce NEC-associated inflammation. The rationale can comprise using a bacteria or bacterial strain(s) that can address multiple underlying causes of NEC. Based on the disease pathogenesis, bacteria or bacterial strain(s) that can target these key underlying microbial drivers of NEC can be selected.

[0093] The compositions provided herein have higher effectiveness, efficiencies, and applicability to subjects’ population, relative to the currently available therapeutics. In some cases, the compositions provided herein can be sufficient to inhibit growth or biofilm by the pathogen, thereby preventing the engraftment of the pathogens. In some cases, the compositions provided herein can be efficient in facilitating the engraftment of the infant gastrointestinal tract by healthy microbiota. In some cases, the bacteria are isolated from the healthy infant gut and can colonize the healthy infant gut. In some cases, the compositions provided herein can sufficiently increase barrier integrity that is comprised in the subjects with the disease. For example, the compositions provided herein can sufficiently adhere to the intestinal epithelial cells. In some cases, the compositions provided herein can sufficiently utilize carbohydrates present within an infant gastrointestinal tract carbohydrate present within an infant gastrointestinal tract(for example, as a nutrient source), rendering them sufficient to proliferate within these organs and reduce the engraftment by the pathogen microbes. In some cases, the compositions provided herein can be sufficient to reduce inflammation that contributes to the diseases as described herein, thereby reducing or improving the symptoms associated with the diseases. In some cases, the compositions provided herein may not inhibit the growth of microbiota associated with the healthy infant gastrointestinal tract, thereby reducing the risk of the subject being suffered from the same disease. In some cases, the compositions provided herein can be based on selection ofAttorney Docket No.: 53206-717601bacteria (as described herein) that can be sufficient to reduce or prevent the disease described herein in a wide population with heterogenicity. For the same reasons as described herein, the compositions provided herein can be used to prevent the development of the diseases.Compositions

[0094] Provided herein, are compositions and / or formulations. The compositions and / or formulations can be used for treating disease or disease conditions associated with microbial dysbiosis, such as those described herein. The compositions and / or formulations can comprise a bacterial population. The bacterial population may comprise at least two bacteria or bacterial strains. The compositions and / or formulations can comprise a mixture comprising a first bacteria or bacterial strain and a bacterial product of a second bacteria or bacterial strain. A bacterial product of a bacteria or bacterial strain my comprise a molecule that is (1) generated or derived by the bacterial product of a bacteria or bacterial strain; (2) generated or derived by a biological process of the a bacteria or bacterial strain. A bacterial product of a bacteria or bacterial strain my comprise a molecule that is generated or derived by the bacterial product of a bacteria or bacterial strain. A bacterial product of a bacteria or bacterial strain my comprise a molecule that is generated or derived by a biological process of the a bacteria or bacterial strain, bacterial product of a bacteria or bacterial strain. A bacterial product may be a bacterial metabolite. The bacterial product or metabolite may comprise a peptide, polypeptide, lipid, organic compound, inorganic compound, nucleic acid, or nucleotide. The compositions and / or formulations can comprise a derivative of: a mixture comprising a first bacteria or bacterial strain and a bacterial product of a second bacteria or bacterial strain; or a bacterial population of at least two bacteria or bacterial strains. The compositions and / or formulations can further comprise a pharmaceutically-acceptable excipient, nutrients for the bacterial population, and other components for administrating to a subject. The compositions and / or formulations described herein can thus also comprise pharmaceutical compositions and / or formulations. A derivative of a mixture comprising a first bacteria or bacterial strain and a bacterial product of a second bacteria or bacterial strain; or a bacterial population of at least two bacteria or bacterial strains, may comprise a supernatant of the mixture or bacterial population. The supernatant may comprise a filtered or purified form of the culture or mixture. The supernatant may comprise a filtered or purified form of the culture or mixture but is enriched for the bacterial product of the bacterial strain or bacteria. In some cases, the supernatant may have an increase of the amount of the bacterial product by at least about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, orAttorney Docket No.: 53206-717601150 %, relative to the culture or mixture the supernatant is derived from. In some cases, the supernatant may have an increase of the amount of the bacterial product by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold%, relative to the culture or mixture the supernatant is derived from. In some cases, the supernatant may have an increase of the amount of the bacterial product by at most about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %, relative to the culture or mixture the supernatant is derived from. In some cases, the supernatant may have an increase of the amount of the bacterial product by at most about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold%, relative to the culture or mixture the supernatant is derived from.

[0095] Provided herein are composition comprising a bacterial population configured to treat a disease or disease condition at least in part by (1) inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition; (2) inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition; (3) increasing an epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition; (4) increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition; or (5) inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition; or (6) any combinations thereof, wherein the control composition does not comprise the first bacteria or bacterial strain and the second bacteria or bacterial strain. In some cases, the composition comprising a bacterial population may be capable of inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition. In some cases, the composition comprising a bacterial population may be capable of inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition. In some cases, the composition comprising a bacterial population may be capable of increasing anAttorney Docket No.: 53206-717601epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition. In some cases, the composition comprising a bacterial population may be capable of increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition. In some cases, the composition comprising a bacterial population may be capable of inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition.

[0096] Provided herein are composition comprising a first bacteria or a cultured medium thereof configured to treat a disease or disease condition at least in part by (1) inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition; (2) inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition; (3) increasing an epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition; (4) increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition; or (5) inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition; or (6) any combinations thereof, wherein when the first bacteria or bacterial strain is cultured with (1) a second bacteria or bacterial strain or (2) a cultured medium of a second bacteria or bacterial strain, wherein the control composition does not comprise the first bacteria or bacterial strain and the second bacteria or bacterial strain. In some cases, the composition comprising the first bacteria or a cultured medium thereof may be capable of inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition. In some cases, the composition comprising first bacteria or a cultured medium thereof may be capable of inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition. In some cases, theAttorney Docket No.: 53206-717601composition comprising first bacteria or a cultured medium thereof may be capable of increasing an epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition. In some cases, the composition comprising first bacteria or a cultured medium thereof may be capable of increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition. In some cases, the composition comprising first bacteria or a cultured medium thereof may be capable of inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition.

[0097] Provided herein are composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof configured to treat a disease or disease condition at least in part by (1) inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition; (2) inhibiting expression of an intestinal immune response signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition; (3) increasing an epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition; (4) increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition; or (5) inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition; or (6) any combinations thereof. In some cases, the composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof may be capable of inhibiting a growth of a pathogen in a gastrointestinal tract of a subject by at least 0.1 % relative to a growth of the pathogen inhibited by a control composition. In some cases, the composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof may be capable of inhibiting expression of an intestinal immune responseAttorney Docket No.: 53206-717601signaling marker by at least 0.1 % relative to expression of the intestinal immune response signaling marker inhibited by the control composition. In some cases, the composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof may be capable of increasing an epithelial integrity of the gastrointestinal tract of the subject by at least 0.1 % relative to an epithelial integrity of the gastrointestinal tract of the subject increased by the control composition. In some cases, the composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof may be capable of increasing a level of the first bacteria or bacterial strain or the second bacterial stain present within the subject by at least 0.1 % relative to a level of the first bacteria or bacterial strain or the second bacteria or bacterial strain present within the subject increased by the control composition. In some cases, the composition comprising a cultured medium or derivative thereof of a bacterial population comprising a first bacteria or bacterial strain and a second bacteria or bacterial strain or a supernatant thereof may be capable of inducing a difference of a level of microbiota structure present within the subject by at least 0.1 % relative to a level of the microbiota structure present within the subject induced by the control composition.Bacterial populations

[0098] The bacterial population provided herein can comprise a bacteria or bacterial strain or a plurality bacteria or bacterial strains. The term “strain” or “bacterial strain” as used herein refers to a group of bacterial cells, isolates, progenies thereof, or derivatives thereof comprising at least 50 %, at least 60 %, at least 70 %, at least 80 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, at least 99 % or more sequence identity in the genome sequences. For example, two bacterial cells, isolates, progenies thereof, derivatives thereof, or any combinations thereof may be the same strain if they share at least 50 %, at least 60 %, at least 70 %, at least 80 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, at least 99 % or more sequence identity in the genome sequences. In some cases, a strain as used herein can also refer to a group of bacterial cells, isolates, progenies thereof, or derivatives thereof comprising at least 50 %, at least 60 %, at least 70 %, at least 80 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, at least 99 % or more sequence identity in the 16S rRNA gene sequences. For example, two bacterial cells, isolates,Attorney Docket No.: 53206-717601progenies thereof, derivatives thereof, or any combinations thereof may be the same strain if they share at least 50 %, at least 60 %, at least 70 %, at least 80 %, at least 90 %, at least 91 %, at least 92 %, at least 93 %, at least 94 %, at least 95 %, at least 96 %, at least 97 %, at least 98 %, at least 99 % or more sequence identity in their 16S rRNA or rDNA sequences. The bacterial population can be used for treating a disease or disease condition as described herein. A bacteria or bacterial strain of the bacterial population can comprise a sufficient ability in a disease or disease condition associated function as described herein (i.e., the bacteria or bacterial strain is sufficiently capable of carrying out a particular disease or disease condition associated function). For example, the disease or disease condition associated function may comprise any of those described in EXAMPLES 2-3, 5, 7-8, and 10- 12. In some cases, the bacterial population may comprise a plurality of bacteria or bacterial strains or at least two bacteria or bacterial strains. In some cases the plurality of bacteria or bacterial strains or at least two bacteria or bacterial strains of the bacterial population can have a collective effect in the disease or disease condition associated function as described herein. In some cases, the plurality of bacteria or bacterial strains or at least two bacteria or bacterial strains of the bacterial population may comprise at least one donor bacteria or bacterial strain and at least one recipient bacteria or bacterial strain.Microbial taxonomy

[0099] The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Firmicutes or Actinomycetota. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Firmicutes. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Actinomycetota. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bacilli or Actinomycetia. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bacilli. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Actinomycetia. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Lactobacillales or Bifidobacteriales. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Lactobacillales. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bifidobacteriales. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Lactobacillaceae or Bifidobacteriaceae. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Lactobacillaceae. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bifidobacteriaceae. The bacteria or bacterial strain described herein can comprise a bacteriaAttorney Docket No.: 53206-717601or bacterial strain of Lactobacillus sp. (or Vertebrate -Associated Lactobacillaceae) or Bifidobacterium sp. The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Lactobacillus sp. (or Vertebrate-Associated Lactobacillaceae). The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bifidobacterium sp. In some cases, a bacteria or bacterial strain described herein can be isolated from a vertebrate (or the bacteria or bacterial strain is vertebrate-associated). In some cases, a bacteria or bacterial strain described herein can be isolated from a human subject. In some cases, a bacteria or bacterial strain described herein can be isolated from a healthy human subject. The healthy human subject can be a female. The healthy human subject can be a male. The healthy human subject can be an infant. For example, the bacteria or bacterial strain can be vertebrate-associated Bifidobacterium sp. The healthy human subject may not have a disease or disease condition as described herein.

[0100] In some instances, a species of Lactobacillus family may comprise a species of the Lactobacillus genus proposed in 1901, which is described in Zheng, J., et. al. hit. J. Syst. Evol. Microbiol. 2020;70:2782-2858 and is entirely incorporated herein by reference. The Lactobacillus genus may comprise Gram-positive, fermentative, facultatively anaerobic, and / or non-spore forming microorganisms. In some cases, the number of microorganisms that can be classified as Lactobacillus genus may increase, compared to those classified in 1901, with the broad definition of the 1901 classification. Lactobacillus genus may comprise about 261 species that comprise distinctive phenotypic, ecological, and / or genotypic characteristics. The number of species in the genus and / or the level of diversity within the Lactobacillus genus may exceed those of other bacterial genera and / or bacterial families. In this case, Lactobacillus can be reclassified. For example, the average nucleotide identity (ANI), average amino acid identity (AAI), core-gene average amino acid identity (cAAI), core genome phylogeny, signature genes, and metabolic, and / or ecological criteria of the bacterial species in the Lactobacillus genus and its sister taxa in the Lactobacillaceae and Leuconostocaceae families are used to reclassify the Lactobacillus genus classified using the definition of 1901 (1901 classification).

[0101] In some cases, under the reclassification system, the species of the Lactobacillaceae family may comprise about 26 different genera (Lactobacillus, Paralactobacillus, Pediococcus, Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacillus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquor ilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfur ilactobacillus, Paucilactobacillus, Limosilactobacillus,Attorney Docket No.: 53206-717601Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus, and Lentilactobacillus), as well as merging the Leuconostocaceae family into the Lactobacillaceae family. A comparison of the reclassified Lactobacllius species can be found using the Lactotax database, which can be found in the link:f Lactobacillus.ualberta.ca / and is entirely incorporated herein by reference. The classification of Lactobacillus described herein, is also provided in Parks, DH et. al. Nat Biotechnol. 2018 Nov;36(10):996-1004; Salvetti, E, et. al. Appl Environ Microbio. 2018 Aug 17;84(17). Print 2018 Sep. 1 Erratum in: Appl Environ Microbio.2018 Oct. l;84(20); Markets and Markets: https: / / www.marketsandmarkets.com / Market-Reports / probiotic-market- advanced-technologies-and-global -market-69.html); Parker, CT, et. al. Int. J. Syst. Evol. Microbiol. 68:1825-1829; Duar, DM, et. al. FEMS Microbiol Rev. 2017 Aug 1;41(Supp_l): S27-S48; or Pane and Vinot 2019: http s: / / www. mi crobi ometi m es. com / the ■■ / »c oZ>ac / / M.s-taxonomy-change-is-coming-why-and-how-to-make-the-most-of-it / , each of which is entirely incorporated herein by reference.

