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The gastrointestinal tract is sterile at birth, but colonization typically begins within a few hours of birth, starting in the small intestine and progressing caudally over a period of several days. In most circumstances, a "mature" microbial flora is established by 3 to 4 weeks of age. The colonic microflora contain up to 400 different species of both aerobic and anaerobic bacteria and make up approximately 30% of faecal dry weight. The most prevalent anaerobes are Bacteroides sp. and Bifidobacterium whilst the most numerous aerobes are Escherichia coli, enterococci and Lactobacillus. The major site of bacterial activity is the caecum where the anaerobic bacteria ferment substrates in a liquid mixture. The principal sources of nutrition for the bacteria are complex carbohydrates including starches, non-starch polysaccharides including dietary fibre (celluloses, gums and pectins) and smaller saccharides such as lactose, sorbitol and xylitol. It is thought that 2-20% of dietary starch escapes absorption in the small bowel. Synthesis of vitamin K by colonic bacteria provides a valuable supplement to dietary sources and makes clinical vitamin K deficiency rare.

Cellulose is a common constituent in the diet of many animals, including man, but no mammalian cell is known to produce a cellulase. Several species of bacteria in the large bowel synthesize cellulases and digest cellulose, and the major end products of digestion of this and other carbohydrates are volatile fatty acids, lactic acid, methane, hydrogen and carbon dioxide. Fermentation is thus the major source of intestinal gas. Volatile fatty acids (acetic, proprionic and butyric acids) generated from fermentation can be absorbed by passive diffusion in the colon and metabolised in the epithelial cells and liver. Short chain fatty acids remaining in the colon are neutralised by bicarbonate ions which are secreted into the lumen.

In man, the metabolic activity of the caecal bacteria can be demonstrated by ingestion of lactulose or baked beans which are fermented by the caecal bacteria, causing a rise in breath hydrogen. This is used as a method of estimating the time of mouth to caecal transit.

Colonic bacteria possess exocellular lipases which are able to hydrolyse fatty acid esters at the 1 and 3 positions of the triglyceride molecule. They also produce enzymes capable of metabolising long chain fatty acids. Approximately 25% of faecal fatty acids are hydroxylated by colonic bacteria, for example oleic acid is hydroxylated to form hydroxystearic acid. The presence of hydroxylated fatty acids in the colon has an inhibitory effect on colonic electrolyte and water transport, and at high concentrations they cause net secretion of water and electrolytes, which results in diarrhoea and therefore a significantly increased colonic transit rate. Infusion of oleic acid (4.3 g per 100 ml) into the mid-ascending colon accelerated colonic transit rate and defaecation when compared to a control infusion12.

The microbial population exerts a profound effect on the structure and function of the digestive tract, as the morphology of the intestine of germ-free animals differs considerably from normal animals. Villi of the small intestine are remarkably regular, the rate of epithelial cell renewal is reduced and, as one would expect, the number and size of Peyer's patches is reduced. The caecum of germ-free rats is roughly 10 times the size of that in a conventional rat.

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