The large intestine houses hundreds of species of bacteria (often referred to as the gut microbiome or microbiota), including Firmicutes and Bacteroidetes. The species that are present can vary between individuals and depend on genetic factors, environmental factors, and diet. Intestinal bacteria feed off undigested material, such as starches and fiber that the body cannot digest on its own, including the carbohydrates in plant cell walls. Bacteria ferment these materials and release some nutrients that can be absorbed by the body. Fermentation reactions also produce flatus, gases such as carbon dioxide and methane, that are released from the intestines. Intestinal bacteria also synthesize vitamins that are important for human health including biotin, vitamin B12, and vitamin K. Furthermore, these bacteria are a critical component of the immune system—they protect the intestines from the colonization of pathogenic microorganisms by competing for space and available nutrients.
People often take antibiotics to help clear bacterial infections. Unfortunately, antibiotics target many types of bacteria, not just those causing the infection. This is a problem because antibiotics can kill the body's "good" intestinal bacteria. For this reason, many doctors suggest taking probiotics, or doses of healthy bacteria, to reconstitute the healthy gut bacterial community after the use of antibiotics. It is also thought that the appendix, a small hollow tube protruding from the large intestine, plays a role in cultivating gut microbiome to repopulate the intestines following illness.Because of the vast diversity of microorganisms that can enter and reside in the large intestine, scientists have categorized where these microorganisms live according to four distinct microenvironments or regions in the large intestine. The first region includes the epithelial surface and inner mucin layer of the large intestine. Very few colonies or groups of microorganisms are found here. Traveling deeper in the large intestine, more colonies of microorganisms are found in the outer mucin layer or diffuse mucin layer. By far, the most diverse group of microbiome reside in the lumen of the large intestine, which includes the lumen-liquid phase and gut-lumen substrate.