[0102] TABLE 1 below shows the names of various Lactobacillus sp. under the 1901 classification and the reclassification.TABLE 1: Lactobacillus sp. names before and after reclassificationName of Lactobacillus species classified in Name of Lactobacillus species under 1901 reclassificationLactobacillus acidipiscis Ligilactobacillus acidipiscis Lactobacillus acidophilus Lactobacillus acidophilusLactobacillus agilis Ligilactobacillus agilisLactobacillus aviarius Ligilactobacillus aviariusLactobacillus brevis Levilactobacillus brevisLactobacillus coleohominis Limosilactobacillus coleohominis Lactobacillus crispatus Lactobacillus crispatusLactobacillus crusiovum Companilactobacillus crusionim Lactobacillus curvatus Latilactobacillus curvatusLactobacillus diolivorans Lentilactobacillus diolivorans Lactobacillus farraginis Lentilactobacillus farraginis Lactobacillus fermentum Limosilactobacillus fermentum Lactobacillus fuchuensis Latilactobacillus fuchuensis Lactobacillus harbinensis Schleiferilactobacillus harbinensis Lactobacillus helve ticus Lactobacillus helveticusLactobacillus hilgardii Lentilactobacillus hilgardii Lactobacillus intestinalis Lactobacillus intestinalisLactobacillus jensenii Lactobacillus jenseniiLactobacillus johnsonii Lactobacillus johnsoniiLactobacillus kefiranofaciens Lactobacillus kefiranofaciensLactobacillus kefiri Lentilactobacillus kefiriAttorney Docket No.: 53206-717601Lactobacillus lindneri Fructilactobacillus lindneri Lactobacillus mali Liquorilactobacillus maliLactobacillus manihoiivovans Lacticaseibacillus manihotivorans Lactobacillus mucosae Limosilactobacillus mucosae Lactobacillus oeni Liquorilactobacillus oeniLactobacillus oligofermentans Paucilactobacillus oligofermentans Lactobacillus panis Limosilactobacillus panisLactobacillus pantheris Lacticaseibacillus pantheris Lactobacillus parabrevis Levilactobacillus parabrevis Lactobacillus paracollinoides Secundilactobacillus paracollinoides Lactobacillus parakefiri Lentilactobacillus parakefiri Lactobacillus paraplantarum Lactiplantibacillus paraplantarum Lactobacillus pentosus Lactiplantibacillus pentosus Lactobacillus ponds Limosilactobacillus pontisLactobacillus reuteri Limosilactobacillus reuteriLactobacillus rhamnosus Lacticaseibacillus rhamnosus Lactobacillus rossiae Furfurilactobacillus rossiae Lactobacillus salivarius Ligilactobacillus salivariusLactobacillus siliginis Furfurilactobacillus siliginis Lactobacillus sucicola Liquorilactobacillus sucicola Lactobacillus vaccinostercus Paucilactobacillus vaccinostercus Lactobacillus vaginalis Limosilactobacillus vaginalis Lactobacillus vini Liquorilactobacillus viniLactobacillus zeae Lacticaseibacillus zeae

[0103] The naming used in this application can be determined using the 1901 classification or the reclassification as described herein, interchangeably. As used herein, Vertebrate- Associated Lactobacillaceae refers to bacterial genera in the Lactobacillaceae family that are associated with vertebrates, which includes Lactobacillus, Limosilactobacillus, Ligilactobacillus, and Lacticaseibacillus. In some instances, the bacterial population may comprise at least one strain of Vertebrate- Associated Lactobacillaceae, or at least one strain of Bifidobacterium sp. In some instances, a bacterial population may comprise at least one strain of Bifidobacterium sp. In some instances, a bacterial population may comprise at least one strain of Vertebrate-Associated Lactobacillaceae.

[0104] The bacteria or bacterial strain described herein can comprise a bacteria or bacterial strain of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus plantarum, or Lactobacillus rhamnosus. The bacteria or bacterial strain described herein for treating or preventing a vaginal disease or a complication associated with a vaginal disease can comprise a bacteria orAttorney Docket No.: 53206-717601bacterial strain of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii. The bacteria or bacterial strain described herein for treating or preventing a vaginal disease or a complication associated with a vaginal disease can comprise a bacteria or bacterial strain of Lactobacillus crispatus. The bacteria or bacterial strain described herein for treating or preventing a vaginal disease or a complication associated with a vaginal disease can comprise a bacteria or bacterial strain of Lactobacillus gasseri. The bacteria or bacterial strain described herein for treating or preventing a vaginal disease or a complication associated with a vaginal disease can comprise a bacteria or bacterial strain of Lactobacillus jensenii. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium adolescentis, Bifidobacterium bifidum.Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Lactobacillus plantarum, or Lactobacillus rhamnosus. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium adolescentis. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium bifidum. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium breve. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium longum. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Bifidobacterium pseudocatenulatum. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Lactobacillus plantarum. The bacteria or bacterial strain described herein for treating or preventing infant gastrointestinal disease can comprise Lac tobacillus rhamnosus.

[0105] The bacterial strain described herein may comprise Lactobacillus crispatus ST100 (or " ST 100"), Bifidobacterium bifidum ST31 (or " ST31"), Bifidobacterium bifidum ST80 (or " ST80"), Lactobacillus crispatus ST20 (or " ST20"), Lactobacillus crispatus STI 12 (or " STI 12"), Lactobacillus gasseri ST105 (or " ST105"), Lactobacillus jensenii ST21 (or " ST21"), Lactobacillus plantarum ST65 (or " ST65"), Bifidobacterium adolescentis ST 101 (or " ST101"), Bifidobacterium breve ST56 (or " ST56"), Bifidobacterium longum ST19 (or " ST 19"), Bifidobacterium longum ST81 (or " ST81"), Bifidobacterium pseudocatenulatum ST37 (or " ST37"), Bifidobacterium pseudocatenulatum ST66 (or " ST66"), Lactobacillus rhamnosus ST116 (or " ST116"), Bifidobacterium breve ST71 (or " ST71"), Bifidobacterium longum ST23 (or " ST23"), Bifidobacterium longum STI 19 (or " STI 19"). The bacterial strain described herein may comprises ST100. The bacterial strain described herein may comprisesAttorney Docket No.: 53206-717601ST31. The bacterial strain described herein may comprises ST80. The bacterial strain described herein may comprises ST20. The bacterial strain described herein may comprises STI 12. The bacterial strain described herein may comprises ST105. The bacterial strain described herein may comprises ST21. The bacterial strain described herein may comprises ST65. The bacterial strain described herein may comprises ST101. The bacterial strain described herein may comprises ST56. The bacterial strain described herein may comprises ST19. The bacterial strain described herein may comprises ST81. The bacterial strain described herein may comprises ST37. The bacterial strain described herein may comprises ST66. The bacterial strain described herein may comprises STI 16. The bacterial strain described herein may comprises ST71. The bacterial strain described herein may comprises ST23. The bacterial strain described herein may comprises STI 19.

[0106] The bacterial strain of Lactobacillus crispatus described herein may comprise ST 100, STI 12, or ST20. The bacterial strain of Lactobacillus crispatus described herein may comprise ST100. The bacterial strain of Lactobacillus crispatus described herein may comprise ST20. The bacterial strain of Lactobacillus crispatus described herein may comprise STI 12. The bacterial strain of Lactobacillus gasseri described herein may comprise ST105. The bacterial strain of Lactobacillus jensenii described herein may comprise ST21. The bacterial strain of Lactobacillus plantarum described herein may comprise ST65. The bacterial strain of Lactobacillus rhamnosus described herein may comprise STI 16. The bacterial strain of Bifidobacterium adolescentis described herein may comprise ST101. The bacterial strain of Bifidobacterium bifidum described herein may comprise ST31 or ST80. The bacterial strain of Bifidobacterium bifidum described herein may comprise ST31. The bacterial strain of Bifidobacterium bifidum described herein may comprise ST80. The bacterial strain of Bifidobacterium breve described herein may comprise ST56 or ST71. The bacterial strain of Bifidobacterium breve described herein may comprise ST56. The bacterial strain of Bifidobacterium breve described herein may comprise ST71. The bacterial strain of Bifidobacterium pseudocatenulatum described herein may comprise ST37 or ST66. The bacterial strain of Bifidobacterium pseudocatenulatum described herein may comprise ST37. The bacterial strain of Bifidobacterium pseudocatenulatum described herein may comprise ST66. The bacterial strain of Bifidobacterium longum described herein may comprise ST19, ST81, ST23, or STI 19. The bacterial strain of Bifidobacterium longum described herein may comprise ST19. The bacterial strain of Bifidobacterium longum described herein may comprise ST81. The bacterial strain of Bifidobacterium longum described herein mayAttorney Docket No.: 53206-717601comprise ST23. The bacterial strain of Bifidobacterium longum described herein may comprise STI 19.

[0107] In some instances, a bacterial population may comprise one or more Bifidobacterium sp. The one or more Bifidobacterium sp. may include Bifidobacterium adolescentis, Bifidobacterium aerophilum, Bifidobacterium angulatum, Bifidobacterium animalis, Bifidobacterium asteroids, Bifidobacterium bifidum, Bifidobacterium bourn, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium choerinum, Bifidobacterium coryneforme, Bifidobacterium cuniculi, Bifidobacterium dentium, Bifidobacterium faecale, Bifidobacterium gallicum, Bifidobacterium globosum, Bifidobacterium indicum, Bifidobacterium infantis, Bifidobacterium longum, Bifidobacterium magnum, Bifidobacterium minimum, Bifidobacterium pseudocatenulatum, Bifidobacterium seudolongum, Bifidobacterium pullorum, Bifidobacterium stercoris. Bifidobacterium subtile, Bifidobacterium suis, or Bifidobacterium thermophilum, or a combination thereof. In some instances, a bacterial population may comprise one or more Lactobacillus sp. The one or more Lactobacillus sp. may include Lactobacillus johnsonii, Lactocaseibacillus rhamnosus, Lactocaseibacillus zeae, Ligilactobacillus acidipiscis, Lactobacillus acidophilus, Ligilactobacillus agilis, Ligilactobacillus aviarius, Levilactobacillus brevis, Limosilactobacillus coleohominis, Lactobacillus crispatus, Companilactobacillus crustorum, Latilactobacillus curvatus, Lentilactobacillus diolivorans, Lentilactobacillus farraginis, Limosilactobacillus fermentum, Latilactobacillus fuchuensis, Schleiferilactobacillus harbinensis, Lactobacillus helveticus, Lentilactobacillus hilgardii, Lactobacillus intestinalis, Lactobacillus jensenii, Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Fructilactobacillus lindneri, Liquorilactobacillus mali, Lactocaseibacillus manihotivorans, Limosilactobacillus mucosae, Liquorilactobacillus oeni, Paucilactobacillus oligofermentans, Limosilactobacillus panis, Lactocaseibacillus pantheris, Levilactobacillus parabrevis, Secundilactobacillus paracollinoides, Lentilactobacillus parakefiri, Lactoplantibacillus paraplantarum, Lactoplantibacillus pentosus, Limosilactobacillus pontis, Limosilactobacillus reuteri, Furfurilactobacillus rossiae, Ligilactobacillus salivarius, Furfurilactobacillus siliginis, Liquorilactobacillus sucicola, Paucilactobacillus vaccinostercus, Limosilactobacillus vaginalis, Liquorilactobacillus vini, Lactococcus garvieae, or Lactococcus lactis, or a combination thereof.

[0108] In some cases, the bacterial population may comprise at least one strain of Akkermansia sp., at least one strain of Blautia sp., at least one strain of Clostridium sp., at least one strain of Coprococcus sp., at least one strain of Dorea sp., at least one strain ofAttorney Docket No.: 53206-717601Faecalibacterium sp., at least one strain of Roseburia sp., at least one strain of Ruminococcus sp., at least one strain of Anaerbutyricum sp., at least one strain of Anaerostipes sp., at least one strain of Anaerotignum sp., at least one strain of Bacillus sp., at least one strain of Bacteroides sp., at least one strain of Clostridium sp., at least one strain of Collinsella sp., at least one strain of Enterococcus sp., at least one strain of Erysipelatoclostridium sp., at least one strain of Escherichia sp., at least one strain of Eubacterium sp., at least one strain of Faecalicatena sp., at least one strain of Holdemanella sp., at least one strain of Lachnospira sp., at least one strain of Longibaculum sp., at least one strain of Paraprevotella sp., at least one strain of Parabacteroides sp., at least one strain of Pediococcus sp., or at least one strain of Veillonella sp. In some instances, a bacterial population may comprise at least one strain of Akkermansia sp. In some instances, a bacterial population may comprise at least one strain of Blautia sp. In some instances, a bacterial population may comprise at least one strain of Clostridium sp. In some instances, a bacterial population may comprise at least one strain of Coprococcus sp. In some instances, a bacterial population may comprise at least one strain of Dorea sp. In some instances, a bacterial population may comprise at least one strain of Faecalibacterium sp. In some instances, a bacterial population may comprise at least one strain of Roseburia sp. In some instances, a bacterial population may comprise at least one strain of Ruminococcus sp. In some instances, a bacterial population may comprise at least one strain of Anaerbutyricum sp. In some instances, a bacterial population may comprise at least one strain of Anaerostipes sp. In some instances, a bacterial population may comprise at least one strain of Anaerotignum sp. In some instances, a bacterial population may comprise at least one strain of Bacillus sp. In some instances, a bacterial population may comprise at least one strain of Bacteroides sp. In some instances, a bacterial population may comprise at least one strain of Clostridium sp. In some instances, a bacterial population may comprise at least one strain of Collinsella sp. In some instances, a bacterial population may comprise at least one strain of Enterococcus sp. In some instances, a bacterial population may comprise at least one strain of Erysipelatoclostridium sp. In some instances, a bacterial population may comprise at least one strain of Escherichia sp. In some instances, a bacterial population may comprise at least one strain of Eubacterium sp. In some instances, a bacterial population may comprise at least one strain of Faecalicatena sp. In some instances, a bacterial population may comprise at least one strain of Holdemanella sp. In some instances, a bacterial population may comprise at least one strain of Lachnospira sp. In some instances, a bacterial population may comprise at least one strain of Longibaculum sp. In some instances, a bacterial population may comprise at least one strain of Paraprevotella sp. In some instances,Attorney Docket No.: 53206-717601a bacterial population may comprise at least one strain of Parabacteroides sp. In some instances, a bacterial population may comprise at least one strain of Pediococcus sp. In some instances, a bacterial population may comprise at least one strain of Veillonella sp.

[0109] In some instances, a bacterial population may comprise at least two strains of Vertebrate-Associated Lactobacillaceae, and / or at least two strains of Bifidobacterium sp., and / or at least two strains of Akkermansia sp., and / or at least two strains of Blautia sp. and / or at least two strains of Clostridium sp., and / or at least two strains of Coprococcus sp., and / or at least two strains of Dorea sp. and / or at least two strains of Faecalibacterium sp., and / or at least two strains of Roseburia sp., and / or at least two strains of Ruminococcus sp., and / or at least two strains of Anaerbutyricum sp., and / or at least two strains of Anaerostipes sp., and / or at least two strains of Anaerotignum sp., and / or at least two strains of Bacillus sp., and / or at least two strains of Bacteroides sp., and / or at least two strains of Clostridium sp., and / or at least two strains of Collinsella sp., and / or at least two strains of Enterococcus sp., and / or at least two strains of Erysipelatoclostridium sp., and / or at least two strains of Escherichia sp., and / or at least two strains of Eubacterium sp., and / or at least two strains of Faecalicatena sp., and / or at least two strains of Holdemanella sp., and / or at least two strains of Lachnospira sp., and / or at least two strains of Longibaculum sp., and / or at least two strains of Paraprevotella sp., and / or at least two strains of Parabacteroides sp., and / or at least two strains of Pediococcus sp., and / or at least two strains of Veillonella sp. In some cases, a bacterial population may comprise at least three strains of Vertebrate-Associated Lactobacillaceae, and / or at least three strains of Bifidobacterium sp., and / or at least three strains of Akkermansia sp., and / or at least three strains of Blautia sp. and / or at least three strains of Clostridium sp., and / or at least three strains of Coprococcus sp., and / or at least three strains of Dorea sp. and / or at least three strains of Faecalibacterium sp., and / or at least three strains of Roseburia sp., and / or at least three strains of Ruminococcus sp., and / or at least three strains of Anaerbutyricum sp., and / or at least three strains of Anaerostipes sp., and / or at least three strains of Anaerotignum sp., and / or at least three strains of Bacillus sp., and / or at least three strains of Bacteroides sp., and / or at least three strains of Clostridium sp., and / or at least three strains of Collinsella sp., and / or at least three strains of Enterococcus sp., and / or at least three strains of Erysipelatoclostridium sp., and / or at least three strains of Escherichia sp., and / or at least three strains of Eubacterium sp., and / or at least three strains of Faecalicatena sp., and / or at least three strains of Holdemanella sp., and / or at least three strains of Lachnospira sp., and / or at least three strains of Longibaculum sp., and / or at least three strains of Paraprevotella sp., and / or at least three strains of Parabacteroides sp., and / or at least threeAttorney Docket No.: 53206-717601strains of Pediococcus sp., and / or at least three strains of Veillonella sp. In some cases, a bacterial population may comprise at least more than three strains of Vertebrate-Associated Lactobacillaceae, or at least more than three strains of Bifidobacterium sp., and / or at least more than three strains of Akkermansia sp., and / or at least more than three strains of Blautia sp. and / or at least more than three strains of Clostridium sp., and / or at least more than three strains of Coprococcus sp., and / or at least more than three strains of Dorea sp. and / or at least more than three strains of Faecalibacterium sp., and / or at least more than three strains of Roseburia sp., and / or at least more than three strains of Ruminococcus sp., and / or at least more than three strains of Anaerbutyricum sp., and / or at least more than three strains of Anaerostipes sp., and / or at least more than three strains of Anaerotignum sp., and / or at least more than three strains of Bacillus sp., and / or at least more than three strains of Bacteroides sp., and / or at least more than three strains of Clostridium sp., and / or at least more than three strains of Collinsella sp., and / or at least more than three strains of Enterococcus sp., and / or at least more than three strains of Erysipelatoclostridium sp., and / or at least more than three strains of Escherichia sp., and / or at least more than three strains of Eubacterium sp., and / or at least more than three strains of Faecalicatena sp., and / or at least more than three strains of Holdemanella sp., and / or at least more than three strains of Lachnospira sp., and / or at least more than three strains of Longibaculum sp., and / or at least more than three strains of Paraprevotella sp., and / or at least more than three strains of Parabacteroides sp., and / or at least more than three strains of Pediococcus sp., and / or at least more than three strains of Veillonella sp.

