Bacterial adaptions in host-microbe interactions.

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PROJECT SUMMARY/ABSTRACT Inflammatory bowel disease (IBD) has long been associated with compositional and metabolic changes in the gut microbiota, yet extensive research efforts have failed to identify a single pathogenic microorganism as the causative agent. In this grant, we investigate an alternative hypothesis in which gut inflammation drives adaptations in commensal bacteria that further exacerbates disease in IBD. Though bacterial adaptations are necessary for commensal survival and persistence in the inflamed gut, we currently do not understand how these adaptive strategies alter the function of commensal microbes. These include metabolic and immunomodulatory activities of commensal bacteria that regulate mucosal immune homeostasis in health and disease. Thus, there is a critical need to understand how the inflamed gut environment shapes commensal bacteria metabolism to further exacerbate inflammation in IBD. The long-term goal of this study is to understand how gut bacteria direct immune responses in order to develop rational microbial therapies for inflammatory diseases. Our central hypothesis is that the oxygenated environment of the inflamed gut drives metabolic adaptations in commensal bacteria, resulting in expansion of bacterial strains that exacerbate intestinal inflammation. The central hypothesis will be tested by pursuing three specific aims: 1) define the genetic and functional variation of commensal Bacteroides fragilis in the IBD gut; 2) determine the metabolic adaptations of commensal bacteria during experimental colitis; and 3) identify the impact of oxygen on anaerobic bacterial metabolism and immune modulation. We will examine the genetic variation of B. fragilis strains from healthy and IBD cohorts. This information will enable the construction of strain-specific B. fragilis genome-scale models to elucidate the metabolic output and phenotypic states of IBD-associated strains. Next, we will determine the genetic adaptations of B. fragilis in mouse models of colitis and test the impact of intestinal inflammation on bacterial metabolism and immune modulation. Finally, we will examine how oxygen-adapted strains of B. fragilis may have metabolic and immunological consequences on intestinal homeostasis. The proposed research is significant because defining commensal bacteria adaptations to early stages of gut inflammation will be a powerful strategy for detecting and treating early stages of IBD and preventing progression into the debilitating chronic phase of IBD.