The human gut is the natural habitat for a large and dynamic bacterial community. Recently developed molecular biology tools suggest that a substantial part of these bacterial populations are still to be described. However, the relevance and impact of resident bacteria on host’s physiology and pathology is well documented. Major functions of the gut microflora include metabolic activities that result in salvage of energy and absorbable nutrients, protection of the colonized host against invasion by alien microbes, and important trophic effects on intestinal epithelia and on immune structure and function. Gut bacteria play an essential role in the development and homeostasis of the immune system. It is important to underscore that the specialised lymphoid follicles of the gut mucosa are the major sites for induction and regulation of the immune system. On the other hand, there is evidence implicating the gut flora in certain pathological conditions, including multisystem organ failure, colon cancer and inflammatory bowel diseases.
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