The microbes that live in and on us direct our immune status, susceptibility to disease, physiological development and metabolism. DNA sequencing of the microbial community in humans and animals during disease and health allows us to examine critical changes in this community that influence our well-being. These studies are supplemented with detailed transcriptomic, proteomic and metabolomic data that reveal the underlying biochemical processes of these microbes that dictate health status. One research area is how the gastrointestinal community (gut microbiota) influences susceptibility to enteric pathogens including Clostridium difficile and E. coli as well as the progression of inflammatory bowel diseases and colorectal cancer. Other research efforts involving the gastrointestinal community includes how individual bacterial species harvest carbohydrate nutrition from the host diet in order to persist in the gut environment. The microbial ecology of mucosal surfaces including the gut, lungs, nasal cavity and vagina and the influence of these microbes in shaping mucosal immunity are also active areas of research. We are also using genomics to understand the evolution of antibiotic resistance and track bacterial pathogen outbreaks.