[0110] In some instances, a pharmaceutical composition that can comprise a bacterial population. Such bacterial population can comprise one or more different bacterial species and / or strains. Such bacterial species and / or strains can belong to one or more different bacterial phyla.

[0111] In some instances, a bacterial population may comprise one or more Akkermansia sp. The one or more Akkermansia sp. may include Akkermansia glycaniphila, or Akkermansia muciniphila, or a combination thereof.

[0112] In some instances, a bacterial population may comprise one or more Blautia sp. The one or more Blautia sp. may include Blautia acetigignens. Blautia ammoniilytica. Blautia argi, Blautia caecimuris. Blautia coccoides. Blautia faecicola. Blautia faecis, Blautia glucerasea, Blautia hansenii. Blautia hominis, Blautia hydrogenotrophica, Blautia intestinalis, Blautia liqüoris. Blautia wexlerae. Blautia obeum. Blautia producta, Blautia schinkii. Blautia stercoris. or Blautia wexlerae or a combination thereof.Attorney Docket No.: 53206-717601

[0113] In some instances, a bacterial population may comprise one or more Coprococcus sp. The one or more Coprococcus sp. may include Coprococcus ammoniilytica. Coprococcus catus, Coprococcus comes, or Coprococcus eutactus or a combination thereof.

[0114] In some instances, a bacterial population may comprise one or more Dorea sp. The one or more Dorea sp. may include Dorea acetigenes, Dorea ammoniilytica, Dorea formicigenerans, or Dorea longicatena, or a combination thereof

[0115] In some instances, a bacterial population may comprise one or more Faecalibacterium sp. The one or more Faecalibacterium sp. may include Faecalibacterium butyr icigenerans, Faecalibacterium duncaniae, Faecalibacterium gallinarum, Faecalibacterium hattorii, Faecalibacterium longum, or Faecalibacterium prausnitzii, or a combination thereof.

[0116] In some instances, a bacterial population may comprise one or more Roseburia sp. The one or more Roseburia sp. may include Roseburia cecicola, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, or Roseburia inulinivorans or a combination thereof.

[0117] In some instances, a bacterial population may comprise one or more Ruminococcus sp. The one or more Ruminococcus sp. may include Ruminococcus albus, Ruminococcus bovis, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus champanellensis, Ruminococcus faecis, Ruminococcus flavefaciens, Ruminococcus gauvreauii, Ruminococcus gnavus, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus lactaris, Ruminococcus luti, Ruminococcus obeum, Ruminococcus palustris, Ruminococcus pasteurii, Ruminococcus productus, Ruminococcus schinkii, or Ruminococcus torques, or a combination thereof.

[0118] In some instances, a bacterial population may comprise one or more Anaerbutyricum sp. The one or more Anaerbutyricum sp. may include Anaerbutyricum hallii, Anaerbutyricum soehngenii, or a combination thereof.

[0119] In some instances, a bacterial population may comprise one or more Anaerostipes sp. The one or more Anaerostipes sp. may include Anaerostipes amylophilus, Anaerostipes butyraticus, Anaerostipes caccae, Anaerostipes faecalis, Anaerostipes hadrus, Anaerostipes hominis, or Anaerostipes rhamnosivorans, or a combination thereof.

[0120] In some instances, a bacterial population may comprise one or more Anaerotignum sp. The one or more Anaerotignum sp. may include Anaerotignum aminivorans, Anaerotignum faecicola, Anaerotignum lactatifermentans, Anaerotignum neopropionicum, or Anaerotignum propionicum, or a combination thereof.

[0121] In some instances, a bacterial population may comprise one or more Bacteroides sp. The one or more Bacteroides sp. may include Bacteroides acidifaciens, Bacteroides caccae,Attorney Docket No.: 53206-717601Bacteroides caecicola, Bacteroides caecigallinarum, Bacteroides caecimuris, Bacteroides cellulolyticus, Bacteroides cellulosilyticus, Bacteroides clarus. Bacteroides corporis, Bacteroides eggerthii, Bacteroides facilis, Bacteroides faecalis, Bacteroides faecichinchillae, Bacteroides faecis, Bacteroides finegoldii, Bacteroides fluxus, Bacteroides fragilis, Bacteroides galacturonicus, Bacteroides gallinaceum, Bacteroides gallinarum, Bacteroides graminisolvens, Bacteroides helcogenes, Bacteroides hominis, Bacteroides intestinalis, Bacteroides koreensis, Bacteroides kribbi, Bacteroides luhongzhouii, Bacteroides luti, Bacteroides nordii, Bacteroides oleiciplenus, Bacteroides ovatus, Bacteroides parvus, Bacteroides pectinophilus, Bacteroides polypragmatus, Bacteroides propionicifaciens, Bacteroides propionicigenes, Bacteroides pyogenes, Bacteroides reticulotermitis, Bacteroides rodentium, Bacteroides salyersiae, Bacteroides stercorovirosa, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides xylanisolvens, or Bacteroides zhangwengongii, or a combination thereof.

[0122] In some instances, a bacterial population may comprise one or more Clostridium sp. The one or more Clostridium sp. may include Clostridium aerotolerans, Clostridium aminophilum, Clostridium coccoides, Clostridium nexile, Clostridium polysaccharolyticum, Clostridium symbiosum, Clostridium sphenoides, Clostridium xylanolyticum, Clostridium leptum, Clostridium cellulosi, Clostridium sordellii, or Clostridium scindens, or a combination thereof.

[0123] In some instances, a bacterial population may comprise one or more Collinsella sp. The one or more Collinsella sp. may include Collinsella aerofaciens, Collinsella intestinalis, Collinsella massiliensis, Collinsella stercoris, Collinsella tanakaei, or Collinsella vaginalis, or a combination thereof.

[0124] In some instances, a bacterial population may comprise one or more Enterococcus sp. The one or more Enterococcus sp. may include Enterococcus alcedinis, Enterococcus alishanensis, Enterococcus aquimarinus, Enterococcus asini, Enterococcus avium, Enterococcus bulliens, Enterococcus caccae, Enterococcus camelliae, Enterococcus canintestini, Enterococcus canis, Enterococcus casseliflavus, Enterococcus cecorum.Enterococcus columbae, Enterococcus crotali, Enterococcus devriesei, Enterococcus diestrammenae, Enterococcus dispar, Enterococcus dongliensis, Enterococcus durans, Enterococcus eurekensis, Enterococcus faecalis, Enterococcus faecium, Enterococcus flavum. Enterococcus gallinarum, Enterococcus gilvus, Enterococcus haemoperoxidus, Enterococcus hermanniensis, Enterococcus hirae, Enterococcus hulanensis, Enterococcus innesii, Enterococcus italicus, Enterococcus lactis, Enterococcus larvae, Enterococcus lemanii,Attorney Docket No.: 53206-717601Enterococcus malodoratus, Enterococcus moraviensis, Enterococcus mundtii, Enterococcus nangangensis, Enterococcus olivae, Enterococcus pallens. Enterococcus phoeniculicola, Enterococcus pingfangensis, Enterococcus plantarum, Enterococcus pseudoavium, Enterococcus quebecensis, Enterococcus raffmosus, Enterococcus ratti, Enterococcus rivorum, Enterococcus rotai, Enterococcus saccharolyticus, Enterococcus saigonensis, Enterococcus silesiacus, Enterococcus songbeiensis, Enterococcus sulfureus, Enterococcus termitis, Enterococcus thailandicus, Enterococcus ureasiticus, Enterococcus ureilyticus, Enterococcus viikkiensis, Enterococcus villorum, Enterococcus wangshanyuanii. or Enterococcus xiangfangensis, or a combination thereof.

[0125] In some instances, a bacterial population may comprise one or more Escherichia sp. The one or more Escherichia sp. may include Escherichia albertii, Escherichia coli, Escherichia fergusonii, Escherichia hermanni, Escherichia marmotae, or Escherichia ruysiae, or a combination thereof.

[0126] In some instances, a bacterial population may comprise one or more Eubacterium sp. The one or more Eubacterium sp. may Eubacterium aggregans, Eubacterium barkeri, Eubacterium brachy, Eubacterium callendera, Eubacterium cellulosolvens, Eubacterium coprostanoligenes, Eubacterium hominis, Eubacterium infirmum, Eubacterium limosum, Eubacterium maltosivorans, Eubacterium minutum, Eubacterium multiforme, Eubacterium nodatum, Eubacterium oxidoreducens, Eubacterium plexicaudatum, Eubacterium pyruvativoxans, Eubacterium ramulus, Eubacterium ruminantium, Eubacterium saphenum, Eubacterium siraeum, Eubacterium tenue, Eubacterium tortuosum, Eubacterium uniforme, Eubacterium ventriosum, Eubacterium xylanophilum, or Eubacterium yurii, or a combination thereof.

[0127] In some instances, a bacterial population may comprise one or more Faecalicatena sp. The one or more Faecalicatena sp. may include Faecalicatena absiana, Faecalicatena acetigenes, Faecalicatena contorta, Faecalicatena fissicatena, or Faecalicatena orotica, or a combination thereof.

[0128] In some instances, a bacterial population may comprise one or more Holdemanella sp. The one or more Holdemanella sp. may include Holdemanella biformis or Holdemanella porci, or a combination thereof.

[0129] In some instances, a bacterial population may comprise one or more Lachnospira sp. The one or more Lachnospira sp. may include Lachnospira eligens, Lachnospira multipara, or Lachnospira pectinoschiza, or a combination thereof.Attorney Docket No.: 53206-717601

[0130] In some instances, a bacterial population may comprise one or more Longibaculum sp. The one or more Longibaculum sp. may include Longibaculum muris.

[0131] In some instances, a bacterial population may comprise one or more Paraprevotella sp. The one or more Paraprevotella sp. may include Paraprevotella clara. o Paraprevotella xylaniphila, or a combination thereof.

[0132] In some instances, a bacterial population may comprise one or more Parabacteroides a sp. The one or more Parabacteroides sp. may include Parabacteroides acidifaciens.Parabacteroides chartae. Parabacteroides chinchilla, Parabacteroides chough, Parabacteroides distasonis, Parabacteroides faecis, Parabacteroides goldsteinii, Parabacteroides gordonii, Parabacteroides hominis, Parabacteroides johnsonii, or Parabacteroides merdae, or a combination thereof.

[0133] In some instances, a bacterial population may comprise one or more Pediococcus sp. The one or more Pediococcus sp. may include Pediococcus acidilactici, Pediococcus argentinicus, Pediococcus cellicola, Pediococcus claussenii, Pediococcus damnosus, Pediococcus ethanolidurans, Pediococcus inopinatus, Pediococcus parvulus, Pediococcus pentosaceus, Pediococcus siamensis, or Pediococcus stilesii, or a combination thereof.

[0134] In some instances, a bacterial population may comprise one or more Veillonella sp. The one or more Veillonella sp. may include Veillonella atypica, Veillonella caviae, Veillonella cricetid, Veillonella denticariosi, Veillonella dispar, Veillonella hominis, Veillonella infantium, Veillonella magna, Veillonella montpellierensis, Veillonella nakazawae, Veillonella parvula, Veillonella ratti, Veillonella rodentium, Veillonella rogosae, Veillonella seminalis, or Veillonella tobetsuensis, or a combination thereof.

[0135] In some instances, a bacteria or bacterial strain described herein may be derived from a subject of an organ or tissue thereof. As used herein, when referring to a microbial organism being “derived from,” a subject or an organ / tissue thereof, is equivalent to the microbial organism being obtained originates from the microbiota of the subject of the organ / tissue thereof.

[0136] In some instances, a bacteria or bacterial strain described herein may be derived from a vagina. In some instances, a bacteria or bacterial strain described herein may be derived from a mammalian vagina. In some instances, a bacteria or bacterial strain described herein may be derived from a human vagina. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have a disease or disease condition. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have a vaginal disease or disease condition, complication of theAttorney Docket No.: 53206-717601vaginal disease or disease condition or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have BV or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from a gastrointestinal tract. In some instances, a bacteria or bacterial strain described herein may be derived from a mammalian gastrointestinal tract. In some instances, a bacteria or bacterial strain described herein may be derived from a human gastrointestinal tract. In some instances, a bacteria or bacterial strain described herein may be derived from a human infant gastrointestinal tract. In some instances, a bacteria or bacterial strain described herein may be derived from a human infant gastrointestinal tract, wherein the infant is a preterm infant. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have a gastrointestinal disease or disease condition or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have an infant gastrointestinal disease or disease condition or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from an infant that does not have NEC or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from a human that does not have a disease or disease condition or a risk thereof. In some instances, a bacteria or bacterial strain described herein may be derived from a human that is healthy. In some cases, when deriving the bacteria or bacterial strain as described herein, the bacteria or bacterial strain can be derived from the microbiota of the subjects, organs, or tissues as described herein. In some instances, a bacterial population may comprise purified bacteria or bacterial strains. In some cases, a bacteria or bacterial strain described herein may not comprise a recombinant genetic modification. In some cases, a bacteria or bacterial strain described herein may not be genetically engineered.Sequences

[0137] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to any one of SEQ ID NOs: 1-30. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, atAttorney Docket No.: 53206-717601most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to any one of SEQ ID NOs: 1-30. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to any one of SEQ ID NOs: 1-30. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to any one of SEQ ID NOs: 1-30.The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to any one of SEQ ID NOs: 1-30.

[0138] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 1. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 1. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 1. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 1. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 1.

[0139] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at leastAttorney Docket No.: 53206-717601about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 2. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 2. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 2. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 2. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 2.

[0140] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 3. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 3. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 3. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at mostAttorney Docket No.: 53206-717601about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 3. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 3.

[0141] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 4. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 4. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 4. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 4. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 4.

