The mucosal surface of the human body, including the gastrointestinal tract, the respiratory tract and the urogenital tract, has a total surface area of more than 400 m2 (11). The gastrointestinal tract's surface area is about 200-300 m2 and is colonized by 1013-14 bacteria with hundreds of bacterial species and subspecies.
The normal microbiota of the gastrointestinal tract has been grouped and defined into two categories, the autochthonous (indigenous) and the allochthonous (nonindigenous) species (12). The autochthonous microbes (1) are always present in the normal adult's gastrointestinal tract, (2) play a role in maintaining the stable bacterial populations in the gastrointestinal tract, (3) colonize particular parts of the tract, (4) can grow anaerobically, (5) colonize their habitats in succession in infants, and (6) often associate intimately with the gastrointestinal mucosal epithelium.
On the other hand, allochthonous species are not characteristic of the normal habitat. Allochthonous microbiota is defined as transient microbes which will not be established but would just be passing through, having arrived in the habitat in food, in water, from another habitat in the gastrointestinal tract, or from elsewhere in the body. These microbes either cannot or find it very challenging to establish themselves since they cannot compete in the various niches or may be killed by host or bacterial factors.
However, the allochthonous microorganisms might colonize the habitats vacated by the autochthonous microbes in the disturbed gastrointestinal system (13). This was evidently seen in the administration of antibiotics which caused severe disturbance in the gastrointestinal microbiota leading to undesirable effects, such as the overgrowth and superinfection with allochthonous microorganisms like yeast (14,15); see also chapter 18 by Sullivan and Nord in this book.
Thus, the main difference between autochthonous and allochthonous species is that an autochthonous microbe naturally colonizes the habitat, whereas an allochthonous one cannot colonize it except under abnormal or atypical situations (13).
In a steady gastrointestinal ecosystem, all the niches are probably occupied by indigenous microbes. The number of microorganisms in the stomach and the upper two-thirds of the small intestine is very scarce: a maximum of 104 per milliliter of intestinal contents. The relatively low number of microbes is due to the low pH (approximately pH 2) of the intestinal contents resulting from gastric acid production and the relatively swift flow (transit time of 4-6 hours) of digesta through the stomach and small intestine. Culturing studies indicate that lactobacilli and streptococci are commonly found microbes in the small intestine (16). Unlike the bulk of the microbes within the gastrointestinal tract, both the lactobacilli and streptococci are acid-tolerant bacteria, and are capable of surviving the passage through the stomach.
The ileum contains larger numbers of microbes (108-109 bacteria per ml of intestinal contents) in comparison to the upper regions of the gastrointestinal tract. The higher bacterial numbers in the ileum are the result of a lower peristalsis and low oxidation-reduction potential. Therefore, lactobacilli, streptococci, enterobacteriacae and anaerobic bacteria are able to establish themselves in the distal region of the small intestine. The main site of microbial colonization in the gastrointestinal tract is the colon. The slow intestinal motility in the colon with a transit time of up to 60 hours and low oxidation-reduction potential are responsible for the large numbers of bacteria present. The colon contains 10n-1012 bacteria per gram of intestinal contents. More than 99% of the colonic microbiota are obligate anaerobes such as Bacteroides spp., Eubacterium, Bifidobacterium and Clostridium spp. (17).
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