The human intestines are colonized by trillions of microorganisms, termed the gut microbiota, which are thought to rival the number of our own cells. Together, these microbes metabolize small molecules within the intestinal lumen through the activities of bacterial enzymes that carry out biochemical transformations. Growing evidence suggests that these small-molecule metabolites confer major benefits to host physiology. However, the enzymes and biochemical pathways that produce these molecules remain poorly understood.

This proposal seeks to develop chemical approaches to understand the metabolic activity of the gut microbiome to better understand metabolite production in the gut and how it contributes to health and disease. The overarching hypothesis guiding this work is that activity-based protein profiling can be used to identify active bile acid metabolizing enzymes within the gut microbiome, which produce secondary bile acids that have critical functions in physiology and disease, and to identify bacterial proteins regulated by bile acids that play important roles in microbial metabolic crosstalk. We will address this hypothesis with the following studies:

Develop chemical probes for identifying active bile acid metabolizing enzymes. Building on our systems biochemistry approach, we will develop activity-based probes to target important enzymes in secondary bile acid metabolism within the gut microbiota. These studies will globally identify individual gut bacteria that are actively producing bile acid metabolites, which cannot be addressed with traditional biochemical approaches.

Characterize bacterial proteins that utilize or are regulated by bile acids. We will apply these chemical probes to identify bacterial proteins that are bile acid interacting proteins and characterize the roles of bile acids in regulating their activities. These results will advance our understanding of metabolic crosstalk between gut bacterial pathogens and commensal bacteria.

Visualize gut microbiota-associated bile salt hydrolase activity in health and disease. We will apply the chemical probes to image active bile acid metabolizing enzymes within the intestinal tissue from mice in both health and disease. These studies will determine the localizations of gut bacterial niches that are actively metabolizing bile acids during gut epithelial damage and inflammation that are affected by maladaptive changes to gut microbial composition.

Current technologies based on metagenomics are limited in their ability to report on genes that are present within the microbiome. Our chemical approach will define how activities of enzymes within the gut microbiome carry out metabolism of important small-molecule metabolites that regulate host physiology and pathology. Broadly, our tools will contribute to a deeper understanding of host-gut microbiota interactions and how this complex relationship influences human health and disease.