Colonization of particulates, mucous, and intestinal tissue

The gastrointestinal system consists of myriad small ecological "niches" within which most bacteria grow in glycocalyx-enclosed microcolonies that form highly structured consortia in biofilms on the surfaces of both tissue and digesta. Bacteria in the lumen of the system are attached to their nutritive substrates by chemotaxis and they then adhere to insoluble nutrients (e.g. cellulose) or position themselves in microcolonies in locations having maximal concentrations of soluble nutrients (e.g. monomeric sugars). Thus, the digestion of even simple foods involves the simultaneous and specific colonization of many different "microniches" by bacteria. Specific bacteria have been shown to colonize tissues within the gastrointestinal tract and some of these taxonomically distinct populations have been shown to cooperate in the physiological activities of some of the colonized tissues. Highly abraded tissues and tissues exposed to extremes of acid concentration may be colonized by a single species of bacteria or yeast, because special adhesion mechanisms or acid resistance are required for persistence, but most nonsecretory epithelia within the tract are heavily colonized by a rich mixture of bacteria. We have developed techniques to retain the mucous blanket on the secretory epithelia of the intestine, and we find that the majority of bacteria and protozoa in these organs are associated with the mobile viscous layer and are thus functionally apposed to the epithelial tissues. Notable exception are the bacteria and protozoa that adhere avidly to the epithelial tissues by special adhesion mechanisms and must therefore remain stationary within the mobile mucous blanket.