Humans harbor large microbial communities in the gastrointestinal tract. This collection of microbes (microbiota) and their associated genes (microbiome) affect many aspects of our physiology. Host diet determines gut microbial metabolism, which in turn modifies the nutritional impact of many dietary components. Thus, in principle, the gut microbiota can be targeted through diet to promote health. However, to successfully manipulate this microbial bioreactor, we need to understand how microbes metabolize nutrients, how they interact with each other as a function of diet, and their impact on the host. The overall goal of our research is to dissect diet by microbiota interactions that impact human health, so that therapeutic/preventive dietary recommendations can be made based on the metabolic potential of a subject’s microbiome. Gut microbial metabolism of specific dietary components (e.g., choline, flavonoids) generates compounds that can impact cardiovascular diseases. The microbes responsible for such transformations, and their representation in humans remain poorly characterized. Projects in my lab aim at identifying human gut bacterial species that transform some of these compounds, the genes involved in these processes, their regulation and their impact in the development of cardiovascular disease. Towards this end, we are using gnotobiotic mouse models of cardiovascular disease, bacterial genetics, transcriptional profiling and metabolomics.