[0142] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 5. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at mostAttorney Docket No.: 53206-717601about 99.9999%, or at most about 99.99999% to SEQ ID NO: 5. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 5. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 5. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 5.

[0143] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 6. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 6. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 6. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 6. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 6.

[0144] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least aboutAttorney Docket No.: 53206-71760199.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 7. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 7. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 7. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 7. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 7.

[0145] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 8. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 8. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 8. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotideAttorney Docket No.: 53206-717601differences relative to SEQ ID NO: 8. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 8.

[0146] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 9. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 9. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 9. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 9. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 9.

[0147] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 10. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 10. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, atAttorney Docket No.: 53206-717601least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 10. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 10. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 10.

[0148] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 11. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 11. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 11. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 11. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 11.

[0149] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 12. The bacteria or bacterial strain described herein canAttorney Docket No.: 53206-717601comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 12. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 12. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 12. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 12.

[0150] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 13. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 13. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 13. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 13. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 13.Attorney Docket No.: 53206-717601

[0151] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 14. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 14. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 14. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 14. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 14.

[0152] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 15. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 15. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or moreAttorney Docket No.: 53206-717601nucleotide differences relative to SEQ ID NO: 15. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 15. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 15.

[0153] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 16. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 16. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 16. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 16. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 16.

[0154] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 17. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at mostAttorney Docket No.: 53206-717601about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 17. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 17. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 17. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 17.

[0155] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 18. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 18. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 18. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 18. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 18.

[0156] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at leastAttorney Docket No.: 53206-717601about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 20. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 20. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 20. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 20. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 20.

[0157] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 21. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 21. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 21. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at mostAttorney Docket No.: 53206-717601about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 21. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 21.

[0158] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 22. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 22. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 22. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 22. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 22.

[0159] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 23. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at mostAttorney Docket No.: 53206-717601about 99.9999%, or at most about 99.99999% to SEQ ID NO: 23. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 23. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 23. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 23.

[0160] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 24. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 24. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 24. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 24. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 24.

[0161] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least aboutAttorney Docket No.: 53206-71760199.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 25. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 25. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 25. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 25. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 25.

[0162] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 26. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 26. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 26. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotideAttorney Docket No.: 53206-717601differences relative to SEQ ID NO: 26. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 26.

[0163] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 27. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 27. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 27. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 27. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 27.

[0164] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 28. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 28. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, atAttorney Docket No.: 53206-717601least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 28. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 28. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 28.

[0165] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 29. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 29. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 29. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 29. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 29.

[0166] The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, at least about 99.99999% or more to SEQ ID NO: 30. The bacteria or bacterial strain described herein canAttorney Docket No.: 53206-717601comprise a sequence having a sequence identity that is at most about 80%, at most about 85%, at most about 90%, at most about 91%, at most about 92%, at most about 93%, at most about 94%, at most about 95%, at most about 96%, at most about 97%, at most about 98%, at most about 99%, at most about 99.9%, at most about 99.99%, at most about 99.999%, at most about 99.9999%, or at most about 99.99999% to SEQ ID NO: 30. The bacteria or bacterial strain described herein can comprise a sequence that has at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 100, at least about 1000, at least about 10000, at least about 100000, at least about 1000000 or more nucleotide differences relative to SEQ ID NO: 30. The bacteria or bacterial strain described herein can comprise a sequence that has at most about 1 nucleotide, at most about 2, at most about 3, at most about 4, at most about 5, at most about 10, at most about 100, at most about 1000, at most about 10000, at most about 100000, or at most about 1000000 nucleotide differences relative to SEQ ID NO: 30. The bacteria or bacterial strain described herein can comprise a sequence having a sequence identity that is 100 % to SEQ ID NO: 30.

[0167] Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 1-4 and 12-15. Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 1-2. Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 1-2. Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 3-4. Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 3-4 Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 12-15. Lactobacillus crispatus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 12-15. Lactobacillus gasseri may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 5-6. Lactobacillus gasseri may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 5-6. Lactobacillus jensenii may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 7.Bifidobacterium bifidum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 8-9. Bifidobacterium bifidum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ IDAttorney Docket No.: 53206-717601NO: 8. Bifidobacterium bifidum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 9. Lactobacillus plantarum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 10-11. Lactobacillus plantarum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 10- 11. Bifidobacterium adolescentis may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 16. Bifidobacterium breve may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 17 and 30. Bifidobacterium breve may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 17. Bifidobacterium breve may have a genome that has a sequence that has a sequence identity that is about 95%- 100% to SEQ ID NO: 30. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 18-26. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 18-19. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 18-19. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 20.Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 21-24. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 21-24. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 25-26. Bifidobacterium longum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to a combination of SEQ ID NOs: 25-26. Bifidobacterium pseudocatenulatum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to any one of SEQ ID NOs: 27-28. Bifidobacterium pseudocatenulatum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 27. Bifidobacterium pseudocatenulatum may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 28.Lactobacillus rhamnosus may have a genome that has a sequence that has a sequence identity that is about 95%-100% to SEQ ID NO: 29.

[0168] Bifidobacterium bifidum ST31 (or “ST31”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 8. Bifidobacterium bifidum ST80 (orAttorney Docket No.: 53206-717601“ST80”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 9 Lactobacillus crispatus ST 100 (or “ST 100”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 12-15. Lactobacillus crispatus ST20 (or “ST20”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 1-2. Lactobacillus crispatus STI 12 (or “STI 12”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NO: 3-4. Lactobacillus gasseri ST105 (or “ST105”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NO: 5-6. Lactobacillus jensenii ST21 (or “ST21”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 7. Lactobacillus plantarum ST65 (or “ST65”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 10-11. Bifidobacterium adolescentis ST101 (or “ST101”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 16. Bifidobacterium breve ST56 (or “ST56”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 17. Bifidobacterium longum ST 19 (or “ST19”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 18-19. Bifidobacterium longum ST81 (or “ST81”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 21-24. Bifidobacterium pseudocatenulatum ST37 (or “ST37”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 27. Bifidobacterium pseudocatenulatum ST66 (or “ST66”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 28. Lactobacillus rhamnosus STI 16 (or “STI 16”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 29. Bifidobacterium longum ST23 (or “ST23”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 20. Bifidobacterium longum STI 19 (or “STI 19”) may have a genome sequence that has a sequence identity that is about 100% to a combination of SEQ ID NOs: 25-26. Bifidobacterium breve ST71 (or “ST71”) may have a genome sequence that has a sequence identity that is about 100% to SEQ ID NO: 30.Sufficient abilities

[0169] In some instances, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) can have a sufficient ability in a disease associated functions. A disease-associated function may comprise a function of a bacteria or bacterial strain or bacterial population that is related to a disease or diseaseAttorney Docket No.: 53206-717601condition as described herein. The disease associated function may be related to a complication associated with the disease or disease condition. The disease-associated function may comprise an alteration of the cellular process of the subject or the pathogen associated with the disease or disease condition. The disease-associated function may comprise an alteration of the cellular process of the bacteria or bacterial strain or bacterial population as described herein. A sufficient ability, as used herein, when referring to a bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium), refers to an ability of the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) to alter the disease-associated function. For example, a bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) having a sufficient ability to alter a disease-associated function may be a bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) capable of altering disease-associated function. The sufficient ability of a bacteria or bacterial strain (or a bacterial population) can be mediated by a bacterial product generated by the bacteria or bacterial strain. The bacterial product may be present within a medium used to culture the bacteria or bacterial strain. The sufficient ability of a bacteria or bacterial strain (or a bacterial population) can be mediated by the metabolic ability of a bacteria or bacterial strain as described herein. The metabolic ability can convert a substance of a nutrient source to a different substance.

[0170] In some instances, the bacteria or bacterial strain can have a sufficient ability in an infant gastrointestinal disease-associated function. The infant gastrointestinal disease-associated function may comprise any NEC-specific MO As and functionalities described in this disclosure. In some cases, an infant gastrointestinal disease-associated function may comprise an adherence to an intestinal epithelial cell (IEC), an integrity of a barrier comprising IEC, epithelial integrity of the gastrointestinal tract, an inhibition of an infant gastrointestinal pathogen, a utilization of carbohydrate present within an infant gastrointestinal tract, an inhibition of an immune response signaling pathway, or a combination thereof. As used herein, an infant gastrointestinal pathogen comprises a microorganism that: (1) causes an infant gastrointestinal disease; (2) associated with an infant gastrointestinal; and / or (3) contributes to the symptoms of the infant gastrointestinal disease. In some instances, inhibiting or eliminating an infant gastrointestinal pathogen can treat or prevent the infant gastrointestinal disease or alleviate the symptoms of the infant gastrointestinal disease. In some cases, an infant gastrointestinal disease-associated functionAttorney Docket No.: 53206-717601may comprise an adherence to an IEC. In some cases, an infant gastrointestinal disease-associated function may comprise an integrity of a barrier comprising IEC. In some cases, an infant gastrointestinal disease-associated function may comprise an inhibition of an infant gastrointestinal pathogen. In some cases, an infant gastrointestinal disease-associated function may comprise a utilization of an infant-relevant carbohydrate. In some cases, an infant gastrointestinal disease-associated function may comprise an inhibition of an immune response signaling pathway. In some instances, the bacteria or bacterial strain can have a sufficient ability in a NEC-associated function. In some cases, an infant gastrointestinal disease-associated function may comprise an adherence to an intestinal epithelial cell (IEC), an integrity of a barrier comprising IEC, an epithelial integrity of the gastrointestinal tract, an inhibition of an infant gastrointestinal pathogen, a utilization of an infant-relevant carbohydrate, and an inhibition of an immune response signaling pathway.NEC-associated functions

[0171] A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of exhibiting an adherence to an IEC. In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an adherence to the IEC by at least about lx 10Al CFU per 9.5 cmA2 of IEC, at least about 2x 10Al CFU per 9.5 cmA2 of IEC, at least about 5x 10Al CFU per 9.5 cmA2 of IEC, at least about lx 10A2 CFU per 9.5 cmA2 of IEC, at least about 2x 10A2 CFU per 9.5 cmA2 of IEC, at least about 5x 10A2 CFU per 9.5 cmA2 of IEC, at least about lx 10A3 CFU per 9.5 cmA2 of IEC, at least about 2x 10A3 CFU per 9.5 cmA2 of IEC, at least about 5x 10A3 CFU per 9.5 cmA2 of IEC, at least about lx 10A4 CFU per 9.5 cmA2 of IEC, at least about 2x 10A4 CFU per 9.5 cmA2 of IEC, at least about 5x 10A4 CFU per 9.5 cmA2 of IEC, at least about lx 10A5 CFU per 9.5 cmA2 of IEC, at least about 2x 10A5 CFU per 9.5 cmA2 of IEC, at least about 5x 10A5 CFU per 9.5 cmA2 of IEC, at least about lx 10A6 CFU per 9.5 cmA2 of IEC, at least about 2x 10A6 CFU per 9.5 cmA2 of IEC, at least about 5x 10A6 CFU per 9.5 cmA2 of IEC, at least about lx 10A7 CFU per 9.5 cmA2 of IEC, at least about 2x 10A7 CFU per 9.5 cmA2 of IEC, at least about 5x 10A7 CFU per 9.5 cmA2 of IEC, at least about lx 10A8 CFU per 9.5 cmA2 of IEC, at least about 2x 10A8 CFU per 9.5 cmA2 of IEC, at least about 5x 10A8 CFU per 9.5 cmA2 of IEC, at least about lx 10A9 CFU per 9.5 cmA2 of IEC, at least about 2x 10A9 CFU per 9.5 cmA2 of IEC, at least about 5x 10A9 CFU per 9.5 cmA2 of IEC, at least about lx 10Al 0 CFU per 9.5 cmA2 of IEC, at least about 2x 10Al 0 CFU per 9.5 cmA2 of IEC, at least about 5x 10Al 0 CFU per 9.5 cmA2 of IEC, at least about lx 10Al 1 CFU per 9.5 cmA2 of IEC,Attorney Docket No.: 53206-717601at least about 2x 10Al 1 CFU per 9.5 cmA2 of IEC, at least about 5x 10Al 1 CFU per 9.5 cmA2 of IEC, at least about lx 10A12 CFU per 9.5 cmA2 of IEC, at least about 2x 10A12 CFU per 9.5 cmA2 of IEC, at least about 5x 10A12 CFU per 9.5 cmA2 of IEC or more. The number of bacteria adhered to a surface area of the IEC may be measured as a score of adherence to the IEC. In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an adherence to the IEC by at most about lx 10Al CFU per 9.5 cmA2 of IEC, at most about 2x 10Al CFU per 9.5 cmA2 of IEC, at most about 5x 10Al CFU per 9.5 cmA2 of IEC, at most about lx 10A2 CFU per 9.5 cmA2 of IEC, at most about 2x 10A2 CFU per 9.5 cmA2 of IEC, at most about 5x 10A2 CFU per 9.5 cmA2 of IEC, at most about lx 10A3 CFU per 9.5 cmA2 of IEC, at most about 2x 10A3 CFU per 9.5 cmA2 of IEC, at most about 5x 10A3 CFU per 9.5 cmA2 of IEC, at most about lx 10A4 CFU per 9.5 cmA2 of IEC, at most about 2x 10A4 CFU per 9.5 cmA2 of IEC, at most about 5x 10A4 CFU per 9.5 cmA2 of IEC, at most about lx 10A5 CFU per 9.5 cmA2 of IEC, at most about 2x 10A5 CFU per 9.5 cmA2 of IEC, at most about 5x 10A5 CFU per 9.5 cmA2 of IEC, at most about lx 10A6 CFU per 9.5 cmA2 of IEC, at most about 2x 10A6 CFU per 9.5 cmA2 of IEC, at most about 5x 10A6 CFU per 9.5 cmA2 of IEC, at most about lx 10A7 CFU per 9.5 cmA2 of IEC, at most about 2x 10A7 CFU per 9.5 cmA2 of IEC, at most about 5x 10A7 CFU per 9.5 cmA2 of IEC, at most about lx 10A8 CFU per 9.5 cmA2 of IEC, at most about 2x 10A8 CFU per 9.5 cmA2 of IEC, at most about 5x 10A8 CFU per 9.5 cmA2 of IEC, at most about lx 10A9 CFU per 9.5 cmA2 of IEC, at most about 2x 10A9 CFU per 9.5 cmA2 of IEC, at most about 5x 10A9 CFU per 9.5 cmA2 of IEC, at most about lx 10Al 0 CFU per 9.5 cmA2 of IEC, at most about 2x 10Al 0 CFU per 9.5 cmA2 of IEC, at most about 5x 10Al 0 CFU per 9.5 cmA2 of IEC, at most about lx 10Al 1 CFU per 9.5 cmA2 of IEC, at most about 2x 10Al 1 CFU per 9.5 cmA2 of IEC, at most about 5x 10Al 1 CFU per 9.5 cmA2 of IEC, at most about lx 10Al 2 CFU per 9.5 cmA2 of IEC, at most about 2x 10A12 CFU per 9.5 cmA2 of IEC, or at most about 5x 10A12 CFU per 9.5 cmA2 of IEC. In some cases, the bacteria or bacterial strain described herein may have an adherence to an IEC that is at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein may have an adherence to an IEC that is at least about 2-fold, at least about 3-fold, at least about 4-fold, at least aboutAttorney Docket No.: 53206-7176015-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about lOOOOO-fold, or at least about 1000000-fold higher than that of a control strain. In some cases, the bacteria or bacterial strain described herein may have an adherence to an IEC that is at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein may have an adherence to an IEC that is at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control strain. The control strain may comprise EV27 (or referred to as evcOOl; described in BMC Pediatr. 2017; 17: 133.); which is herein incorporated by reference in its entirety); BG49 (or referred to as IBP-9414; described in U. S. clinical trial no. NCT03978000; which is herein incorporated by reference in its entirety. The adherence to the IEC can be measured by contacting a population of a bacteria or bacterial strains to an IEC and measuring the number of the bacteria cells attached or adhered to the IEC at a period of time after the contacting. When measuring the NEC-associated function as described herein, the measurements may span a period of time. The period of time may be at least about: 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29 hours, 30 hours, 31 hours, 32 hours, 33 hours, 34 hours, 35 hours, 36 hours, 37 hours, 38 hours, 39 hours, 40 hours, 41 hours, 42 hours, 43 hours, 44 hours, 45 hours, 46 hours, 47 hours, 48 hours, 49 hours, 50 hours, 51 hours, 52 hours, 53 hours, 54 hours, 55 hours, 56 hours, 57 hours, 58 hours, 59 hours, 60 hours, 61 hours, 62 hours, 63 hours, 64 hours, 65 hours, 66 hours, 67 hours, 68 hours, 69 hours, 70 hours, 71 hours, 72 hours, 73 hours, 74 hours, 75 hours, 76 hours, 77 hours, 78 hours, 79 hours, 80 hours, 81 hours, 82 hours, 83 hours, 84 hours, 85 hours, 86 hours, 87 hours, 88 hours, 89 hours, 90 hours, 91 hours, 92 hours, 93 hours, 94 hours, 95 hours, 96 hours, 97 hours, 98 hours, 99 hours, 100 hours, 120 hours. The period of time may be at least about: 1, day, 2 days, 3 days, 4 days, 5Attorney Docket No.: 53206-717601days, 6 days, 7 days. The period of time may be at least about: 2 weeks, 3 weeks, 4 weeks. The period of time may be at least about: 2 months, 3 months 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months or more. The period of time may be at most about: 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29 hours, 30 hours, 31 hours, 32 hours, 33 hours, 34 hours, 35 hours, 36 hours, 37 hours, 38 hours, 39 hours, 40 hours, 41 hours, 42 hours, 43 hours, 44 hours, 45 hours, 46 hours, 47 hours, 48 hours, 49 hours, 50 hours, 51 hours, 52 hours, 53 hours, 54 hours, 55 hours, 56 hours, 57 hours, 58 hours, 59 hours, 60 hours, 61 hours, 62 hours, 63 hours, 64 hours, 65 hours, 66 hours, 67 hours, 68 hours, 69 hours, 70 hours, 71 hours, 72 hours, 73 hours, 74 hours, 75 hours, 76 hours, 77 hours, 78 hours, 79 hours, 80 hours, 81 hours, 82 hours, 83 hours, 84 hours, 85 hours, 86 hours, 87 hours, 88 hours, 89 hours, 90 hours, 91 hours, 92 hours, 93 hours, 94 hours, 95 hours, 96 hours, 97 hours, 98 hours, 99 hours, 100 hours, 120 hours. The period of time may be at most about: 1, day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days. The period of time may be at most about: 2 weeks, 3 weeks, 4 weeks, or 2 months, 3 months 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, or 12 months. For example, the adherence to the IEC can be measured by the methods described herein, such as those described in EXAMPLE 3. A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may not be capable of exhibiting of adherence to an IEC.

