The human ‘metagenome’ is a composite of Homo sapiens genes and genes present in the genomes of the trillions of microbes that colonize our adult bodies (the ‘microbiome’). Our largest collection of microbes resides in the gut, where an estimated 10-100 trillion organisms reside (the gut microbiota). The gut microbiome encodes metabolic capacities that remain largely unexplored but include the degradation of otherwise indigestible components of our diet. Our recent metagenomic analyses of humans and mice have revealed linkages between distal gut microbial ecology, microbial community gene content, and host energy balance. Other studies have also demonstrated links between microbial ecology and human disorders such as Crohn’s disease, ulcerative colitis, and diabetes.
Despite the recent surge in human gut microbiome research (e.g. NIH HMP), a number of basic questions regarding the assembly, structure, and functional operations of the gut microbiome remain unanswered. Our research involves the development and application of computational and experimental methods for the analysis of community structure, gene content, and function of complex microbial communities. We plan to couple these techniques to additional experimental techniques such as functional metagenomics and in vitro cell culture to study the metabolic functions of the human gut microbiome, with potential implications for human health and nutrition.