The microbiota is now well-accepted as a major contributor to human health. However, the molecular bases for its impacts remain largely unknown. To address this knowledge gap, my lab has pioneered the development of “functional profiling” technologies that use microbial interactions with the host as a lens to identify causal microbes and their mechanisms of action. Many of these technologies leverage recent developments in synthetic biology and next-generation sequencing to explore thousands of possible molecular-level interactions between indigenous microbes (and their products) and potential host receptors. We assess the causal effects of these interactions on mammalian physiology using a combination of anaerobic ‘culturomics’ (to isolate microbial strains of interest) and reductionist gnotobiotic mouse models (e.g., germ-free mice colonized with simplified microbial communities). Finally, we have a long-standing interest in discovering and characterizing novel immunostimulatory strains from the human gut microbiota and dissecting the co-evolutionary dynamics of host-microbiota interactions. Overall, our studies establish both conceptual frameworks and experimental tools to understand how and why our microbial inhabitants have such wide-reaching impacts on human health and disease.
Allergy and Immunology; Gastrointestinal Diseases; Homeostasis; Humans; Inflammation; Microbiology; Microbiota