Bacteria in the intestine, helpful residents or enemies from within?

Humans evolved in the presence of numerous microbial communities that preceded the appearance of mammals on planet Earth. The role of these microbial communities in our evolution is a matter of considerable interest. Indeed, comparative studies with germfree and conventional animals have established that the intestinal microflora is essential for the development and function of the mucosal immune system during early life, a process that is now known to be important to overall immunity in adults. An absence of intestinal bacteria is associated with reductions in mucosal cell turnover, vascularity, muscle wall thickness, motility, baseline cytokine production, and digestive enzyme activity and with defective cell-mediated immunity (83). Furthermore, the intestinal microflora makes important metabolic contributions to vitamin K, folate, and short-chain fatty acids, such as butyrate, a major energy source for enterocytes, and also mediates the breakdown of dietary carcinogens (7, 50). The bacterial flora of the gastrointestinal tract varies longitudinally; the oral cavity contains about 200 different species, the stomach is almost sterile, and the bacterial content increases distally, with approximately 10 bacteria per g (dry weight) of ileal contents and up to 10 bacteria per g (dry weight) of colonic contents (7). The conclusions of studies on the bacterial flora carried out some decades ago are still thought to be true. The large intestine contains organisms belonging to over 30 identified genera and as many as 500 separate species or phenotypes. The main types of bacteria in the colon are obligate anaerobes, and the most abundant bacteria are members of the genus Bacteroides, anaerobic gram-positive cocci, such as Peptostreptococcus sp., Eubacterium sp., Lactobacillus sp., and Clostridium sp. More recent studies of large bowel biopsies confirmed that Bacteroides was a dominant genus in the specimens examined (142). Thus, intestinal bacteria represent a complex and incompletely understood microbiome. Since certain organisms are thought to play a role in the onset of inflammatory diseases of the bowel, whereas other organisms are considered protective, this review explores the relationship between bacteria that reside in the gastrointestinal tract and the host. There is an emphasis on bacterial interactions with epithelial cells, as well as on the role of bacteria in the development of inflammation and in defense mechanisms deployed by the host to counter such attacks. Selected homeostatic processes and mediators that may maintain the intestine in a state of “controlled inflammation” are also discussed.