The human gut microbiome is made up of a diverse set of bacterial species that have the potential to impact biological processes such as drug metabolism. Gut bacterial species and their enzymes have been shown to metabolize some drugs through enzymatic conversion into their metabolites, known as microbiome-derived metabolism (MDM). One such drug is the immunosuppressant mycophenolate mofetil (MMF), commonly used in organ transplantation and known to be metabolized into its active metabolite, MPA, by bacterial esterases. However, the specific bacterial strains and their corresponding enzymes responsible for this metabolism remains unclear. This thesis identifies a bacterial strain isolate and an enzyme responsible for MMF metabolism by the gut microbiome. Using MDM assays, I screened six gut bacterial strain isolates for their ability to convert MMF to MPA, identifying the gut bacterial strain, Prevotella copri, as a robust metabolizer of MMF. To investigate which P. copri enzyme drove this metabolism, I heterologously expressed six P. copri-encoded esterase enzymes and similarly screened their ability to convert MMF to MPA. This revealed a P. copri carboxylesterase, PC5, as the primary enzyme responsible for MMF metabolism by the strain. To evaluate whether these findings of MMF metabolism in bacterial isolation predict MMF metabolism in gut microbial communities, I correlated P. copri relative abundance and PC5 abundance with MMF metabolism across 20 individual gut microbial communities. Neither P. copri nor PC5 significantly predicted MMF metabolism across gut microbial communities, suggesting that additional bacterial strains and enzymes also contribute to MMF metabolism when in complex microbial communities. These findings provide insight into the role of P. copri in MMF metabolism and highlight the need for further characterization of MMF metabolism within microbial communities to improve predictions of microbiome-driven drug metabolism.

The symbiotic relationship between bacteria and humans can be readily observed in the human gastrointestinal (GI) tract, where gut bacteria play a role in immune system functions and metabolism. Healthy individuals have diverse and stable microbiomes, and disruption of this microbiome composition correlates with disease. To understand bacterial involvement in human processes and elucidate microbe-host interactions, it is important to study how bacteria regulate their own behavior. Small regulatory RNAs (sRNAs) are one of the mechanisms by which bacteria control gene expression and respond to environmental stimuli. Cis-encoded antisense sRNAs bind mRNA targets with full complementarity and post-transcriptionally regulate mRNA translation. Since few asRNAs have been experimentally confirmed, this study computationally selected two potential mRNA-asRNA pairs from Bacteroides thetaiotaomicron using sequencing data of bacterial RNA transcripts from human fecal samples. A previously designed computational pipeline annotated noncoding RNAs in this metatranscriptomic dataset by potential gene, identifying the selected sod and cshA genes as encoding superoxide dismutase [Mn/Fe] and ATP-dependent RNA helicase CshA, respectively. This work establishes a model for experimentally identifying biologically relevant asRNAs by co-expressing asRNAs and their mRNA targets in Escherichia coli.