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

January 2010

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Jeffrey Gordon


The adult human gut microbiota consists of hundreds to thousands of bacterial species, the majority belonging to the Bacteroidetes and the Firmicutes. Differences in the balance between these phyla has been linked to obesity in mice and humans. However, little is known about their interactions in vivo. I have used comparative and functional genomics, proteomics and biochemical assays to identify the ways they marshal their genomic resources to adapt to life together in the distal gut. I first annotated the complete genome sequences of two human gut Bacteroidetes (Bacteroides vulgatus and Parabacteroides distasonis) and two Firmicutes (Eubacterium rectale and E. eligens). By comparing the genomes of all sequenced gut Bacteroidetes and Firmicutes, I found that gut Bacteroidetes' genomes contain large groups of genes responsible for: i) sensing, binding, and metabolizing the varied polysaccharides that they encounter in the distal intestine; and: ii) constructing their polysaccharide capsules. These portions of their genomes have been shaped by lateral gene transfer, including phage and conjugative transposons, as well as by gene duplication. By colonizing germ-free mice with B. thetaiotaomicron, or B. vulgatus, or both species together, I documented that B. vulgatus upregulates its unique glycan-degrading enzymes to adapt to the presence of B. thetaiotaomicron. In contrast to the Bacteroidetes, the Firmicutes have smaller genomes, a significantly smaller proportion of glycan-degrading genes, and are suited to degrade a more specialized assortment of dietary carbohydrates. By colonizing germ-free mice with E. rectale and/or B. thetaiotaomicron, I showed that B. thetaiotaomicron, like B. vulgatus, upregulates its unique glycoside hydrolase activities to adapt to the presence of E. rectale, increasing its degradation of host-derived glycans that E. rectale cannot use. In contrast, E. rectale downregulates its polysaccharide degradation genes and upregulates nutrient transporters, likely allowing it to access sugars released by B. thetaiotaomicron's glycoside hydrolases. These models of the human gut microbiota illustrate niche specialization and functional redundancy within the Bacteroidetes, the adaptable niche specialization that likely underlies the success of Firmicutes in this habitat, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.


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