Physiology of bacterial metabolism in the human gut microbiome

Summary: One of the biggest gaps in our knowledge of the human gut microbiome is how microbes secure the energy and nutrients required to sustain their growth. This is an important deficit in light of the fact that microbial pathways produce short chain fatty acids like butyrate, indoles like indolepropionic acid, and amines like trimethylamine, all of which play a critical role in host physiology and disease. Understanding the metabolic processes that underlie why microbes make these molecules is critical for developing strategies to predictably control the metabolic output of the gut microbiota. Despite the importance of microbial metabolism in the gut to human physiology, we know very little about the nature of these metabolic pathways. A key gap in knowledge is how pathways for high abundance metabolites is linked to the physiology of commensal bacteria. Knowledge of these metabolic strategies is critical to developing strategies aimed at predictably modulating the metabolic output of the gut microbiota. One of the major challenges to studying the gut microbiota is that genetic tools are only available for a small subset of bacteria. Therefore, new tools are urgently needed to study the physiology and metabolism of genetically intractable microbes. In this project, we will use techniques in bacterial physiology and genetics to uncover how microbes in the gut capture energy from dietary nutrients, and how these processes contribute to drug-like small molecules that influence host physiology. We will also develop a new metabolomics approach to generate genome-wide maps of genetic determinants of microbial small molecules in genetically tractable and intractable gut bacteria. These studies will provide fundamental insights into several of the microbiome's core functions and will stimulate future avenues for inquiry into the human gut microbiome.