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Some indigenous microbes form climax communities on gastrointestinal epithelial surfaces during succession in animals of many types. Most communities form in mucous layers on the surfaces, where some microbes in the communities may utilize the mucin as a source of carbon and energy. The mucous gel may also serve physically to stabilize the community. Some microbial types that colonize early during succession may serve, perhaps synergistically with dietary components, to lower the oxygen tension and oxidation-reduction potential so that oxygen-intolerant anaerobes can colonize the epithelial surfaces. Microbes in the communities may adhere to the epithelial surface; the mechanisms by which they adhere may depend upon a variety of factors, including the type of epithelium and the rate of flow of lumenal contents in the areas. Dietary fiber may influence the composition of these communities by providing nutrients for the microbes or altering their environmental conditions including peristaltic rate, mucous concentration and composition, and oxygen tension and oxidation-reduction potential.

Indigenous microorganisms of numerous types associate with epithelial surfaces in the gastrointestinal tracts of mammals and birds. Some of the microbial types, e.g., Lactobacillus sp. in the stomachs of laboratory rodents, adhere to a surface without altering it ultrastructurely. In such cases, the adherence is mediated undoubtedly by macromolecules on the bacterial surfaces, possibly polysaccharides in most cases, interacting in specific ways with receptor macromolecules on the epithelial surface. Other microbial types that associate with epithelial surfaces without altering them ultrastructurally, e.g., Clostridium 109-2 in the mouse large bowel, may adhere to the surface only weakly or not at all, and maintain the association because they are motile and attracted to the epithelium by chemotactic substances. Microbial types that alter the ultrastructure of the epithelial cells to which they attach interact intimately with the membranes of the epithelial cells. In such cases, the microbes have specialized segments or ends for adhering to the membranes, and probably elaborate systems for stabilizing the membranes and cytoplasm at the site in the epithelial cell to which they attach. Some such organisms may have evolved unique reproductive mechanisms to maintain their populations on the epithelial surface.