Dietary fiber and soy protein-based microbiome metabolites for IBD prevention

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Summary The precise etiology of inflammatory bowel disease (IBD) remains unknown. Despite identification of >100 human genetic polymorphisms that are thought to play a role in IBD, genetic predisposition typically explains only a fraction of disease risk. Important contributions for environmental factors—including diet and the gut microbiota—have become prominent suspects as additional disease drivers. However, the functional interconnections between these potential contributors remain unknown. Using a gnotobiotic mouse model, in which animals were colonized with a synthetic human gut microbiota composed of fully sequenced and metabolically characterized commensal bacteria, we have begun to elucidate the mechanistic interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defense against encroachment by intestinal bacteria. During dietary fiber deficiency, the gut microbiota resorts to host- secreted mucus glycoproteins as a nutrient source, leading to erosion of the mucus layer. Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium. More strikingly, when this same synthetic microbiota is assembled in mice deficient in interleukin 10 (IL-10), a cytokine for which loss of function defects have been associated with human IBD, animals develop lethal spontaneous inflammation in the absence of an overt pathogen, but only on a low fiber diet. Our work has therefore revealed functional interconnections between diet, the gut microbiota, mucosal barrier function and spontaneous IBD development. Our central hypothesis is that there is a dynamic balance between fiber- and mucus-degrading bacteria, such that in low fiber conditions the mucus layer is increasingly eroded resulting in temporal disease progression that can be ameliorated by preventative or therapeutic fiber consumption or other bacterial metabolites that counterbalance inflammation. The proposed work will extend the findings outlined above by first measuring the respective contributions of mucin-degrading bacteria and their functions towards eroding the mucosal barrier and precipitating inflammation. We have already established that addition of several pure fibers to our fiber deficient diet reduces disease and have fortuitously discovered that inclusion of soy (but not milk) protein also reduces disease in part by promoting production of the branched chain fatty acid isobutyrate. Isobutyrate is produced from L-valine and our hypothesis is that soy protein delivers a peptide-based source of this amino acid to the colon for bacterial metabolism. Because isobutyrate is a poorly studied metabolite, we will investigate its microbial source(s) and mechanism of action in dampening host inflammation. We anticipate that our findings will provide functional insight into the constellation of genetic and environmental triggers that conspire to precipitate IBD. As such, our findings will provide paths to future research in humans, which are built on a foundation of functional knowledge of diet-microbiota interactions gathered in a tractable model.