Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity

The
metagenome of the gut microbiome encodes tremendous potential
for biosynthesizing and transforming small-molecule metabolites through
the activities of enzymes expressed by intestinal bacteria. Accordingly,
elucidating this metabolic network is critical for understanding how
the gut microbiota contributes to health and disease. Bile acids,
which are first biosynthesized in the liver, are modified in the gut
by enzymes expressed by commensal bacteria into secondary bile acids,
which regulate myriad host processes, including lipid metabolism,
glucose metabolism, and immune homeostasis. The gateway reaction of
secondary bile acid biosynthesis is mediated by bile salt hydrolases
(BSHs), bacterial cysteine hydrolases whose action precedes other
bile acid modifications within the gut. To assess how changes in bile
acid metabolism mediated by certain intestinal microbiota impact gut
physiology and pathobiology, methods are needed to directly examine
the activities of BSHs because they are master regulators of intestinal
bile acid metabolism. Here, we developed chemoproteomic tools to profile
changes in gut microbiome-associated BSH activity. We showed that
these probes can label active BSHs in model microorganisms, including
relevant gut anaerobes, and in mouse gut microbiomes. Using these
tools, we identified altered BSH activities in a murine model of inflammatory
bowel disease, in this case, colitis induced by dextran sodium sulfate,
leading to changes in bile acid metabolism that could impact host
metabolism and immunity. Importantly, our findings reveal that alterations
in BSH enzymatic activities within the gut microbiome do not correlate
with changes in gene abundance as determined by metagenomic sequencing,
highlighting the utility of chemoproteomic approaches for interrogating
the metabolic activities of the gut microbiota.