The gut microbiota in humans evolve throughout life and appear to play a pivotal role in both health and disease. In a healthy state, the gut microbiota have myriad positive functions, including energy recovery from metabolism of nondigestible components of foods, protection of a host from pathogenic invasion, and modulation of the immune system. A dysbiotic state of the gut microbiota is becoming recognized as an environmental factor that interacts with a host’s metabolism and has a role in pathological conditions, both systemic—obesity, diabetes, and atopy—and gut-related IBS and IBD, although the specific contribution of the gut microbiota to these diseases is unclear. The heterogeneous etiology of metabolic and gastrointestinal diseases has been associated with different microbes, although little information exists about the causal direction of the association.