Feces are a complex microbial habitat, with many niches occupied by bacteria. It is estimated that bacteria account for about 30% of the fecal mass, and 40-55% of fecal solids. All of the bacteria in feces are exposed to the influences of dehydrating and concentrating mechanisms of the colon and rectum, and intense biochemical activity of the organisms living in the material. When the samples consist of only feces, the composition and localization of communities anywhere in the tract cannot be revealed. Bacteroides accounts for nearly 20% of the species that can be cultivated from feces (10). The Bacteroides and Prevotella group (gram-negative anaerobes), and Eubacterium rectale and Clostridium coccoides species (gram-positive anaerobes) are predominantly present in the fecal samples (90,92). The predominant bacterial community in feces is stable in time, host specific, affected by ageing, and not significantly altered after consumption of probiotic strains (97).
Fecal samples have to be collected in sterile bags, and kept at low temperature ( — 80°C to +4°C) before processing (88). Stool specimens or rectal swabs can be used for the diagnosis of cholera. Dipsticks in rectal swabs are used for the rapid diagnosis of cholera caused by Vibrio cholerae. Dipstick analysis uses colloidal gold particles, and is based on a one-step immunochomatography principle. The sensitivity and the specificity of the dipsticks is greater than 92% and 91% respectively. This rapid test (diagnosis within 10 minutes) requires minimal technical skills (98,99).
Most knowledge of the gastrointestinal microbiota stems from colon or feces bacteriology. A major limitation in studying the proximal human colonic microbiota is the lack of suitable sampling methods. Studies in which only feces are sampled can never reveal the composition and localization of epithelial and cryptal communities anywhere in the tract. Such studies reveal little about the composition of lumenal communities in any area except perhaps the large bowel (29).
Low fecal pH is caused by ingestion of poorly absorbed carbohydrates or carbohydrate malabsorption in the small intestine, and consequently, the bacteria in the colon ferment the carbohydrate. Fecal pH of less than six is highly suggestive of carbohydrate malabsorption. A breath hydrogen test with lactose can confirm carbohydrate malabsorption. In this test a fasting patient is given 25 g of lactose dissolved in water, and exhaled breath is assayed for hydrogen content at baseline, and at intervals
for several hours as described in Figure 4. As explained above, because hydrogen is not a normal product of human metabolism, any increase in breath hydrogen concentration represents bacterial fermentation, and indicates that unabsorbed lactose has reached the colon.
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