The lower intestine of mammals is a marvellous habitat for microorganisms. The temperature is a steady 34-40°C and there is a reliable supply of carbon sources, vitamins, minerals and water. It is therefore not surprising that immense numbers of bacteria inhabit the distal small intestine (ileum), the caecum, and the colon. Their densities range up to 1012 organisms/ml intestinal contents, so overall the bacteria that we carry outnumber our own cells, and within about 1,000 species present there are approximately 100 times as many genes as on our own chromosomes (Hooper et al. 2001). In normal circumstances, this habitat can never remain sterile for long, so we are colonised just after birth and carry these microbial passengers throughout life (Mackie et al. 1999).
This review summarises experiments carried out to examine the way in which the immune system has adapted to the presence of commensal intestinal bacteria for mutual co-existence, with an emphasis on the secretory IgA response.
The relationship with intestinal bacteria, and microbes that colonise other body surfaces, is usually mutually beneficial. In the intestine, bacteria salvage energy from carbon sources that cannot be digested by mammalian enzymes and supply the host with vitamin precursors. They also appear to compete effectively with pathogenic bacteria, leading to the use of commensal bacteria
(Tvede and Rask-Madsen 1989) or non-pathogenic Saccharomyces (McFar-land et al. 1994) as therapeutic 'probiotics' to treat recurrent infections with toxigenic Clostridium difficile or some forms of relapsing inflammatory bowel disease (Cummings and Kong 2004). Although there is epidemiological evidence that these treatments work, the mechanisms are largely speculative because we understand so little about the complex consortia of bacteria that live in or adjacent to the mucus layer overlying the single-cell-thick sheet of epithelia cells. This has immense practical importance, because the bacteria that are seen by the immune system are probably mainly those intimately associated with the epithelium in biofilms. Conversely, we assume that mucosal immunity has an important effect on the composition and density of these biofilms, but there is very little information to show whether this is true in vivo. We still need much better information about the dynamics and plasticity of the commensal intestinal flora.
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