Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Molecular Microbiology and Microbial Pathogenesis


English (en)

Date of Award

Spring 4-25-2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Jeffrey I Gordon


The human gut is colonized by a diverse array of microbes, collectively referred to as the microbiota. The microbiota's complexity poses significant challenges in characterizing the rules dictating its assembly, inferring the functional roles of its component species, and understanding how communities sense and respond to changes in their habitat. We developed defined, representative model communities comprised of sequenced human gut bacteria that could be characterized in a highly controlled manner in gnotobiotic mice, plus a suite of scalable molecular tools for assaying community properties. These tools were first used to evaluate how the microbiota is impacted by probiotic bacterial strains found in fermented milk products: FMP). Introduction of a consortium of five FMP strains resulted in only minimal changes in the structural configuration of a 15-member model microbiota. However, RNA-Seq and follow-up mass spectrometry revealed numerous functional responses, many related to carbohydrate metabolism. Results from a study performed in monozygotic twin pairs confirmed many of our observations in the model microbiota, showing that lessons learned from preclinical models can inform the design and interpretation of human studies. In a second set of experiments, we evaluated the impact of food on both a model community and its constituent taxa by feeding gnotobiotic mice oscillating diets of disparate composition. In addition to prompt and reversible structural reconfigurations suggesting rules-based diet effects, we noted consistent, staggered changes in the representation of many functions within the metatranscriptome related to carbohydrate and amino acid metabolism. One prominent community member, Bacteroides cellulosilyticus WH2, was identified as an adaptive forager that tailors its versatile carbohydrate utilization strategy to the dietary polysaccharides available. The specific carbohydrates that trigger expression of many of this organism's 113 predicted polysaccharide utilization loci were identified by RNA-Seq analysis during in vitro growth on 31 distinct carbohydrate substrates, aiding our interpretation of in vivo RNA-Seq and high resolution proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota.


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