Fecal microbiota, short chain fatty acids, bile acids, and colonic transit in Irritable Bowel Syndrome

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PROJECT SUMMARY The precise mechanisms by which the gut microbiome and contributes to irritable bowel syndrome (IBS) symptoms are unclear. However , it is recognized that microbial metabolites such as short chain fatty acids (SCFA) and bile acids exert important effects on gastrointestinal physiology. Thus, an enhanced understanding of the relationships between the gut microbiome, SCFAs, and bile acids will be essential to developing novel strategies for effective IBS treatment. This career development application is submitted on response to PA-18- 374 in which the candidate proposes a hypothesis-driven research strategy to (1) identify changes in the fecal microbiota that are associated with SCFA and bile acid profiles in IBS, (2) establish SCFAs as an actionable IBS biomarker, and (3) interrogate interactions between SCFA and bile acids in IBS. This proposal builds on preliminary data acquired through the support of an institutional KL2. The specific aims of this research strategy are to (1) identify shifts in the relative abundance of SCFA-producing bacteria that are associated with fecal SCFA levels, markers of SCFA production through inulin fermentation (residual fecal inulin after inulin challenge), and colonic transit in IBS with constipation (IBS-C), IBS with diarrhea (IBS-D), and controls and (2) identify shifts in the relative abundance of bile acid dehydroxylating bacteria that are associated with fecal bile acids and markers of SCFA production in IBS-C, IBS-D, and controls and test if bile acid profiles are associated with markers of SCFA production. To achieve these aims, the candidate will develop a prospective cohort of well- phenotyped IBS patients and matched-controls who will undergo (1) baseline assessments of their fecal microbiota, fecal SCFAs, fecal bile acids, and colonic transit, followed by (2) repeat assessments of fecal microbiota, fecal SCFAs, fecal bile acids, as well as measurement of fecal inulin after standardized dietary intervention with inulin supplementation. The proposed career development plan integrates in-depth mentoring from a multidisciplinary team of senior scientists, advanced coursework in bioinformatics and microbiome analysis, experiential learning through the conduct of the proposed research, and a highly supportive research environment. The mentorship team, which includes independent investigators with expertise in clinical and translational research in microbiome science (Nelson) and functional gastrointestinal disorders (Camilleri); data analysis and biostatistics (Xu); bioinformatics (Dong); and career development (Chalasani) will guide the candidate's research and career development. The superb institutional infrastructure for facilitating junior investigators and substantial institutional commitment greatly strengthen this application. At the conclusion of the program, the candidate will be well positioned to become an independent physician investigator studying novel microbial and metabolomics biomarkers and novel interventions in IBS.