Abstract

Learning how members of the human gut microbiota compete and cooperate for dietary nutrients, such as fiber-associated glycans, should help facilitate development of more precise nutritional recommendations for improving health. To model how bacteria prioritize the utilization of different fiber glycans in the mammalian gut, germ-free mice were colonized with a 13-member consortium of cultured, genome-sequenced human bacterial strains, including seven Bacteroides species. Animals were fed a Western diet supplemented with pea fiber. Once the consortium had time to assemble, an inducible CRISPR-based system was used to deplete the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each type of knockdown resulted in specific, reproducible increases in the absolute abundances of other Bacteroides, with accompanying changes in their glycan prioritization, most notably involving changes in the expression of their polysaccharide utilization loci (PULs). The emergence of these ‘alternate consumers’ was associated with preservation of the community’s capacity to metabolize fiber glycans, as judged by measurements of degradation of polysaccharides covalently attached to orally administered artificial food particles, and of monosaccharides and glycosidic linkages remaining in cecal contents. Finally, using a Cas9-PmCDA1 base editing system, we disrupted translation of transporters critical for utilizing abundant dietary polysaccharides in Bacteroides vulgatus, a B. cellulosilyticus knockdown-responsive taxon, to further characterize mechanisms associated with its increased fitness following knockdown. Using this approach to define how nutrient resource utilization is prioritized among community members could help delineate the origins of robustness and resiliency in the microbiota, as well as aid in the design of microbiota-directed therapeutics.

Committee Chair

Jeffrey Gordon

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

5-9-2024

Language

English (en)

Author's ORCID

0000-0003-3965-9147

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