Exploring the mechanisms of immunomodulation by a commensal Clostridium species

The microbiome is intricately linked to human health and, when dysregulated, can cause disease. It has been shown that specific members of the intestinal microbiota regulate immunity, a finding that offers an approach for treating autoimmune disease through microbiome engineering. In previously published work, we identified Clostridium immunis, a new human-derived commensal bacterial species that protects mice against colitis. To understand the host immunological response to C. immunis, we performed comprehensive flow cytometric analysis of the colonic immune system of C. immunis-treated mice. We observed a significant decrease in the number of group 3 innate lymphoid cells (ILC3s), a rare but critical tissue-resident immune cell population that has been implicated in autoimmune diseases. We hypothesize that C. immunisproduces a bioactive molecule that downregulates ILC3s. To identify the genetic determinants of ILC3 downregulation by C. immunis, we compared the ability of closely related clostridia to modulate ILC3-produced cytokines in a colonic explant model. By excluding genes encoded by two inactive clostridia strains, we managed to identify 40 genes that are associated with ILC3 modulation. We similarly observed that C. immunis culture supernatant contained activity. By excluding genes that have predicted intracellular products, we further narrowed this list to 8 candidate genes. Critically, we have recently developed a method to perform targeted genetic knockouts in C. immunis, and are currently generating mutants for these genes. This work will therefore identify the gene product required for ILC3 modulation and potentially identify novel classes of bacterially derived molecules to treat ILC3-driven disease.