[0172] A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of exhibiting of inhibiting a growth of an infant gastrointestinal pathogen. A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of exhibiting of inhibiting a growth of an infant gastrointestinal pathogen within a subject when the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) is administer into the subject. The gastrointestinal tract can comprise ileum or distal ileum. The infant gastrointestinal pathogen may comprise E. coli, K. pneumoniae, C. perfringens, S. aureus, S.flexneri, or a combination thereof. The infant gastrointestinal pathogen may comprise E. coli. The infant gastrointestinal pathogen may comprise K. pneumoniae. The infant gastrointestinal pathogen may comprise C. perfringens. The infantAttorney Docket No.: 53206-717601gastrointestinal pathogen may comprise S. aureus. The infant gastrointestinal pathogen may comprise S.flexneri. The infant gastrointestinal pathogen may comprise E. coli, K. pneumoniae, C. perfringens, S. aureus, and S.flexneri. A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may not be capable of exhibiting of inhibiting a growth of an infant gastrointestinal pathogen.

[0173] In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the growth of an infant gastrointestinal pathogen, in vitro or within the subject, by at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100%, relative to a growth of the pathogen when inhibited by a control. The amount of cell growth of an infant gastrointestinal pathogen that is inhibited, in vitro or within the subject, may be measured as a score of inhibition of a growth of an infant gastrointestinal pathogen. The control may comprise growing the infant gastrointestinal pathogen with a media control or without the bacteria or bacterial strain (such as those described in EXAMPLE 3). The control may comprise growing the infant gastrointestinal pathogen without the bacteria or bacterial strain. In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the growth of an infant gastrointestinal pathogen, in vitro or within the subject, by at most about 1%, at most about 2%, at most about 3%, at most about 4%, at most about 5%, at most about 10%, at most about 15%, at most about 20%, at most about 25%, at most about 30%, at most about 35%, at most about 40%, at most about 45%, at most about 50%, at most about 55%, at most about 60%, at most about 65%, at most about 70%, at most about 75%, at most about 80%, at most about 85%, at most about 90%, at most about 95%, or at most about 100%, relative to a growth of the pathogen when inhibited by the control.

[0174] In some cases, the ability of a bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) to inhibit the growth of an infant gastrointestinal pathogen may be increased when the bacteria or bacterial strain is cultured with the human milk or a derivative of the human milk, compared to when the bacteria or bacterial strain is not cultured with the human milk or a derivative of theAttorney Docket No.: 53206-717601human milk. For example, the inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at least about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. For example, the inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, when the bacteria or bacterial strain is cultured with the human milk or a derivative of the human milk, compared to when the bacteria or bacterial strain is not cultured with the human milk or a derivative of the human milk. The inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at most about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. The inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at most about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, when the bacteria or bacterial strain is cultured with the human milk or a derivative of the human milk, compared to when the bacteria or bacterial strain is not cultured with the human milk or a derivative of the human milk. The derivative of the human milk may comprise milk filtered whey liquid (see, for example, Example 12).

[0175] In some cases, the ability of bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) to inhibit the growth of an infant gastrointestinal pathogen may be increased when the bacteria or bacterial strain is cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract, compared to when the bacteria or bacterial strain is not cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract. For example, the inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at least about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %,Attorney Docket No.: 53206-71760120 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. For example, the inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, when the bacteria or bacterial strain is cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract, compared to when the bacteria or bacterial strain is not cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract. The inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at most about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. The inhibition of the growth of an infant gastrointestinal pathogen by the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be increased by at most about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, when the bacteria or bacterial strain is cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract, compared to when the bacteria or bacterial strain is not cultured with the human milk oligosaccharide (HMO) or the carbohydrate present within an infant gastrointestinal tract.

[0176] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the growth of an infant gastrointestinal pathogen, in vitro or within the subject, that is at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the growth of an infant gastrointestinal pathogen, in vitro or within the subject, that is at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at leastAttorney Docket No.: 53206-717601about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the growth of an infant gastrointestinal pathogen, in vitro or within the subject, that is at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the growth of an infant gastrointestinal pathogen, in vitro or within the subject, that is at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49. The inhibition of the growth of the pathogen can be measured by contacting the bacteria or bacterial strains to the infant gastrointestinal pathogen and measuring the growth of the infant gastrointestinal pathogen. Inhibition of a growth of the infant gastrointestinal pathogen may be measured as a ratio of (1) the number of the infant gastrointestinal pathogen present within a culture medium before the infant gastrointestinal pathogen is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) and (2) the number of the infant gastrointestinal pathogen present within a culture medium at the period of time subsequent to when the infant gastrointestinal pathogen is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). Inhibition of a growth of the infant gastrointestinal pathogen in the GI tract of a subject may be measured as a ratio of (1) the number of the infant gastrointestinal pathogen present within a stool sample of the subject and (2) the number of the infant gastrointestinal pathogen present within a stool sample of theAttorney Docket No.: 53206-717601subject at the period of time subsequent to when the subject is administered with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). For example, the inhibition of the growth of the infant gastrointestinal pathogen can be measured by the methods described herein, such as those described in EXAMPLE 3 or 12

[0177] A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of exhibiting of inhibiting a signaling pathway of a cell. In some cases, the signaling pathway may comprise an intestinal immune response signaling. Alteration of a signaling pathway may comprise altering an output of that signaling pathway. The output of that signaling pathway can comprise a transcriptional, translational, post-transcriptional, post-translational, metabolic, or cellular output; or a combination thereof. Inhibition (or activation) of a signaling pathway may comprise decreasing (or increasing) an output of that signaling pathway. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) capable of exhibiting of inhibiting (or activating) a signaling pathway can inhibit (or activate) a signal of a reporter of the signaling pathway. The reporter can comprise a transcriptional, translational, post-transcriptional, post-translational, metabolic, or cellular reporter; or a combination thereof. The reporter can be genetically engineered. The reporter can generate or facilitate a generation of the signal. The signal can be optical. The signal can be fluorescence. The signaling pathway may comprise an immune response signaling pathway. In some cases, the immune response signaling pathway may comprise an innate immune response signaling pathway. In some cases, the immune response signaling pathway may comprise an adaptive immune response signaling pathway. In some cases, the immune response signaling pathway may comprise an inflammatory immune response signaling pathway. The innate immune response signaling pathway may comprise Pattern Recognition Receptor (PRR) signaling pathway. The PRR signaling pathway may recognize molecules of by pathogens (Pathogen- Associated Molecular Patterns / PAMPs) or by damaged cells (the Damage-Associated Molecular Patterns / DAMPs). In some cases, the innate immune response signaling pathway may comprise toll-like receptor (TLR) signaling pathway. The TLR signaling pathway may comprise signaling pathways mediated by TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, TLR12, TLR13, or a combination thereof. In some cases, the immune response signaling pathway may comprise TLR1 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR2 signaling pathway. In some cases,Attorney Docket No.: 53206-717601the immune response signaling pathway may comprise TLR3 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR4 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR5 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR6 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR7 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR8 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR9 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR10 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR11 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR12 signaling pathway. In some cases, the immune response signaling pathway may comprise TLR13 signaling pathway. In some cases, the immune response signaling pathway may comprise nuclear factor kappa-light-chain-enhancer of activated B cells (NF-KB). In some cases, the immune response signaling pathway may comprise a ligand. The ligand can comprise a PAMP. The ligand can comprise a DAMP. The ligand can comprise a ligand of a gram-positive bacteria. The ligand can comprise a ligand of a gram-negative bacteria. The ligand of a gram-negative bacteria can comprise lipopolysaccharide (LPS). In some cases, the immune response signaling pathway may comprise nuclear factor kappa-light-chain-enhancer of activated B cells (NF-KB) signaling pathway. In some cases, the immune response signaling pathway may comprise interferon signaling pathway. In some cases, the bacteria or bacterial strain or bacterial population described herein can inhibit the immune response pathway of a cell of a subject being administered with the composition or formulation comprising the bacteria or bacterial strain or bacterial population. The cell may comprise an immune cell. The immune cell may comprise a macrophage, B-cell, or a T-cell. A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may not have a sufficient ability in inhibiting a signaling pathway of a cell.

[0178] In some cases, the intestinal immune signaling pathway may be assayed or characterized by a marker of the pathway. The marker of the intestinal immune signaling pathway may comprise interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), fecal calprotectin, cytokine, pattern recognition receptor, toll-like receptor, nucleotide binding oligomerization domain containing 2 (NOD2), Cluster of Differentiation 244 (CD244), nuclear factor of kappa light polypeptide gene enhancer in B-cells, toll-like receptors, Signal Transducer And Activator Of Transcription 3 (STAT), or a combinationAttorney Docket No.: 53206-717601thereof. The marker of the intestinal immune signaling pathway may comprise IL6. The marker of the intestinal immune signaling pathway may comprise IL1B. The marker of the intestinal immune signaling pathway may comprise Lcn2. The marker of the intestinal immune signaling pathway may comprise fecal calprotectin. The marker of the intestinal immune signaling pathway may comprise cytokine. The marker of the intestinal immune signaling pathway may comprise pattern recognition receptor. The marker of the intestinal immune signaling pathway may comprise toll-like receptor. The marker of the intestinal immune signaling pathway may comprise nucleotide binding oligomerization domain containing 2 (NOD2). The marker of the intestinal immune signaling pathway may comprise Cluster of Differentiation 244 (CD244). The marker of the intestinal immune signaling pathway may comprise nuclear factor of kappa light polypeptide gene enhancer in B-cells. The marker of the intestinal immune signaling pathway may comprise toll-like receptors. The marker of the intestinal immune signaling pathway may comprise Signal Transducer And Activator Of Transcription 3 (STAT3).

[0179] In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the immune response signaling pathway by at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100%, relative to immune response signaling pathway when inhibited by a control. The amount of an immune response signaling pathway that is inhibited, in vitro or within the subject, may be measured as a score of inhibition of an immune response signaling pathway. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control may comprise inhibiting the immune response signaling pathway with a media control or without the bacteria or bacterial strain (such as those described in EXAMPLE 3).In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the immune response signaling pathway by at most about 1%, at most about 2%, at most about 3%, at most about 4%, at most about 5%, at most about 10%, at most about 15%, at most about 20%, at most about 25%, at most about 30%, at most about 35%, at most about 40%, at most about 45%, atAttomey Docket No.: 53206-717601most about 50%, at most about 55%, at most about 60%, at most about 65%, at most about 70%, at most about 75%, at most about 80%, at most about 85%, at most about 90%, at most about 95%, or at most about 100%, relative to the immune response signaling pathway when inhibited by the control.

