Host-microbe interactions shaping the gastrointestinal environment

Tremendous advances have been made in mapping the complexity of the human gut microbiota in both health and disease states. These analyses have revealed that, rather than a constellation of individual species, a healthy microbiota comprises an interdependent network of microbes. The microbial and host interactions that shape both this network and the gastrointestinal environment are areas of intense investigation. Here we review emerg-ing concepts of how microbial metabolic processes con-trol commensal composition, invading pathogens, immune activation, and intestinal barrier function. We posit that all of these factors are critical for the mainte-nance of homeostasis and avoidance of overt inflamma- tory disease. A greater understanding of the underlying mechanisms will shed light on the pathogenesis of many diseases and guide new therapeutic interventions.