The Host and Microbial Determinants of Activity by Commensal Clostridium immunis

Abstract

The microbiota—the diverse collection of commensal microorganisms that normally colonizes mucosal and skin surfaces—plays a fundamental role in controlling various biological processes, including metabolism, immune responses and behavior. Although there have been increasing successes in identifying commensal bacteria that causally impact different host functions, the specific mechanisms by which these bacteria work remain poorly understood. Using Clostridium immunis—a human gut commensal bacterium—as a prototypical immunomodulatory microbe, we dissect the host and bacterial mechanisms of its activity. Through this, we unravel an intriguing and potentially generalizable strategy by which certain commensal bacteria uniquely regulate certain immune cells. In Chapters 3 and 4, we define the host cellular and molecular requirements for immunomodulation by C. immunis. In Chapter 3, we use transcriptomic analysis of C. immunis treated mice to reveal that C. immunis negatively regulates a lipid metabolism pathway driven by group 3 innate lymphoid cell (ILC3) activity. Using mice genetically deficient in ILC3s, we demonstrate using two distinct animal models—lipid metabolism and adiposity, as well as colonic inflammation, that group 3 innate lymphoid cell (ILC3) function is regulated by C. immunis. In Chapter 4, we further show that C. immunis regulates adiposity and colitis in a context- and ILC3 effector-dependent manner. In Chapters 5 and 6, we delineate the bacterial mechanisms of activity. In Chapter 5, using comparative genomics and biochemical fractionation, we identify a C. immunis-derived exopolysaccharide (EPS) that is sufficient to recapitulate its ILC3-regulating activity. In Chapter 6, we demonstrate that a phosphocholine moiety on the EPS is associated with bioactivity. To attribute a causative role for phosphocholine on EPS, we performed targeted reverse genetics in C. immunis to disrupt the cognate phosphocholine processing locus. Through this, we show that phosphocholine-modification of the EPS is essential for activity. Considered together, we identify a commensal bacterial species, its biochemical product, and a molecular determinant thereof that regulate ILC3 function in vivo. Broadly, our findings suggest that the specific ability of certain commensal bacteria to modulate host immunity is dependent on small-molecule modifications of classical microbial products.