ABSTRACT
This chapter argues that the gastrointestinal tract (GIT) is essentially a tubelike structure consisting of a number of anatomically distinct regions each of which has different environmental characteristics and, consequently, harbors a distinct microbiota. It finds that the GIT is one of the largest body surfaces in contact with the external environment, harbors the vast majority of human microbial symbionts, and is home to an overwhelming variety of bacteria, archaea, fungi, viruses, and protozoa. The GIT consists of a number of anatomically and functionally distinct regions—the oral cavity, the pharynx, esophagus, stomach, small intestine and the large intestine. Mucosa-associated lymphoid tissue is also abundant in the small intestine and is present both as solitary lymphatic nodules and as aggregated lymphatic follicles known as Peyer's patches. Many environmental features of the GIT remain unknown because most of its regions are difficult to access and/or involve sampling procedures that are uncomfortable or embarrassing for the individual or are unethical.
