Project Summary / Abstract The human microbiome plays a vital role in health and disease. However, the ways in which bacteria affect the human host at a molecular level remain poorly understood. In order to harness connections between the microbiome and disease to improve human health, we need to know more about the molecules and chemical mechanisms driving host-microbiota interactions. The long-term goal of my laboratory is to understand and control the chemistry of human-associated bacteria in order to uncover how the microbiome affects human health and disease. We are prioritizing the study of human gut bacterial metabolism of host-produced small molecules (endobiotics) and how the resultant compounds affect host physiology. Endobiotics such as steroids and vitamins act as crucial signaling molecules and regulators of host biology, but their metabolism by gut bacteria has been relatively unexplored. We aim to uncover the biosynthetic pathways and biological roles of host-produced, bacterially modified metabolites. We are also expanding the scope of our studies of microbiome metabolites to study novel transformations of host- and diet-derived metabolites by microbiome bacteria and how these metabolites affect the host. With the support of an NIH ESI MIRA grant, my group has established a track record of discovering gut microbial metabolites of bile acids, elucidating how these compounds are biosynthesized, and determining the effects of these compounds on the host. We have demonstrated that we can advance microbiome research from molecule discovery to in vivo effects. These studies have allowed us to establish a roadmap for the proposed studies investigating microbiome metabolites more broadly. Over the next five years, we will (1) discover new chemical transformations by human-associated bacteria that lead to bioactive metabolites, (2) investigate the effects of microbiome metabolites on host physiology, including host immune response, metabolism, and neurological function and behavior, and (3) identify active enzymes responsible for keystone microbiome transformations using comparative metabolomics and chemoproteomics. By taking a chemically guided approach to understanding both the production and in vivo functions of microbiome metabolites, we will gain a more complete understanding of these molecules and their biological activities than has ever been established. This work will provide us with a deeper understanding of how gut bacterial metabolism of host- and diet-derived compounds functions on a molecular level and how this activity affects host physiology. Our research program will also lay the groundwork for the rational manipulation of the microbiome in a clinical context to treat disease and improve health.