Individuals vary widely in drug response. Microbes in the human gastrointestinal tract influence drug metabolism at multiple levels, but we cannot currently predict whether an individual's gut microbial community (microbiota) predisposes them towards efficient or inefficient metabolism of almost any drug. The long-term goals of this research program are to understand the mechanisms that create interpersonal variation in human gut microbial communities and to measure how this variation impacts drug metabolism. We describe experiments that will uncover how three general mechanisms (direct bacterial interaction, small molecule exchange, and host modulation of the microbiota) determine microbiome dynamics. First, wildtype and genetically manipulated human gut symbionts will be studied in vitro and in gnotobiotic mouse models. Next, genomic analyses and epidemiological modeling will be used to connect experimental results from genetically tractable human gut anaerobes to the entire microbiome. Defined assemblies of human gut microbes will then be examined in vitro and in gnotobiotic mice in order to test predictions from the experimental and computational data. In parallel, we will also apply these approaches to dissect the consequences of microbiome variation on metabolism of 5-aminosalicylate (5-ASA), a front-line drug for ulcerative colitis that is directly modified by bacterial enzymes. This proposal presents plan to integrate drug responsiveness results from patients initiating or currently taking 5-ASA with in vitro and gnotobiotic animal studies of 5-ASA metabolism by their microbiomes. Together, these studies will provide key mechanistic insights critical for adding or removing species in human gut microbiomes in a predictable and stable manner; for manipulating individuals' microbiomes in order to improve medical therapy, and for measuring the contribution of the microbiome to individual drug responses.
Humans carry enormous gut microbial communities that vary widely between individuals. Because interactions between these bacteria and with the host are not understood, we lack the ability to predict how these communities will function or to manipulate the microbiome to promote health or desired responses to medical therapy. This research program will identify mechanisms that shape microbial community variation and define how this variation impacts drug response.
