Gut Environment and Evolution of Mutualistic Fermentative Digestion

The gastrointestinal tract is a specialized tube divided into various well-defined anatomical regions extending from the lips to the anus. However, for the purposes of this series concerning the ecology, physiology, metabolism, and genetics of gastrointestinal microbes, discussion is restricted to the stomach (rumen-reticulum, crop, gizzard), small intestine, and large intestine (cecum and colon). Large populations of microorganisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture comprising bacteria, ciliate and flagellate protozoa, anaerobic phycomycete fungi, and bacteriophage can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological, and protective functions of the host animal. Development of microbial populations in the alimentary tract of higher animals commences soon after birth. The processes involved in the establishment of microbial populations are complex, involving succession of microorganisms and many microbial and host interactions eventually resulting in dense, stable populations inhabiting characteristic regions of the gut.