The goals of the Sonnenburg Lab research program are to (i) elucidate the basic mechanisms that underlie dynamics within the gut microbiota and (ii) devise and implement strategies to prevent and treat disease in humans via the gut microbiota. We investigate the principles that govern gut microbial community function and interaction with the host using experimental systems ranging from gnotobiotic mice to humans. We pursue molecular mechanisms of host-microbial interaction using an array of technologies including gnotobiotic and conventional mouse models, quantitative imaging, molecular genetics and synthetic biology, and a metabolomics pipeline focused on defining microbiota-dependent metabolites. The synergy of these diverse techniques provides insight into the dynamics of a microbial ecosystem in response to cues ranging from nutrition to pathogen-induced inflammation. Studies of microbiomes diverse human cohorts, ranging from indigenous populations in Africa, Asia, and South America to dietary intervention trials in cohorts of US residents, have provided great insight into