●The surface of the intestinal tract in healthy individuals is free of bacteria in all bowel segments. Adherence of bacteria to epithelial cells is thus a sign of infection. By contrast, the intestinal lumen is never sterile.
●The occurrence, composition, and organization of intestinal microbiota in each gut segment depend upon whether suppression (mechanisms that suppress bacterial growth) or separation (mechanisms that create a physical barrier from the host such as the mucus layer) dominates.
●It was initially believed that the immune system was tightly regulated to respond to pathogenic intestinal bacteria while tolerating commensal bacterial. However, it is increasingly recognized that bacterial residents of the large bowel cannot be easily divided as being pathogenic or nonpathogenic. Many indigenous bacteria are known pathogens. As examples, E. coli cause sepsis, Bacteroides cause abscesses, Enterococci cause endocarditis, and C. histolyticum causes gas gangrene. The control of pathogens and the regulation of the colonic bioreactor require proper function of the intestinal mucus layer. Before bacteria can adhere and invade the mucosa, they must first traverse the mucus layer.
●The structure and composition of intestinal bacteria can be markedly affected in the presence of a variety of diseases states. For example, inflammatory bowel disease is a polymicrobial infection that is characterized by a sustained broken mucus barrier, subsequent bacterial migration towards the mucosa and proliferation of a complex bacterial biofilm on the epithelial surface with resulting invasive and cytopathologic effects.
●The composition and structure of fecal microbiota changes as a consequence of the inflammatory response. Active Crohn disease and ulcerative colitis can be distinguished from each other and other disease controls based upon the biostructure of fecal cylinders.