[0180] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the immune response signaling pathway that is at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the immune response signaling pathway that is at least about 0.001 %, at least about at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the immune response signaling pathway that is at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the immune response signaling pathway that is at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-Attorney Docket No.: 53206-717601fold, or at most about 1000000-fold higher than that of a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49. The inhibition (or activation) of a signaling pathway or the immune response signaling pathway can be measured by contacting the bacteria or bacterial strains (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) to a cell comprising a reporter or an immune response reporter of the immune response signaling pathway and measuring the reporter or immune response reporter. The cell may comprise an engineered cell. The engineered cell may comprise a mammalian cell. The mammalian cell may comprise an immune cell. The immune cell may comprise a macrophage, B-cell, or a T-cell. In some cases, when measuring the immune response signaling pathway using the immune response reporter, the immune response reporter may be activated by a ligand (by contacting the ligand to the cell comprising the reporter), and the cell is then contacted with the bacteria or bacterial strain. The activation (or inhibition or lack of activation) is then measured. The ligand can comprise a PAMP. The ligand can comprise a DAMP. The ligand can comprise a ligand of a grampositive bacteria. The ligand can comprise a ligand of a gram-negative bacteria. The ligand of a gram-negative bacteria can comprise lipopolysaccharide (LPS). The immune response reporter may comprise a reporter for the TLR. In some cases, the immune response reporter may comprise a TLR4 reporter. In some embodiments, the engineered cell can comprise a macrophage. In some embodiments, the reporter can comprise a NFkB reporter or an interferon-sensitive response element reporter (ISRE). In some embodiments, the TLR4 reporter can comprise a NFkB reporter or an interferon-sensitive response element reporter (ISRE). In some embodiments, the TLR4 reporter can comprise a NFkB reporter. In some embodiments, the TLR4 reporter can comprise a ISRE reporter In some embodiments, the NFkB reporter can comprise a secreted embryonic alkaline phosphatase (SEAP) reporter. In some embodiments, the ISRE reporter can comprise a Lucia luciferase. Inhibition of the immune response pathway may be measured as a difference in (1) the level of the reporter present within a cell comprising the reporter before the cell is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) and (2) the level of the reporter present within the cell at the period of time subsequent after the cell is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). For example, the inhibition of the growth of the immune response pathway can be measured by the methods described herein, such as those described in EXAMPLE 3.Attorney Docket No.: 53206-717601

[0181] In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the intestinal immune response signaling pathway by at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 100%, relative to intestinal immune response signaling pathway when inhibited by the control. In some cases, the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may inhibit the intestinal immune response signaling pathway by at most about 1%, at most about 2%, at most about 3%, at most about 4%, at most about 5%, at most about 10%, at most about 15%, at most about 20%, at most about 25%, at most about 30%, at most about 35%, at most about 40%, at most about 45%, at most about 50%, at most about 55%, at most about 60%, at most about 65%, at most about 70%, at most about 75%, at most about 80%, at most about 85%, at most about 90%, at most about 95%, or at most about 100%, relative to the intestinal immune response signaling pathway when inhibited by the control. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49. Inhibition of the intestinal immune response pathway may be measured as a difference in (1) the level of the marker of the immune response pathway present within a serum sample before the subject is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) and (2) the level of the marker of the immune response pathway present within a serum sample at a period of time after the subject is contacted with the bacteria or bacterial strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The inhibition of the intestinal immune signaling pathway can be measured by the methods described herein, such as those described in EXAMPLE 14.

[0182] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the intestinal immune response signaling pathway that is at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6Attorney Docket No.: 53206-717601%, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the intestinal immune response signaling pathway that is at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the intestinal immune response signaling pathway that is at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may exhibit an inhibition of the intestinal immune response signaling pathway that is at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49.

[0183] A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of increasing the integrity of a barrier comprising IEC. The method to measure the integrity of the barrier comprising IEC may comprise contacting a bacteria or bacterial strain with a barrier comprising IEC and measuring the difference of the cellular impedance of the barrier between (1) before the IEC is contacted with the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that culturedAttorney Docket No.: 53206-717601medium) and at the period of time after the IEC is contacted with the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The methods for measuring the barrier integrity are described herein, for example, in EXAMPLE 3. In some cases, a bacteria or bacterial strain described herein may increase the cellular impedance of a barrier comprising IEC by at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, a bacteria or bacterial strain described herein may increase the cellular impedance of a barrier comprising IEC by at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control. The control may comprise growing the infant gastrointestinal pathogen with a media control or without the bacteria or bacterial strain (such as those described in EXAMPLE 3). In some cases, a bacteria or bacterial strain described herein may increase the cellular impedance of a barrier comprising IEC by at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, a bacteria or bacterial strain described herein may increase the cellular impedance of a barrier comprising IEC by at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control. A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may not be capable of increasing the integrity of a barrier comprising IEC.

[0184] A bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may be capable of increasingAttorney Docket No.: 53206-717601the integrity of the epithelium of the gastrointestinal tract of a subject. The methods for measuring the epithelial integrity of a gastrointestinal tract are described herein, for example, in EXAMPLE 14. In some cases, a bacteria or bacterial strain described herein may increase the epithelial integrity of a gastrointestinal tract of a subject by at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, a bacteria or bacterial strain described herein may increase the epithelial integrity of a gastrointestinal tract of a subject by at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control. In some cases, a bacteria or bacterial strain described herein may increase the epithelial integrity of a gastrointestinal tract of a subject by at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, a bacteria or bacterial strain described herein may increase the epithelial integrity of a gastrointestinal tract of a subject by at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control. The gastrointestinal tract may comprise ileum or distal ileum. The method to measure epithelial integrity of a gastrointestinal tract of a subject is measured by using hematoxylin and eosin staining of the gastrointestinal tract. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium).

[0185] A bacteria or bacterial strain described herein may be capable of utilizing a carbohydrate present within an infant gastrointestinal tract. An carbohydrate present withinAttorney Docket No.: 53206-717601an infant gastrointestinal tract can comprise a carbohydrate present in an infant gastrointestinal tract. In some cases, the carbohydrate present within an infant gastrointestinal tract may comprise human milk oligosaccharides (HMOs). In some cases, the carbohydrate present within an infant gastrointestinal tract may comprise a carbohydrate present in infant formula. In some cases, the carbohydrate present within an infant gastrointestinal tract may comprise 2’-Fucosyllactose, Lacto-N-difucohexaose I (LNDFH-I), Lacto-N-fucopentaose I (LNFP-I), Lacto-N-fucopentaose II (LNFP-II), Lacto-N-tetraose (LNT), 3-Fucosyllactose (3-FL), 6’-Sialyllactose (6’-SL), Disialyllacto-N-tetraose (DSLNT), Lacto-N-neotetraose (LNnT), Difucosyllactose (DFL), Fucosyldisialyllacto-N-hexaose I (FDS-LNH), Lacto-N-fucopentaose III (LNFP-III), 3’-Sialyllactose (3’SL), N-Acetylglucosamine (GlcNAc), fructooligosaccharides (FOS), galactose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, fructose, pectin, fucose, or a combination thereof.

[0186] human milk oligosaccharide (HMO)s may comprise 2’-Fucosyllactose (2’FL), Lacto-N-difucohexaose I (LNDFH-I), Lacto-N-fucopentaose I (LNFP-I), Lacto-N-fucopentaose II (LNFP-II), Lacto-N-tetraose (Lacto-N-tetraose), 3-Fucosyllactose (3-FL), 6’-Sialyllactose (6’-SL), Disialyllacto-N-tetraose (DSLNT), Lacto-N-neotetraose (LNnT), Difucosyllactose (DFL), Fucosyldisialyllacto-N-hexaose I (FDS-LNH), Lacto-N-fucopentaose III (LNFP-III), 3’-Sialyllactose (3’SL), or any combination thereof. In some cases, bacterial strain described herein may be capable of utilizing human milk oligosaccharide (HMO)s as described herein.

[0187] In some cases, bacteria or bacterial strain described herein may be capable of utilizing ’2’-Fucosyllactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-tetraose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-difucohexaose I. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-fucopentaose I. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-fucopentaose II. In some cases, bacteria or bacterial strain described herein may be capable of utilizing 3-Fucosyllactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing 6’-Sialyllactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Disialyllacto-N-tetraose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-neotetraose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Difucosyllactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Fucosyldisialyllacto-N-hexaose I. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Lacto-N-fucopentaose III. In some cases,Attorney Docket No.: 53206-717601bacteria or bacterial strain described herein may be capable of utilizing 3’-Sialyllactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing N-Acetylglucosamine. In some cases, bacteria or bacterial strain described herein may be capable of utilizing fructooligosaccharides. In some cases, bacteria or bacterial strain described herein may be capable of utilizing galactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing Galacto-Oligosaccharides. In some cases, bacteria or bacterial strain described herein may be capable of utilizing lactose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing inulin. In some cases, bacteria or bacterial strain described herein may be capable of utilizing mucin. In some cases, bacteria or bacterial strain described herein may be capable of utilizing fructose. In some cases, bacteria or bacterial strain described herein may be capable of utilizing pectin. In some cases, bacteria or bacterial strain described herein may be capable of utilizing fucose. A bacteria or bacterial strain described herein may not be capable of utilizing an carbohydrate present within an infant gastrointestinal tract. A bacteria or bacterial strain described herein may not be capable of utilizing carbohydrate of the mucus intestinal barrier. For example, a bacteria or bacterial strain described herein may not have a sufficient ability in utilizing mucin. In some cases, utilization of infant gastrointestinal-relevant can be measured by the growth ratio between the bacteria or bacterial strain grown in a culture having a carbon source comprising the carbohydrate present within an infant gastrointestinal tract and the bacteria or bacterial strain grown in a culture having a carbon source comprising glucose (referred to as carbohydrate present within an infant gastrointestinal tract growth ratio). For example, methods to determine the carbohydrate present within an infant gastrointestinal tract growth ratio are described herein, such as those described in EXAMPLE 3 or 12. The growth ratio of a bacteria or bacterial strain in a culture medium comprising a carbohydrate as an energy source may be used to measure as a score of growth of the bacteria or bacterial strain in the culture medium. In some cases, the carbohydrate present within an infant gastrointestinal tract growth ratio is measured at least about: 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29 hours, 30 hours, 31 hours, 32 hours, 33 hours, 34 hours, 35 hours, 36 hours, 37 hours, 38 hours, 39 hours, 40 hours, 41 hours, 42 hours, 43 hours, 44 hours, 45 hours, 46 hours, 47 hours, 48 hours, 49 hours, 50 hours, 51 hours, 52 hours, 53 hours, 54 hours, 55 hours, 56 hours, 57 hours, 58 hours, 59 hours, 60 hours, 61 hours, 62 hours, 63 hours, 64 hours, 65 hours, 66 hours, 67 hours, 68 hours, 69Attorney Docket No.: 53206-717601hours, 70 hours, 71 hours, 72 hours, 73 hours, 74 hours, 75 hours, 76 hours, 77 hours, 78 hours, 79 hours, 80 hours, 81 hours, 82 hours, 83 hours, 84 hours, 85 hours, 86 hours, 87 hours, 88 hours, 89 hours, 90 hours, 91 hours, 92 hours, 93 hours, 94 hours, 95 hours, 96 hours, 97 hours, 98 hours, 99 hours, or 100 hours, subsequent to when a bacteria is inoculated. When used herein, “inoculation” of a microbe or a bacteria in a culture medium refers to within at most about 5 minutes subsequent to the microbe or bacteria is cultured within the culture medium. In some cases, the carbohydrate present within an infant gastrointestinal tract growth ratio is measured at most about: 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29 hours, 30 hours, 31 hours, 32 hours, 33 hours, 34 hours, 35 hours, 36 hours, 37 hours, 38 hours, 39 hours, 40 hours, 41 hours, 42 hours, 43 hours, 44 hours, 45 hours, 46 hours, 47 hours, 48 hours, 49 hours, 50 hours, 51 hours, 52 hours, 53 hours, 54 hours, 55 hours, 56 hours, 57 hours, 58 hours, 59 hours, 60 hours, 61 hours, 62 hours, 63 hours, 64 hours, 65 hours, 66 hours, 67 hours, 68 hours, 69 hours, 70 hours, 71 hours, 72 hours, 73 hours, 74 hours, 75 hours, 76 hours, 77 hours, 78 hours, 79 hours, 80 hours, 81 hours, 82 hours, 83 hours, 84 hours, 85 hours, 86 hours, 87 hours, 88 hours, 89 hours, 90 hours, 91 hours, 92 hours, 93 hours, 94 hours, 95 hours, 96 hours, 97 hours, 98 hours, 99 hours, or 100 hours, subsequent to when a bacteria is inoculated.

[0188] In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio of at least about 0.01, at least about 0.02, at least about 0.05, at least about 0.1, at least about 0.2, at least about 0.3, at least about 0.4, at least about 0.5, at least about 0.6, at least about 0.7, at least about 0.8, at least about 0.9, at least about 1, at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5 or more. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio of at most about 0.01, at most about 0.02, at most about 0.05, at most about 0.1, at most about 0.2, at most about 0.3, at most about 0.4, at most about 0.5, at most about 0.6, at most about 0.7, at most about 0.8, at most about 0.9, at most about 1, at most about 1.1, at most about 1.2, at most about 1.3, at most about 1.4, at most about 1.5, at most about 1.6, atAttorney Docket No.: 53206-717601most about 1.7, at most about 1.8, at most about 1.9, at most about 2, at most about 2.5, at most about 3, at most about 3.5, at most about 4, at most about 4.5, or at most about 5.

[0189] In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio (for ’2’-Fucosyllactose) of at least about 0.01, at least about 0.02, at least about 0.05, at least about 0.1, at least about 0.2, at least about 0.3, at least about 0.4, at least about 0.5, at least about 0.6, at least about 0.7, at least about 0.8, at least about 0.9, at least about 1, at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5 or more. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio (for ’2’-Fucosyllactose) of at most about 0.01, at most about 0.02, at most about 0.05, at most about 0.1, at most about 0.2, at most about 0.3, at most about 0.4, at most about 0.5, at most about 0.6, at most about 0.7, at most about 0.8, at most about 0.9, at most about 1, at most about 1.1, at most about 1.2, at most about 1.3, at most about 1.4, at most about 1.5, at most about 1.6, at most about 1.7, at most about 1.8, at most about 1.9, at most about 2, at most about 2.5, at most about 3, at most about 3.5, at most about 4, at most about 4.5, or at most about 5. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio (for Lacto-N-tetraose) of at least about 0.01, at least about 0.02, at least about 0.05, at least about 0.1, at least about 0.2, at least about 0.3, at least about 0.4, at least about 0.5, at least about 0.6, at least about 0.7, at least about 0.8, at least about 0.9, at least about 1, at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5 or more. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth ratio (for Lacto-N-tetraose) of at most about 0.01, at most about 0.02, at most about 0.05, at most about 0.1, at most about 0.2, at most about 0.3, at most about 0.4, at most about 0.5, at most about 0.6, at most about 0.7, at most about 0.8, at most about 0.9, at most about 1, at most about 1.1, at most about 1.2, at most about 1.3, at most about 1.4, at most about 1.5, at most about 1.6, at most about 1.7, at most about 1.8, at most about 1.9, at most about 2, at most about 2.5, at most about 3, at most about 3.5, at most about 4, at most about 4.5, or at most about 5.Attorney Docket No.: 53206-717601

[0190] In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth (for example, for ’2’-Fucosyllactose or Lacto-N-tetraose) ratio that is at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth (for example, for ’2’-Fucosyllactose or Lacto-N-tetraose) ratio that is at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control strain. In some cases, the bacteria or bacterial strain described herein may have a vaginally relevant carbohydrate growth (for glycogen, bioglycogen, dextrin, or maltodextrin) ratio that is at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein may have an carbohydrate present within an infant gastrointestinal tract growth (for example, for ’2’-Fucosyllactose or Lacto-N-tetraose) ratio that is at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control strain. The control strain may comprise EV27 or BG49.

