An engineered Clostridial consortia to interrogate immune modulation by secondary bile acids

We, and others, have linked the increasing prevalence of non-communicable chronic diseases (NCCDs), to changes in the composition and function of resident intestinal microbes. To gain insight into the mechanisms responsible for a bacteria-induced barrier protective response, we have examined the roles of various Lachnospiraceae products, including the short chain fatty acid butyrate and tryptophan metabolites and commensal flagellins. In this proposal we explore the immunomodulatory capacity of Lachnospiraceae-derived secondary bile acids (SBAs). Bile acids (BAs) have long been known as emulsifying agents which facilitate the absorption of dietary lipids in the small intestine. Emerging evidence shows that BAs also potently regulate mucosal and systemic immunity. In collaboration with the Mimee laboratory at the University of Chicago, we have used a group II intron-based approach to target 3b-HSDH, a terminal enzyme in the biosynthesis of isoDCA, in the prominent Lachnospiraceae species [Ruminococcus] gnavus. R. gnavus is among a small group of gut bacteria which possess both the 3a- and 3b- HSDHs required to epimerize DCA into isoDCA. By pairing this novel mutant R. gnavus with the Clostridial strain P. hiranonis we have created a two-strain consortium that allows us to toggle isoDCA production on and off (while keeping other bacterial products and metabolites constant) in mice with a replete microbiome. This innovative approach will enable an interrogation of the mechanisms by which Lachnospiraceae-derived isoDCA modulates host immunity at homeostasis and an assessment of its immunomodulatory potential in well-established models of intestinal inflammation. We hypothesize that isoDCA has anti-inflammatory effects on all levels of the intestinal immune system including intestinal epithelial cells and CD11c+ antigen presenting cells through the Farnesoid X receptor (FXR) and the G-protein coupled bile acid receptor (GPBAR1/TGR5). In the first Aim we will identify key cell types and signaling mechanisms involved in the immunomodulatory activity of isoDCA. We will then examine the mechanisms by which isoDCA ameliorates intestinal inflammation in Aim 2.