An Engineered Clostridial Mini-Consortium Modulates Intestinal Inflammation

We have proposed that 21st century lifestyle factors have changed the composition and function of the commensal microbiota. We identified bacteria in the Clostridia class as key immunomodulatory taxa and examined the mechanisms by which Clostridial products protect against noncommunicable chronic diseases. Recent evidence suggests that secondary bile acids (SBAs), unique metabolites of Clostridia, can directly modulate host immunity. Here we report a novel system to study isodeoxycholic acid (isoDCA), one such SBA, and interrogate its immunomodulatory effects relevant to maintaining intestinal homeostasis. In this first report of mutagenesis of bile acid epimerization genes, we engineered [Ruminococcus] gnavus (now classified as Mediterraneibacter gnavus) to ablate isoDCA production. Combining R. gnavus (WT or KO) with Peptacetobacter hiranonis created a unique two-member consortium that allowed us to turn isoDCA production “on” or “off” holding everything else constant. Using this system, we showed that isoDCA induces colonic lamina propria RORγt⁺Foxp3⁺ regulatory T cells (pTregs), an immunosuppressive subset of gut Tregs that are implicated in protection from chronic diseases both clinically and in murine disease models. We demonstrated a requirement for the Takeda G protein-coupled receptor 5 (TGR5) in isoDCA-mediated colonic lamina propria RORγt⁺Foxp3⁺ pTreg induction. Lastly, we used our system to demonstrate that our isoDCA+ consortium protects from colitis in the CD45RB^hi adoptive T cell transfer model by both modulating microbiota composition and inhibiting host inflammatory responses. Taken together, this work defines a novel approach for studying a prominent gut metabolite, highlighting its immunosuppressive effects and importance for the maintenance of intestinal homeostasis.