Deconvoluting host‐gut microbiota co‐metabolism

Abstract

The metagenome of the gut microbiome encodes tremendous potential for the biosynthesis and transformation of small‐molecule metabolites through the activity of many enzymes expressed by the intestinal bacteria. The metabolic activity of this gut bioreactor provides numerous important functions for the host, including breaking down indigestible components of our diet, biosynthesizing essential vitamins and nutrients, and regulating the development of our immune system. Accordingly, elucidating the metabolic potential of the multitude of potential enzymatic reactions is critical for understanding how the activities of the gut microbiota contribute to human health and physiology. Therefore, there is a critical need for new technologies that can determine the enzymatic activities of the gut microbiome because these activities cannot be directly determined by existing metagenomic approaches used to profile microbial taxonomy by genetic content. Activity‐based probes, which are mechanism‐based covalent tags for enzyme active sites, represent a powerful chemical approach for directly identifying and profiling enzymatic activities. Here, we have developed activity‐based probes for a class of cysteine proteases known as bile salt hydrolases (BSHs), which are master regulators of gut microbial transformation of host‐derived, or primary, bile acids into a large and diverse group of secondary bile acids. These important metabolites regulate myriad host biological processes, including lipid metabolism, energy metabolism, and immune homeostasis. In addition, changes in bile acid levels are known to accompany different physiological states. However, the role of BSH activity in these processes remains poorly understood due to the lack of adequate tools to address its function. To address this critical gap in knowledge, we have applied our chemical approach to profile BSH activity in gut microbiomes using healthy and diseased samples.