The gastrointestinal tract can be divided into various distinct anatomical areas. These include esophagus, stomach, jejunum and upper ileum, distal small intestine, and large intestine. The microbial flora present on the mucosa, within crypts, and in the lumen is different. Complete information has been obtained for the stomach and large intestine by studying the microbial composition of feces or the specimens collected during the intra-abdominal surgery.
Sufficient information is not available about the microbial flora of the esophagus. However, transient colonization by oropharyngeal bacteria and yeasts is known to occur.
Stomach is an inhospitable organ containing hydrochloric acid and pepsinogen. For this reason, the normal microbial flora is very sparse. The organisms present in the stomach are acid-tolerant Lactobacillus spp., Streptococcus spp., and Helicobacterpylori. H. pylori causes gastritis and gastric and duodenal ulcersand is associated with gastric malignancy.
The number of microbes in the upper part of the small intestine is less than 105/mL of fluid. They are predominantly anaero-bic, consisting of Lactobacillus, Peptostreptococcus, Streptococcus, Porphyromonas, and Prevotella. If upper tract obstruction andstasis occur, then the microbial flora shifts to resemble colonic bacteria, thereby leading to malabsorption syndrome.
This is the transition area between the stomach (where a sparse number of acid-tolerant bacteria are found) and the large intes-tine (which is inhabited by a plethora of microbes). The micro-bial population is large (108–109 organisms/g of feces) and diverse with the predominance of anaerobes.
This is the most densely populated organ in the human body. It consists of more than 108 aerobic bacteria and 1011 anaerobic bacteria per gram of feces. Various yeasts and nonpathogenic parasites reside in this area. The bacteria in the large intestine that are present in large numbers include Bifidobacterium spp.,Bacteroides fragilis, Eubacterium spp., Enterococcus spp., and E. coli. Although B. fragilis is the most virulent species, Bacteroidesthetaiotaomicron is more numerous in the colon. Eubacterium spp.is the second most common bacterium in the large intestine. The most commonly isolated species are Eubacterium aerofaciens, Eubacterium cylindroides, Eubacterium lentum, and Eubacterium rectale. Nine species of Bifidobacterium have been isolated infeces. Among Enterococcus species, the most frequently isolated ones are Enterococcus faecalis and Enterococcus faecium.
E. coli causes colonization soon after an infant is born. It isthe most common facultative organism responsible for intra-abdominal infections. Other members of Enterobacteriaceae like Citrobacter spp., Klebsiella spp., Enterobacter spp., and Proteus spp.can establish residence in the intestine.
Streptococcus species and Actinomyces have been isolated fromfecal specimens. A variety of Peptostreptococcus and Gemella species are members of the normal intestinal flora. The spore-forming Bacillus species and Clostridium species are isolated from fecal specimens. Vibrio parahaemolyticus can also colo-nize the intestinal tract, but only in small numbers. Other organisms commonly isolated in small numbers include species of Fusobacterium, Porphyromonas, and Prevotella species. Various species of Candida and protozoa colonize the large intestine.