Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: Provided are nucleic acids that include a promoter, where the promoter is operable in a Bacteroides cell and is operably linked to a heterologous nucleotide sequence of interest. Also provided are nucleic acids that include a promoter (operable in a prokaryotic cell such as a Bacteroides cell) operably linked to a sequence encoding a synthetic ribosomal binding site (RBS). Also provided are fusion proteins (and nucleic acids encoding them) in which a secreted Bacteroides polypeptide is fused to a heterologous polypeptide of interest. Also provided are prokaryotic cells (e.g., E. coli, a Bacteroides cell, and the like) that include one more nucleic acids such as those described above. Also provided are methods of expression in a prokaryotic cell, methods of detectably labeling a Bacteroides cell in an animal's gut, and methods of delivering a protein to an individual's gut.

Abstract: Provided are nucleic acids that include a promoter, where the promoter is operable in a Bacteroides cell and is operably linked to a heterologous nucleotide sequence of interest. Also provided are nucleic acids that include a promoter (operable in a prokaryotic cell such as a Bacteroides cell) operably linked to a sequence encoding a synthetic ribosomal binding site (RBS). Also provided are fusion proteins (and nucleic acids encoding them) in which a secreted Bacteroides polypeptide is fused to a heterologous polypeptide of interest. Also provided are prokaryotic cells (e.g., E. coli, a Bacteroides cell, and the like) that include one more nucleic acids such as those described above. Also provided are methods of expression in a prokaryotic cell, methods of detectably labeling a Bacteroides cell in an animal's gut, and methods of delivering a protein to an individual's gut.

Abstract: The present invention provides high-complexity defined gut microbial communities capable of achieving substantial engraftment and having stability following human fecal community microbial challenge and methods of producing the same. Also provided are methods of using high-complexity defined gut microbial communities for the treatment of dysbiosis or a pathological condition in an animal.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: Provided are nucleic acids that include a promoter, where the promoter is operable in a Bacteroides cell and is operably linked to a heterologous nucleotide sequence of interest. Also provided are nucleic acids that include a promoter (operable in a prokaryotic cell such as a Bacteroides cell) operably linked to a sequence encoding a synthetic ribosomal binding site (RBS). Also provided are fusion proteins (and nucleic acids encoding them) in which a secreted Bacteroides polypeptide is fused to a heterologous polypeptide of interest. Also provided are prokaryotic cells (e.g., E. coli, a Bacteroides cell, and the like) that include one more nucleic acids such as those described above. Also provided are methods of expression in a prokaryotic cell, methods of detectably labeling a Bacteroides cell in an animal's gut, and methods of delivering a protein to an individual's gut.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: The present invention provides high-complexity defined gut microbial communities capable of achieving substantial engraftment and having stability following human fecal community microbial challenge and methods of producing the same. Also provided are methods of using high-complexity defined gut microbial communities for the treatment of dysbiosis or a pathological condition in an animal.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: A therapeutic formulation containing mucin glycans derived from one or a number of nutritionally appropriate sources is described.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: Compositions and methods are provided for modulating growth of a genetically modified bacterial cell present in a human organ, for modulating growth of a genetically modified bacterial cell in an organ (e.g., gut), for displacing at least a portion of a population of bacterial cells in an organ, and for facilitating gut colonization by a genetically modified bacterial cell. Also provided are genetically modified bacterial cells, e.g., cells that include a heterologous carbohydrate-utilization gene or gene set that provides for the ability to utilize as a carbon source a rare carbohydrate of interest that is utilized as a carbon source by less than 50% of bacterial cells present in a human microbiome.

Abstract: A therapeutic formulation containing mucin glycans derived from one or a number of nutritionally appropriate sources is described.

Abstract: A therapeutic formulation containing mucin glycans derived from one or a number of nutritionally appropriate sources is described.

Abstract: Antibiotic-associated enteric pathogens are shown to increase in mucosal carbohydrate availability that occur upon disruption of the competitive ecosystem. Transient post-antibiotic increase in monosaccharides liberated by the resident microbiota from host mucus provides a window of opportunity for these pathogens to expand to densities sufficient to induce self-promoting host inflammation.

Abstract: A therapeutic formulation containing mucin glycans derived from one or a number of nutritionally appropriate sources is described.

Abstract: Methods and compositions are provided for the screening of candidate agents for their effect on the growth and colonization of hosts by anaerobic microorganisms, particularly microorganisms that comprise the gut microbiota of mammals. In some embodiments of the invention, candidate agents are screened for the ability to modulate growth of multiple microbes within a taxon, or functionally related microbes. In some embodiments of the invention, candidate agents are screened for the ability to modulate growth across a genus or functionally-defined group when the microorganisms are presented with a substrate of interest, which substrates include, without limitation, prebiotic compounds that promote expansion of divergent taxa within the microbiota, e.g. starch, fats, isoflavones, etc.