[First part: the intestinal microbiota]

The human gastrointestinal tract contains a large number of commensal (non pathogenic) and pathogenic microbial species that have co-evolved with the human genome and differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host and we can in fact consider the human body as a mix of human and bacterial cells. It is now evident that the large intestine is much more than an organ for waste material and absorption of water, salts and drugs, and indeed has a very important impact on human health, for a major part related to the specific composition of the complex microbial community in the colon. In man, the large gut receives material from the ileum which has already been digested and the contents are then mixed and retained for 6-12 hours in the caecum and right colon. Thus, the large intestine is an open system, with nutrients flowing in the caecum, and bacteria, their metabolic products, and undigested foodstuffs being excreted as faeces. The anaerobic brakdown of carbohydrate and protein by bacteria is known conventionally as fermentation. In man the major end products are the short-chain fatty acids (SCFA) acetate, propionate, butirate, the gases H2 and CO2, ammonia, amines, phenols and energy, which the bacteria use for growth and the maintenance of cellular function. The microbiota is also an important factor in the development of the immune response. The interaction between the gastrointestinal tract and resident microbiota is well balanced in healthy individuals, but its breakdown can lead to intestinal and extraintestinal disease.