The Gut Microbiota

Of all human body sites, the gastrointestinal tract (gut) houses the most substantial collection of microorganisms. The colonic microbiota, to a lesser extent the oral microbiota, appears especially important in health and disease. Major factors that influence bacterial colonization throughout the digestive tract are oxygen, pH, and peristalsis; as food travels downward through the digestive tract, it encounters a series of environments with generally increasing bacterial loads and different bacterial taxa. In the small intestine, the body must defend against pathogenic bacteria while allowing the uptake of nutrients, water, and electrolytes; many of the body's immune defenses are located in this region. Thus, the gastrointestinal immune system known as the gut-associated lymphoid tissue has a complex system for protecting the intestinal epithelium from bacteria. Gut microbiota can influence the brain via the gut-brain axis: through neuronal activation (with the vagus nerve being particularly important), endocrine signals, and immune pathways. And while bacterial members of the microbiota have been the most studied to date, an abundance of other microorganisms is present in the normal gut microbiota—including eukaryotes, viruses, and archaea—but scientists know very little about their influence on bacterial communities or on health and disease.