Humans are colonized by trillions of microorganisms that exert a profound influence on health and disease. The unique chemical capabilities of the human microbiome play an important role in this process, but the microbial pathways and enzymes involved in these metabolic interactions are largely unknown. We believe that linking microbial activities with genes and enzymes holds the key to deciphering the biological roles of these organisms and unlocking their therapeutic potential, and we are forging these crucial connections by combining bioinformatics approaches with a chemical understanding of enzymes and metabolic pathways. We are investigating how gut microbes consume essential dietary nutrients (choline), produce DNA-damaging genotoxins (colibactin), and metabolize drugs (digoxin). By studying uncharacterized genes and enzymes in microbiome sequencing data, we are uncovering previously unknown microbial activities. Finally, we are demonstrating that a molecular understanding of gut microbial enzymes is critical for elucidating how these organisms influence host biology and developing methods to modulate their functions. Overall, our work is delineating a general experimental strategy for investigating gut microbial metabolism and its links to human health and disease. We believe these studies will lay the foundation for new therapeutic strategies targeting microbiomes rather than the human host.