[0191] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) within a bacterial population comprising at least two bacteria or bacterial strains may increase the abundance of any bacteria or bacterial strains within the bacterial composition within the subject by at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least aboutAttorney Docket No.: 53206-7176010.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) within a bacterial population comprising at least two bacteria or bacterial strains may increase the abundance of any bacteria or bacterial strains within the bacterial composition within the subject by at least about 2-fold, at least about 3 -fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) within a bacterial population comprising at least two bacteria or bacterial strains may increase the abundance of any bacteria or bacterial strains within the bacterial composition within the subject by at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) within a bacterial population comprising at least two bacteria or bacterial strains may increase the abundance of any bacteria or bacterial strains within the bacterial composition within the subject by at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49. The methods of measuring the abundance of the bacteria within a subject are described in EXAMPLE 14.Attorney Docket No.: 53206-717601

[0192] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference in the microbiota within a subject. The difference in microbiota may be measured by a difference in the number of species present within the microbiota of a subject between (1) before the subject is administered with the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) and after the period of time the subject is administered with the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The microbiota structure within a subject can be measured by Bray-Curtis dissimilarity, as described in EXAMPLE 14. In some cases, the bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the microbiota within a subject by at least about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. In some cases, the bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the microbiota within a subject by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold higher than that of a control. In some cases, the bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the Bray-Curtis dissimilarity in the microbiota within a subject by at most about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. In some cases, the bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the microbiota within a subject by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold higher than that of a control. A difference of the microbiota within a subject may be measured using alpha diversity, beta diversity, Bray-Curtis dissimilarity, Euclidean distance, Manhattan distance, Canberra distance, Chebyshev distance, Minkowski distance, Cosine distance, Pearson Correlation distance, Spearman correlation, Mahalanobis distance, Standardized Euclidian distance, Chi-square distance, Jensen-Shannon distance, Levenshtein distance, Hamming distance, Jaccard / Tanimoto distance, Sorensen-Dice, a derivative thereof, or a combination thereof.Attorney Docket No.: 53206-717601

[0193] In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the Bray-Curtis dissimilarity in the microbiota within a subject by at least about 0.001 %, at least about 0.001 %, at least about 0.01%, at least about 0.1 %, at least about 1 %, at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 6 %, at least about 7 %, at least about 8 %, at least about 9 %, at least about 10 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, at least about 90 %, at least about 100 %, or at least about 150 %. In some cases, the bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the microbiota within a subject by at least about 2-fold, at least about 3-fold, at least about 4-fold, at least about 5-fold, at least about 6-fold, at least about 7-fold, at least about 8-fold, at least about 9-fold, at least about 10-fold, at least about 100-fold, at least about 1000-fold, at least about 10000-fold, at least about 100000-fold, or at least about 1000000-fold higher than that of a control. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the Bray-Curtis dissimilarity in the microbiota within a subject by at most about 0.001 %, at most about 0.001 %, at most about 0.01%, at most about 0.1 %, at most about 1 %, at most about 2 %, at most about 3 %, at most about 4 %, at most about 5 %, at most about 6 %, at most about 7 %, at most about 8 %, at most about 9 %, at most about 10 %, at most about 20 %, at most about 30 %, at most about 40 %, at most about 50 %, at most about 60 %, at most about 70 %, at most about 80 %, at most about 90 %, at most about 100 %, or at most about 150 %. In some cases, the bacteria or bacterial strain described herein (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium) may induce a difference of the Bray-Curtis dissimilarity in the microbiota within a subject by at most about 2-fold, at most about 3-fold, at most about 4-fold, at most about 5-fold, at most about 6-fold, at most about 7-fold, at most about 8-fold, at most about 9-fold, at most about 10-fold, at most about 100-fold, at most about 1000-fold, at most about 10000-fold, at most about 100000-fold, or at most about 1000000-fold higher than that of a control. The control may comprise a subject not administered with the bacteria or has NEC. The control may also comprise a control strain (or the cultured medium thereof; or a bacterial product encompassed within that cultured medium). The control strain may comprise EV27 or BG49.Attorney Docket No.: 53206-717601

[0194] A control composition or control formulation may comprise any control or control strain as described herein.

[0195] In some cases, the bacteria or bacterial strain described herein may exhibit a growth when cultured in a culture medium having an carbohydrate present within an infant gastrointestinal tract. In some cases, the bacteria or bacterial strain described herein may exhibit an increase of cell numbers by at least about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. In some cases, the bacteria or bacterial strain described herein may exhibit an increase of cell numbers by at least about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, subsequent to the bacteria or bacterial strain being inoculated in the culture medium. In some cases, the bacteria or bacterial strain described herein may exhibit an increase of cell numbers by at most about: 0.001 %, 0.001 %, 0.01%, 0.1 %, 1 %, 2 %, 3 %, 4 %, 5 %, 6 %, 7 %, 8 %, 9 %, 10 %, 20 %, 30 %, 40 %, 50 %, 60 %, 70 %, 80 %, 90 %, 100 %, or 150 %. In some cases, the bacteria or bacterial strain described herein may exhibit an increase of cell numbers by at most about: 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 100-fold, 1000-fold, 10000-fold, 100000-fold, or 1000000-fold, subsequent to the bacteria or bacterial strain being inoculated in the culture medium. The increase in cell numbers as described herein may be measured after a period of time subsequent to the bacteria or bacterial strain being inoculated in the culture medium.

[0196] The growth of any microbe as described herein (such as any bacteria or bacterial strain as described herein or any pathogens as described herein) can be measured as a growth rate that comprises the difference the numbers of cells or weight of the microbe in a period of time as described herein. In some cases, the period of time may start when a bacteria is administered into a subject.

[0197] In some cases, the sufficient ability or a capability to alter NEC-associated functions can be measured as a difference in the functionality period in a period of time as described herein. In some cases, the period of time may start when a bacteria is administered into a subject. In some cases, the period of time may start when a bacteria is inoculated. In some cases, the period of time may start when a bacteria is contacted with a different cell, organism, or marker, as described herein. In some cases, the period of time may start when any experiment or method described herein is initiated.Microbial combinationsAttorney Docket No.: 53206-717601

[0198] The bacterial population can comprise a plurality or at least two bacteria or bacterial strains as described herein. The bacterial population can comprise a plurality or at least two bacterial species as described herein. The term “plurality” can comprise at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more. The plurality of bacteria or bacterial strains can comprise any bacteria or bacterial strains as descried herein. For a bacterial population comprising at least two bacteria or bacterial strains, each of the at least two bacteria or bacterial strains are different bacteria or bacterial strains. When used herein, two different bacteria may comprise: two bacteria cells that are different from each other; two different species of bacteria; or two bacterial isolates. In some cases, each of the at least two bacteria or bacterial strains may comprise the bacterial species as described herein. In some cases, the bacterial population can comprise a plurality of bacteria or bacterial strains of Bifidobacterium sp. or Lactobacillus sp. (or Vertebrate-Associated Lactobacillaceae). In some cases, the bacterial population can comprise a plurality of bacteria or bacterial strains of Bifidobacterium adolescentis.Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii. Lactobacillus plantarum, or Lactobacillus rhamnosus. A plurality of bacteria or bacterial strains of Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus plantarum, or Lactobacillus rhamnosus can comprise any individual bacteria or bacterial strain or combinations of ST101, ST31, ST80, ST56, ST71, ST23, ST19, ST81, ST119, ST37, ST66, ST20, ST100, ST112, ST105, ST21, ST65, and / or STI 16. In some cases, the bacterial population can comprise any of the aforementioned bacteria or bacterial strains in addition to one or more additional bacteria or bacterial strains from Bifidobacterium sp. or Lactobacillus sp. (or Vertebrate-Associated Lactobacillaceae).

[0199] The bacterial population can comprise any combinations of at least two bacteria or bacterial strains of the following bacteria or bacterial strains: a bacterial of Lactobacillus crispatus as described herein, a bacterial of Lactobacillus gasseri as described herein, a bacteria of Lactobacillus jensenii as described herein, a bacteria of Bifidobacterium bifidum as described herein, a bacteria of Lactobacillus plantarum as described herein, a bacteria of Bifidobacterium adolescentis as described herein, a bacteria of Bifidobacterium breve as described herein, a bacteria of Bifidobacterium longum as described herein, a bacteria of Bifidobacterium pseudocatenulatum as described herein, and / or a bacteria of Lactobacillus rhamnosus as described herein. The bacterial population can comprise any combinations of atAttorney Docket No.: 53206-717601least two bacteria or bacterial strains of the following bacteria or bacterial strains: a bacteria of Lactobacillus crispatus as described herein, a bacteria of Lactobacillus gasseri as described herein, and / or a bacteria of Lactobacillus jensenii as described herein. In some cases, the composition may be used for treating or preventing a disease or disease condition. A disease or disease condition may comprise a disease or complication associated with the disease. In some cases, the composition for treating or preventing a vaginal disease as described herein (e.g., BV or recurrent BV or a complication associated with the vaginal disease (e.g., pre-term birth, birth / pregnancy complications, STIs (such as HIV, Chlamydia, Gonorrhea, Suphilis, Trichomoniasis), pelvic inflammatory disease (PID), vulvovaginitis, or a combination thereof can comprise a bacterial population comprising any combinations of at least two bacteria or bacterial strains of the following bacteria or bacterial strains: a bacteria of Lactobacillus crispatus as described herein, a bacteria of Lactobacillus gasseri as described herein, and / or a bacteria of Lactobacillus jensenii as described herein. The bacterial population can comprise any combinations of at least two bacteria or bacterial strains of the following bacteria or bacterial strains: a bacteria of Bifidobacterium bifidum as described herein, a bacteria of Lactobacillus plantarum as described herein, a bacteria of Bifidobacterium adolescentis as described herein, a bacteria of Bifidobacterium breve as described herein, a bacteria of Bifidobacterium longum as described herein, a bacteria of Bifidobacterium pseudocatenulatum as described herein, and / or a bacteria of Lactobacillus rhamnosus as described herein. In some cases, the composition for treating or preventing an infant gastrointestinal disease as described herein (e.g., NEC, infectious gastroenteritis, neonatal cholestasis, or pediatric intestinal motility disorder) can comprise a bacterial population comprising any combinations of at least two bacteria or bacterial strains of the following bacteria or bacterial strains: a bacteria of Bifidobacterium bifidum as described herein, a bacteria of Lactobacillus plantarum as described herein, a bacteria of Bifidobacterium adolescentis as described herein, a bacteria of Bifidobacterium breve as described herein, a bacteria of Bifidobacterium longum as described herein, a bacteria of Bifidobacterium pseudocatenulatum as described herein, and / or a bacteria of Lactobacillus rhamnosus as described herein.

[0200] The bacterial population can comprise at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20 or more bacteria or bacterial strain(s). The bacterial population can comprise atAttorney Docket No.: 53206-717601most about 1, at most about 2, at most about 3, at most about 4, at most about 5, at most about 6, at most about 7, at most about 8, at most about 9, at most about 10, at most about 11, at most about 12, at most about 13, at most about 14, at most about 15, at most about 16, at most about 17, at most about 18, at most about 19, or at most about 20 bacteria or bacterial strain(s). The bacterial population can comprise at least about 1 bacteria or bacterial strain. The bacterial population can comprise at least about 2 bacteria or bacterial strains. The bacterial population can comprise at least about 3 bacteria or bacterial strains. The bacterial population can comprise at least about 4 bacteria or bacterial strains. The bacterial population can comprise at least about 5 bacteria or bacterial strains. The bacterial population can comprise at least about 6 bacteria or bacterial strains. The bacterial population can comprise at least about 7 bacteria or bacterial strains. The bacterial population can comprise at least about 8 bacteria or bacterial strains. The bacterial population can comprise at least about 9 bacteria or bacterial strains. The bacterial population can comprise at least about 10 bacteria or bacterial strains. The bacterial population can comprise at least about 11 bacteria or bacterial strains. The bacterial population can comprise at least about 12 bacteria or bacterial strains. The bacterial population can comprise at least about 13 bacteria or bacterial strains. The bacterial population can comprise at least about 14 bacteria or bacterial strains. The bacterial population can comprise at least about 15 bacteria or bacterial strains. The bacterial population can comprise at least about 16 bacteria or bacterial strains. The bacterial population can comprise at least about 17 bacteria or bacterial strains. The bacterial population can comprise at least about 18 bacteria or bacterial strains. The bacterial population can comprise at least about 19 bacteria or bacterial strains. The bacterial population can comprise at least about 20 bacteria or bacterial strains. The bacterial population can comprise more than 20 bacteria or bacterial strains. The bacterial population can comprise at most about 1 bacteria or bacterial strain. The bacterial population can comprise at most about 2 bacteria or bacterial strains. The bacterial population can comprise at most about 3 bacteria or bacterial strains. The bacterial population can comprise at most about 4 bacteria or bacterial strains. The bacterial population can comprise at most about 5 bacteria or bacterial strains. The bacterial population can comprise at most about 6 bacteria or bacterial strains. The bacterial population can comprise at most about 7 bacteria or bacterial strains. The bacterial population can comprise at most about 8 bacteria or bacterial strains. The bacterial population can comprise at most about 9 bacteria or bacterial strains. The bacterial population can comprise at most about 10 bacteria or bacterial strains. The bacterial population can comprise at most about 11 bacteria or bacterial strains. The bacterialAttorney Docket No.: 53206-717601population can comprise at most about 12 bacteria or bacterial strains. The bacterial population can comprise at most about 13 bacteria or bacterial strains. The bacterial population can comprise at most about 14 bacteria or bacterial strains. The bacterial population can comprise at most about 15 bacteria or bacterial strains. The bacterial population can comprise at most about 16 bacteria or bacterial strains. The bacterial population can comprise at most about 17 bacteria or bacterial strains. The bacterial population can comprise at most about 18 bacteria or bacterial strains. The bacterial population can comprise at most about 19 bacteria or bacterial strains. The bacterial population can comprise at most about 20 bacteria or bacterial strains. In some cases, the plurality of bacteria or bacterial strains may not comprise strains from a...

Claims

Attorney Docket No.: 53206-717601CLAIMS WHAT IS CLAIMED IS:

1. A method of treating or preventing a disease or condition in a subject in need thereof, wherein said method comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source,wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium,and wherein said first growth ratio is at least about 10 % different than said second growth ratio.

2. The method of claim 1, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, and wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source.

3. The method of claim 2, wherein said energy source or said second energy comprises a carbohydrate.

4. The method of any one of claims 2-3, wherein said second energy source comprises glucose.

5. The method of any one of claims 1-4, wherein said energy source comprises a humanAttorney Docket No.: 53206-717601milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract.

6. The method of any one of claims 1-4, wherein said energy source comprises fructooligosaccharides (FOS), guar gum, corn syrup, poly dextrose, Galacto- Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N- Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’- Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin, or a combination thereof.

7. The method of any one of claims 1-6, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said third growth ratio is at least about 10 % different than said fourth growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, and wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source.

8. The method of claim 7, wherein said first growth ratio is at least about 10 % or at least about 25 % higher than said second growth ratio, and wherein said fourth growth ratio is at least about 10 % or at least about 25 % higher than said third growth ratio.

9. The method of claim 7 or 8, wherein said energy source comprises LNnT or GlcNAc, and wherein said third energy source comprises galactose.

10. The method of any one of claims 1-9, wherein said composition comprises said bacterial population.

11. The method of any one of claims 1-9, wherein said composition comprises said mixture.

12. The method of any one of claims 1-9, wherein said composition comprises said derivative of said mixture or said bacterial population.

13. A method of treating or preventing a disease or condition in a subject in need thereof,Attorney Docket No.: 53206-717601wherein said method comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein when administered into said subject, said composition:(1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by a control composition; or(2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise (a), (b), (c), or (d).

14. The method of claim 13, wherein when administered into said subject, said composition inhibits said expression of said intestinal immune response signaling marker by at least about 0.1 % relative to said expression of said intestinal immune response signaling marker inhibited by said control composition.

