The human body is colonized by trillions of microorganisms that exert a profound influence on human biology, in part by providing functional capabilities that extend beyond those of host cells. In particular, there is growing evidence linking chemical processes carried out by the microbial inhabitants of the gastrointestinal tract and cervicovaginal environment to both health and disease. However, we still do not understand the vast majority of the molecular mechanisms underlying this phenomenon. This talk will discuss my lab’s efforts to discover, characterize, and manipulate gut and vaginal microbial enzymes and metabolic pathways, including transformations that produce disease-associated microbial secondary metabolites. Gaining a molecular understanding of microbial biosynthetic pathways will not only enhance our ability to identify the genes encoding these activities in microbiome sequencing data but will also help to elucidate the mechanisms by which these organisms affect human biology. Ultimately, this work could enable efforts to improve health outcomes by manipulating gut and vaginal microbial metabolism.