The human gastrointestinal tract is colonized by up to 100 trillion commensal microorganisms, termed the gut microbiota, which are known to influence host immunity and physiology through their metabolic activities. However, the biotransformations carried out by these bacteria remain poorly characterized at the enzymatic level, including which enzymes are active and how their activities influence host biology. This research will elucidate these host-microbe interactions and ultimately provide a mechanistic basis for the development of therapeutics and prophylactics for diseases that are influenced by the gut microbiota, including inflammatory bowel disease (IBD), cancer, allergy, and metabolic syndrome.