Dissecting the effect of diet on gut microbiome metabolism - Project Summary Gut microbiome products such as indole and phenol metabolites have major impacts on host physiology. Decreased production of these important metabolites is linked with many diseases, and increasing circulating concentrations of indole or phenol metabolites ameliorates inflammatory bowel disease or obesity in mouse models, respectively. Diet is a promising tool for treating microbiome-related diseases, as dietary modifications can affect both microbial composition and metabolism, but dietary control of indole and phenol production is still underexplored. Here, this work will dissect the effect of dietary components such as protein, fiber, and processing on microbial production of phenol and indole metabolites. The overarching hypothesis driving this work is that diet controls microbial metabolism through altering the balance of dietary or secreted protein available to the microbiome. Aim 1 will investigate the effect of protein digestibility and dietary processing on microbial metabolites. Liquid chromatography-mass spectrometry (LC-MS) will be used to measure circulating and fecal metabolites and 16S rRNA sequencing will be used to measure microbial composition in mice fed differentially processed (e.g. cooking, grinding) diets. Additionally, the contribution of dietary protein fermentation will be directly measured via 13C-labeled protein diets. Aim 2 will examine the effect of dietary fiber and mucin production on microbiome metabolism. Through isotope tracing and techniques developed by the Rabinowitz lab, and we will measure the contribution of microbial fermentation of host-secreted proteins to microbial metabolites. Additionally, dietary fiber can impact both the production of host-derived mucin as well as the abundance of bacteria that can ferment the mucin. In mice fed diets with different types of fiber (e.g. inulin, pectin, cellulose), mucous layer thickness will be measured through histologic staining, microbiome composition will be assessed by 16S rRNA sequencing of fecal samples, and metabolite concentrations in feces and serum will be analyzed via LC-MS. Completion of the work proposed here will provide a critical foundation for the understanding of dietary control on production of indole and phenol metabolites. By unlocking the potential for targeted dietary control of desired metabolites, this work could eventually facilitate dietary formulations to help treat patients suffering from microbiome-related diseases such as inflammatory bowel disease and obesity.
