We are colonized by trillions of microorganisms, including bacteria and fungi, which inhabit the external and internal surfaces of our bodies. It is becoming increasingly evident that these microbes play an important role in regulating many aspects of host physiology, including the immune system. For example, the bacteria in the gut are critical for the development and function of the immune system, as germ-free mice have an underdeveloped intestinal immune system.  In addition, perturbations to the populations of commensal bacteria have been linked to autoimmunity and chronic inflammatory conditions, such as inflammatory bowel diseases and metabolic syndrome.

The overall theme of our research is to understand how the host immune system is regulated by the gut microbiota through their secretion of small molecule metabolites. Our research focuses primarily on two areas: (1) the identification of metabolites produced by the gut microbiota that regulate inflammation during inflammatory bowel diseases and host defense during gastrointestinal infection with enteric pathogens; and building on these discoveries, (2) the development of chemical tools to modulate the immune response and to probe metabolic reactions catalyzed by the gut microbiome. We employ biological and chemical approaches including the tools of molecular and cellular immunology, microbiology, chemical biology, chemistry, biochemistry, and cell biology to elucidate key communication pathways between the gut microbiota and the host immune system. Our ultimate goal is to understand how immune homeostasis and host defense are regulated in the intestines, as such discoveries would have broad implications for the development of therapeutics and prophylactics for many inflammatory diseases.