The concentration and population of microorganisms that constitute the normal intestinal flora vary with the location along the intestine. Flora in the stomach, duodenum, jejunum and proximal ileum are sparse, usually less than 10⁵/mL. The distal ileum represents a transitional zone between the sparse flora of the proximal small intestine and the luxuriant flora of the lower bowel, where microorganism concentrations reach 10¹¹/mL. The predominant species are strict anaerobes, including bacteroides, anaerobic streptococci, bifidobacteria and Clostridium. The commonest aerobic organisms are E. coli; however, their concentration (10⁸/mL) is only 1/1,000 of the usual concentration of anaerobes in the colon.

Normally, bacterial flora are present in the intestinal lumen and in the mucus layer overlying the epithelium, and attached to the mucosal cells themselves. There is a specific tissue or cell type to which each microbial species attaches. For example, Streptococcus mutans, the oral organism that causes tooth decay, attaches only to the enamel surface of teeth; removal of the teeth leads to the disappearance of S. mutans from the oral microflora. This phenomenon of adherence may play an important role in the establishment and maintenance of a normal flora.

What are the mechanisms controlling normal small intestinal flora? First, in the stomach, acid suppresses the growth of most organisms that enter from the oropharynx. Bile added in the duodenum has additional antibacterial properties. Second, small intestinal motility mechanically sweeps bacteria downstream, helping to maintain a low concentration of organisms in the proximal small intestine. Third, the ileocecal valve plays an important role in preventing reflux of large amounts of colonic organisms. Additionally, mucus secreted by goblet cells and immunoglobulins has antibacterial properties.

Whereas the small intestine regulates the number of organisms present, in the colon the microorganisms themselves are responsible for maintaining their own population levels. Volatile fatty acids (e.g., acetic, butyric and propionic acid) are produced by anaerobes as well as by some coliforms. These short-chain fatty acids reduce the intraluminal pH and suppress the growth of certain organisms, thereby serving to control proliferation. In addition, some organisms produce other substances that inhibit bacterial growth, called bacteriocins.

Thus far we have considered what the microorganisms are, where they are located, and how their numbers are controlled. We next examine the concept that the normal flora exert a profound influence on intraluminal constituents, including food, urea, bilirubin, bile salts, drugs and potential toxins. Bacteria ferment dietary carbohydrates, yielding short-chain fatty acids, hydrogen and carbon dioxide. Fatty acids from carbohydrates and those from fat in the diet are hydroxylated by the intestinal flora. The hydroxy fatty acids formed stimulate fluid secretion and are thus cathartics. Similarly, bacteria alter protein and amino acids. Tryptophan is converted to indole compounds, glycine to ammonia, and methionine to hydrogen sulfide. Urea is converted to ammonia, a reaction that may contribute to hepatic encephalopathy. Bilirubin is metabolized to urobilinogen; bile salts may be deconjugated (removing glycine and taurine) and dehydroxylated (cholic acid becomes deoxycholic acid, and chenodeoxycholic acid becomes lithocholic acid). This deconjugation and dehydroxylation renders bile acids more insoluble and less capable of forming micelles. Bacteria also can affect vitamin synthesis and metabolism. Vitamin B₁₂ may be bound, thereby becoming unavailable for absorption (hence the abnormal Schilling test in bacterial overgrowth) and vitamin K and folic acid produced.

The normal flora also affect drugs and other ingested materials. Sulfasalazine, a drug used in ulcerative colitis, is unabsorbed in its native form. Intestinal bacteria, however, convert the substance into two moieties, a therapeutically active aminosalicylic acid and an inactive sulfapyridine. The sulfa drug succinylsulfathiazole is itself inactive, but is converted by intestinal bacteria to sulfathiazole, which is an active antimicrobial agent. Another example is cyclamate, unabsorbed and inert in its native form. Intestinal bacteria produce cyclohexylamine, a potential carcinogenic agent. Thus, bacteria can activate pro-drugs and produce carcinogens.