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


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Thaddeus Stappenbeck


Inflammatory bowel disease: IBD) arises from complex interactions of genetic, environmental, and microbial factors. The intestinal microbiota is crucial for IBD induction and complex shifts in microbiota composition occur in IBD, but disease has not been consistently associated with presence or absence of a specific microbe. It is thus controversial whether fulfilling Koch's postulates for individual bacterial species is relevant to IBD and whether disease-associated alterations in microbial colonization are predictive of underlying etiology. Resolving these controversies has been challenging due to paucity of animal models with rapid disease onset, experimental reliance on gnotobiotic animals, and difficulty specifically isolating many commensal intestinal bacteria. We fulfilled Koch's postulates in a host genotype-specific fashion, using non-gnotobiotic methods to show that common commensal Bacteroides species induced disease in a genetic mouse model of IBD whereas an Enterobacteriaceae species that was significantly enriched during spontaneous disease was not itself sufficient for disease induction. We studied mice with a human-relevant IBD-susceptibility mutation which spontaneously develop intestinal inflammation resembling human ulcerative colitis. Antibiotics blocked colitis induction and mice remained disease-free after treatment cessation but developed disease if subsequently colonized with intestinal contents from untreated donors or with intestinal contents grown in mixed culture on media selective for Gram-negative obligate anaerobes. We therefore isolated common commensal Bacteroides species, introduced them into antibiotic-pre-treated mice, and confirmed colonization by specific, quantitative re-isolation in culture. Isolates colonized susceptible and non-susceptible mice equivalently but induced disease exclusively in susceptible animals, suggesting susceptibility was due to differences in host response rather than altered colonization susceptibility. In contrast to commensal Bacteroides, Enterobacteriaceae were >100-fold enriched in the microbiota during spontaneous disease in our mice, supporting observations in other animal models and in human patients. However an Enterobacteriaceae isolate from a spontaneously colitic mouse was not sufficient to induce disease in antibiotic-pre-treated animals despite robust colonization. We thus identified distinct subsets of commensals with and without IBD-inducing potential and showed that these subsets would not have been predicted based on disease-associated shifts in the microbiota. Our findings establish experimental criteria and a conceptual framework for understanding the intestinal microbiota's involvement in IBD.


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