15. The method of claim 13 or 14, wherein said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof.

16. The method of any one of claims 13-15, wherein when administered into said subject, said composition increases said level of said first bacterial strain or said second bacterial strain present within said subject by at least about 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition.

17. The method of any one of claims 13-16, wherein when administered into said subject, said composition inhibits a growth of a pathogen in a gastrointestinal tract of said subject by at least about 0.1 % relative to said growth of said pathogen inhibited byAttorney Docket No.: 53206-717601said control composition.

18. The method of claim 17, wherein said pathogen comprises E. coli, K. pneumoniae, C.perfringens, S. aureus, S. flexneri, or a combination thereof.

19. The method of any one of claims 13-18, wherein when administered into said subject, said composition increases an epithelial integrity of a gastrointestinal tract of said subject by at least about 0.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject increased by said control composition.

20. The method of any one of claims 17-19, wherein said gastrointestinal tract comprises ileum or distal ileum.

21. The method of any one of claims 13-20, wherein when administered into said subject, said composition induces a difference of a level of microbiota structure present within said subject by at least about 0.1 % relative to said level of said microbiota structure present within said subject induced by said control composition.

22. The method of any one of claims 10-21, wherein said composition comprises said bacterial population, and wherein said control composition does not comprise said bacterial population.

23. The method of any one of claims 10-21, wherein said composition comprises said mixture, and wherein said control composition does not comprise said mixture.

24. The method of any one of claims 10-21, wherein said composition comprises said derivative of said mixture or said bacterial population, and wherein said control composition does not comprise said derivative of said mixture.

25. The method of any one of claims 1-24, wherein said bacterial population comprises at least 3 different bacteria species.

26. The method of any one of claims 1-25, wherein said bacterial population comprises at least 4 different bacteria species.

27. The method of any one of claims 1-26, wherein said first bacterial strain and said second bacterial strain comprises Bifidobacterium longum, Bifidobacterium bifidum, or Lactobacillus plantarum.

28. The method of any one of claims 1-26, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium bifidum, or Lactobacillus plantarum.

29. The method of any one of claims 1-26, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, or Bifidobacterium bifidum.Attorney Docket No.: 53206-71760130. The method of any one of claims 1-29, wherein said disease or condition comprises a gastrointestinal disease or condition.

31. A method of preventing a gastrointestinal disease or condition in a subject in need thereof, wherein said method comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein administration of said formulation into said subject is initiated within about 48 hours from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

32. A method of treating a gastrointestinal disease or condition in a subject in need thereof, wherein said method comprises administering a formulation comprising a composition to said subject, wherein said composition comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate-Associated Lactobacillaceae, and wherein administration of said formulation into said subject is initiated within about 30 days from birth of said subject to at most about 40 weeks of gestation age (GA) of said subject.

33. The method of any one of claims 30-32, wherein said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC), infectious gastroenteritis, neonatal cholestasis, pediatric intestinal motility disorders, gastroenteritis, Inflammatory bowel disease (IBD), Irritable bowel syndrome (IBS), or a combination thereof.

34. The method of any one of claims 30-32, wherein said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC).

35. The method of any one of claims 1-34, wherein said subject is an infant.

36. The method of any one of claims 1-34, wherein said subject is a preterm infant or a neonate.

37. The method of any one of claims 1-4 or 7-36, wherein said composition further comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract.

38. The method of any one of claims 1-4 or 7-36, wherein said composition furtherAttomey Docket No.: 53206-717601comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’- Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin.

39. A method, comprising:a. providing a plurality of bacterial strains;b. identifying a bacterial strain from said plurality bacterial strains that ranks at top 50 percentile among said plurality bacterial strains in:i. a score of adherence to an intestinal epithelial cell (IEC),ii. a score of growth in a culture medium comprising a carbohydrate as an energy source, wherein said carbohydrate is present within an infant gastrointestinal tract,iii. a score of inhibition of a growth of an infant gastrointestinal pathogen, iv. a score of inhibition of an immune response signaling pathway of a cell, orv. any combination of (i)-(iv); andc. selecting said bacterial strain for generating a composition for treating or preventing a gastrointestinal disease or condition of a subject, wherein said composition comprises a bacterial strain of Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae.

40. The method of claim 39, wherein said plurality bacterial strains is derived from a fecal sample of a human.

41. The method of claim 40, wherein said human does not have said gastrointestinal disease or condition.

42. The method of claim 40 or 41, wherein said human is an adult.

43. The method of claim 40 or 41, wherein said human is an infant.

44. The method of any one of claims 39-43, wherein said bacterial strain ranks at top 10 percentile among said plurality bacterial strains in (i) or (ii).

45. The method of any one of claims 39-43, wherein said bacterial strain ranks at top 10 percentile among said plurality bacterial strains in (i) and (ii).

46. The method of any one of claims 39-45, wherein said carbohydrate comprises fructooligosaccharides (FOS), guar gum, corn syrup, poly dextrose, Galacto- Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N- Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2'-Attorney Docket No.: 53206-717601Fucosyllactose (2'-FL), galactose, fucose, maltodextrin, pectin, or a combination thereof, optionally lactose, galactose, GlnNAc, or LNnT.

47. The method of any one of claims 39-46, wherein said bacterial strain exhibits a growth ratio of about at least about 0.7 between (1) a number of bacterial cells of said bacterial strain within about 48 hours after said bacterial strain is inoculated in said culture medium and (2) a number of bacterial cells of said bacterial strain within about 48 hours after said bacterial strain is inoculated in a culture medium comprising glucose.

48. The method of any one of claims 39-47, wherein said bacterial strain exhibits an adherence value of at least 1x104[colony-forming units (CFU) / 9.5 centimeter square (cmA2) of a surface area of said IEC], optionally of at least 1x107log CFU / cm2of said surface area of said IEC.

49. The method of any one of claims 39-48, wherein said bacterial strain inhibits the growth of said infant gastrointestinal pathogen in vitro by at least 50%, relative to a growth of said infant gastrointestinal pathogen in vitro when inhibited by a control bacteria strain that is not said bacterial strain.

50. The method of any one of claims 39-49, wherein said bacterial strain inhibits said immune response signaling pathway of said cell by at least 50%, relative to an immune response signaling pathway when inhibited by a control bacteria strain that is not said bacterial strain.

51. A composition for treating or preventing a disease or condition in a subject in need thereof, comprising:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source,wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium,Attorney Docket No.: 53206-717601and wherein said first growth ratio is at least about 10 % different than said second growth ratio.

52. The composition of claim 51, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source, and wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source.

53. The composition of claim 52, wherein said energy source or said second energy comprises a carbohydrate.

54. The composition of any one of claims 52-53, wherein said second energy source comprises glucose.

55. The composition of any one of claims 51-54, wherein said energy source comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract.

56. The composition of any one of claims 51-54, wherein said energy source comprises fructooligosaccharides (FOS), guar gum, corn syrup, poly dextrose, Galacto- Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N- Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’- Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin, or a combination thereof.

57. The composition of any one of claims 51-55, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said third growth ratio is at least about 10 % different than said fourth growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterialAttorney Docket No.: 53206-717601cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, and wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source.

58. The composition of claim 56, wherein said first growth ratio is at least about 10 % or at least about 25 % higher than said second growth ratio, and wherein said fourth growth ratio is at least about 10 % or at least about 25 % higher than said third growth ratio.

59. The composition of claim 57 or 58, wherein said energy source comprises LNnT or GlcNAc, and wherein said second energy source comprises galactose.

60. The composition of any one of claims 51-59, wherein said composition comprises said bacterial population.

61. The composition of any one of claims 51-59, wherein said composition comprises said mixture.

62. The composition of any one of claims 51-59, wherein said composition comprises said derivative of said mixture or said bacterial population.

63. A composition for treating or preventing a disease or condition in a subject in need thereof, comprising:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein when administered into said subject, said composition is configured to:(1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by said control composition; orAttorney Docket No.: 53206-717601(2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, andwherein said control composition does not comprise (a), (b), (c), or (d).

64. The composition of claim 63, wherein when administered into said subject, said composition is configured to inhibit said expression of said intestinal immune response signaling marker by at least about 0.1 % relative to said expression of said intestinal immune response signaling marker inhibited by said control composition.

65. The composition of claim 63 or 64, wherein said intestinal immune response signaling marker comprises interleukin-6 (IL6), interleukin- lb (IL1B), or Lipocalin-2 (Lcn2), or a combination thereof.

66. The composition of any one of claims 63-65, wherein when administered into said subject, said composition is configured to increase said level of said first bacterial strain or said second bacterial strain present within said subject by at least about 0.1 % relative to said level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition.

67. The composition of any one of claims 63-66, wherein when administered into said subject, wherein said composition is configured to inhibit a growth of a pathogen in a gastrointestinal tract of said subject by at least about 0.1 % relative to said growth of said pathogen inhibited by said control composition.

68. The composition of claim 67, wherein said pathogen comprises E. coli, K.pneumoniae, C. perfringens, S. aureus, S. flexneri, or a combination thereof.

69. The composition of any one of claims 63-68, wherein when administered into said subject, said composition increases an epithelial integrity of said gastrointestinal tract of said subject by at least about 0.1 % relative to said epithelial integrity of said gastrointestinal tract of said subject increased by said control composition.

70. The composition of any one of claims 67-69, wherein said gastrointestinal tract comprises ileum or distal ileum.

71. The composition of any one of claims 63-70, wherein when administered into said subject, said composition induces a difference of a level of microbiota structure present within said subject by at least about 0.1 % relative to said level of said microbiota structure present within said subject induced by said control composition.

72. The composition of any one of claims 63-71, wherein said composition comprisesAttorney Docket No.: 53206-717601said bacterial population, and wherein said control composition does not comprise said bacterial population.

73. The composition of any one of claims 63-71, wherein said composition comprises said mixture, and wherein said control composition does not comprise said mixture.

74. The composition of any one of claims 63-71, wherein said composition comprises said derivative of said mixture or said bacterial population, and wherein said control composition does not comprise said derivative of said mixture.

75. The composition of any one of claims 51-74, wherein said bacterial population comprises at least 3 different bacteria species.

76. The composition of any one of claims 51-75, wherein said bacterial population comprises at least 4 different bacteria species.

77. The composition of any one of claims 51-76, wherein said first bacterial strain and said second bacterial strain comprises Bifidobacterium longum, Bifidobacterium bifidum, or Lactobacillus plantarum.

78. The composition of any one of claims 51-77, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium bifidum, or Lactobacillus plantarum.

79. The composition of any one of claims 51-77, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium longum, Bifidobacterium pseudocatenulatum, or Bifidobacterium bifidum.

80. The composition of any one of claims 51-78, wherein said disease or condition comprises a gastrointestinal disease or condition.

81. The composition of claim 80, wherein said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC), infectious gastroenteritis, neonatal cholestasis, pediatric intestinal motility disorders, gastroenteritis, Inflammatory bowel disease (IBD), Irritable bowel syndrome (IBS), or a combination thereof.

82. The composition of claim 80, wherein said gastrointestinal disease or condition comprises necrotizing enterocolitis (NEC).

83. The composition of any one of claims 51-82, wherein said subject is an infant.

84. The composition of any one of claims 51-82, wherein said subject is a preterm infant or a neonate.

85. The composition of any one of claims 51-54 or 58-84, wherein the composition further comprises a human milk oligosaccharide or a carbohydrate present within an infant gastrointestinal tract.Attorney Docket No.: 53206-71760186. The composition of any one of claims 51-54 or 58-84, wherein the composition further comprises fructooligosaccharides (FOS), guar gum, corn syrup, polydextrose, Galacto-Oligosaccharides (GOS), lactose, inulin, mucin, sialic acid, glucan, fructose, N-Acetylglucosamine (GlcNAc), mannose, Lacto-N-neotetraose (LNnT), glucose, 2’- Fucosyllactose (2’ -FL), galactose, fucose, maltodextrin, pectin.

87. A method of treating or preventing a disease or condition in a subject in need thereof, wherein said method comprises administering a formulation to said subject, wherein said formulation comprises a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Verlebrale-, QC\&iQ Laclobacillaceae. and wherein a first growth ratio of said first bacterial strain is at least about 10 % different than a second growth ratio of said second bacterial strain.

88. A method of treating or preventing a disease or condition in a subject in need thereof, wherein said method comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein when administered into said subject, said composition: (1) inhibits expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by a control composition, or (2) increases a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise said first bacterial strain and said second bacterial strain.

89. A composition for treating or preventing a disease or condition in a subject in need thereof, comprising a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source, wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium, wherein said first growth ratio is at least about 10 % different than saidAttorney Docket No.: 53206-717601second growth ratio.

90. A composition for treating or preventing a disease or condition in a subject in need thereof, comprising a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain, wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae, and wherein when administered into said subject, said composition is configured to: (1) inhibit expression of an intestinal immune response signaling marker by at least about 0.1 % relative to expression of said intestinal immune response signaling marker inhibited by said control composition, or (2) increase a level of said first bacterial strain or said second bacterial stain present within said subject by at least about 0.1 % relative to a level of said first bacterial strain or said second bacterial strain present within said subject increased by said control composition, and wherein said control composition does not comprise first bacterial strain and said second bacterial strain.

91. A method of treating or preventing a disease or condition in a subject in need thereof, wherein said method comprises administering a formulation to said subject, wherein said formulation comprises a composition comprising:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein said first bacterial strain exhibits a first growth ratio when cultured in a medium comprising an energy source,wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium,wherein said first growth ratio is at least about 10 % higher than said second growth ratio, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain isAttorney Docket No.: 53206-717601inoculated in a medium comprising a second energy source different from said energy source, wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said fourth growth ratio is at least about 10 % higher than said third growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source, wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said energy source comprises LNnT or GlcNAc,wherein said second energy source comprises glucose, andwherein said third energy source comprises galactose.

92. A composition for treating or preventing a disease or condition in a subject in need thereof, wherein said composition comprises:a. a bacterial population comprising a first bacterial strain and a second bacterial strain different from said first bacterial strain;b. a mixture comprising said first bacterial strain and a bacterial product of said second bacterial strain;c. a derivative of said mixture or said bacterial population; ord. any combination of (a)-(c),wherein said first bacterial strain and said second bacterial strain comprise Bifidobacterium sp. or Vertebrate- Associated Lactobacillaceae,wherein said first bacterial strain exhibits a first growth ratio when cultured inAttorney Docket No.: 53206-717601a medium comprising an energy source,wherein said second bacterial strain exhibits a second growth ratio when cultured in said medium,wherein said first growth ratio is at least about 10 % higher than said second growth ratio, wherein said first growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in a medium comprising a second energy source different from said energy source,wherein said second growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said first bacterial strain exhibits a third growth ratio when cultured in a second medium comprising a third energy source different from said energy source, wherein said second bacterial strain exhibits a fourth growth ratio when cultured in said second medium, wherein said fourth growth ratio is at least about 10 % higher than said third growth ratio, wherein said third growth ratio is measured as a ratio between (1) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said first bacterial strain within about 48 hours after said first bacterial strain is inoculated in said medium comprising said second energy source,wherein said fourth growth ratio is measured as a ratio between (1) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said second medium and (2) a number of bacterial cells of said second bacterial strain within about 48 hours after said second bacterial strain is inoculated in said medium comprising said second energy source, wherein said energy source comprises LNnT or GlcNAc,wherein said second energy source comprises glucose, andwherein said third energy source comprises galactose.

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