Bile acid metabolism by gut bacteria

Abstract

The human gut microbiome significantly affects host biology. In particular, gut bacteria modify important pools of molecules that impact host physiology. Therefore, further studies of gut bacterial metabolism will provide insights into the significance of gut bacteria and their impact on host health and disease. Here, I describe my projects that aimed to contribute to our understanding on the gut bacterial modifications of bile acids. Chapter 2 describes our use of a chemical tool to modulate gut bacterial metabolism in vivo. AAA-10 inhibits bile salt hydrolase (BSHs), enzymes that catalyze the gateway step for all gut bacterial metabolism of bile acids. We showed successful modulation of bile acid pools using AAA-10 in both monocolonized and conventional mice, which led to significant changes in metabolic phenotypes and host gene expression, respectively. AAA-10 treatment improved glucose tolerance and reduced liver steatosis in monocolonized mice, while AAA-10 treatment led to preliminary gene expression changes in genes related to the circadian rhythm and immune response in conventional mice. These studies will serve as a guide for future in vivo experiments modulating gut bacterial metabolism of bile acids. However, AAA-10’s effectiveness as a BSH inhibitor in vivo has room for improvement, and my efforts to understand mechanisms of insensitivity to AAA-10 are presented in Chapter 3. Here, we describe our discovery of a bacteria strain, Lactobacillus intestinalis ASF 360, that has a strong BSH activity that is insensitive to AAA-10 inhibition. Using heterologous expression and bacterial assays, we showed evidence for a transport mechanism that may be involved in removing the inhibitor from the cell during normal growing conditions. We also discovered a new lead inhibitor, DCA-FMK, that inhibited BSH activity in L. intestinalis. Our new lead inhibitor together with our understanding of the resistance mechanism will guide us towards developing a next-generation BSH inhibitor. Finally, Chapter 4 describes our efforts to elucidate the biosynthesis of the bile acid metabolite isoallolithocholic acid (isoalloLCA), a compound that enhances the differentiation of naïve T cells into Treg cells both in vitro and in vivo. Using a combination of microbial genetics, protein expression, analytical chemistry, and synthetic organic chemistry, we identified a gene cluster that is responsible for isoalloLCA production in the abundant gut bacterial phylum Bacteroidetes. We showed that the gene cluster is necessary and sufficient for both in vitro and in vivo production of isoalloLCA, and both isoalloLCA and the isoalloLCA-producing genes are associated with inflammatory bowel disease (IBD) in human patients. These results highlight a new mechanism by which gut bacterial metabolism mediate host immune tolerance. Overall, my projects cover a range of topics about gut bacterial metabolism of bile acids. Together, these studies contribute to our understanding of how gut bacteria impact on host health and disease by chemically modifying compounds found in the gut.