The gastrointestinal (GI) tract receives, moves, digests, and absorbs food and removes waste. It encompasses the oral cavity, esophagus, stomach, small intestine, large intestine, rectum, and anus. Stating that the GI tract harbors residents may seem to contradict our earlier statement that internal organs are generally sterile, but it is not an exception to the rule. How can this be true? In reality, the GI tract is a long, hollow tube (with numerous pockets and curves), bounded by the mucous membranes of the oral cavity on one extreme and those of the anus on the other. Because the innermost surface of this tube is exposed to the environment, it is topographically outside the body, so to speak.
The shifting conditions of pH and oxygen tension and differences in the microscopic anatomy of the GI tract are reflected by the variations in or distribution of the microbiota (figure 1). Some microbes remain attached to the mucous epithelium or its associated structures, and others dwell in the lumen. Although the abundance of nutrients invites microbial growth, the only areas that harbor appreciable permanent microbes are the oral cavity, large intestine, and rectum. The esophagus contains an extremely light load of microbiota, primarily bacteria swallowed with saliva. The stomach acid inhibits most microbes, although small numbers of lactobacilli and Helicobacter pylori (associated with stomach ulcers) can become established there. The small intestine has a sparse population of lactobacilli and streptococci except for its terminal segment, which has microbiota more similar to that of the adjacent large intestine.
Fig1. Distribution of microbes in the GI tract. Areas of the gastrointestinal tract that shelter major communities of resident microbes are highlighted in color. Noncolored areas do not harbor residents in significant numbers.
Microbiota of the Mouth
The oral cavity has unique residents that are some of the most diverse and abundant of the body. Microhabitats, including the cheek epithelium, gingiva, tongue, floor of the mouth, and tooth enamel, provide numerous adaptive niches. By one estimate, there are more than 700 species residing there. The most common residents are aerobic Streptococcus species—S. sanguinis, S. salivarius, S. mitis—that colonize the smooth superficial epithelial surfaces. Two species, S. mutans and S. sanguinis, make a major contribution to dental caries by forming sticky dextran slime layers in the presence of simple sugars. The adherence of dextrans to the tooth surface establishes the basis for a biofilm that attracts other bacteria.
Eruption of the teeth establishes an anaerobic habitat in the gingival crevice that favors the colonization by anaerobic bacteria that can be involved in dental caries and periodontal2 infections. The instant that saliva is secreted from ducts into the oral cavity, it becomes laden with resident and transient bacteria. Saliva normally has a high bacterial count (up to 5 × 109 cells per milliliter), a fact that tends to make mouthwashes rather ineffective and a human bite quite dangerous.
Microbiota of the Large Intestine
Microbes inhabiting the intestinal tract have complex and profound interactions with the host. The large intestine (cecum and colon) and the rectum harbor a huge population of microbes (108−1011 per gram of feces). So abundant and prolific are these microbes that they constitute 30% or more of the fecal volume. Even an individual on a long-term fast passes feces consisting primarily of bacteria.
The appendix has been considered an organ without much use, but recent research is verifying its importance in replenishment of the normal microbiota (see Clinical Connections). The lack of oxygen within the large intestine favors strictly anaerobic bacteria (Bacteroides, Bifidobacterium, Fusobacterium, and Clostridium). Coliforms such as E. coli, Enterobacter, and Citrobacter are present in smaller numbers. Many species ferment waste materials in the feces, generating vitamins (B12, K, pyridoxine, riboflavin, and thiamine) and acids (ace tic, butyric, and propionic) of potential value to the host. Occasionally significant are bacterial digestive enzymes that convert disaccharides to monosaccharides or promote steroid metabolism.
Intestinal bacteria contribute to intestinal odor by producing skatole, amines, and gases (CO2, H2, CH4, and H2S). Intestinal gas is known in polite circles as flatus, and the expulsion of it as flatulence. Some of the gas arises through the action of bacteria on dietary carbohydrate residues from vegetables such as cabbage, corn, and beans. The bacteria produce an average of 8.5 liters of gas daily, but only a small amount is ejected in flatus. Combustible gases occasion ally form an explosive mixture in the presence of oxygen that has reportedly ignited during intestinal surgery and ruptured the colon!
Late in childhood many people lose the ability to secrete the enzyme lactase, a condition known as lactase deficiency or intolerance. Difficulties arise when an individual with this condition ingests milk or other lactose-containing dairy products. Lactose is a disaccharide that cannot be absorbed, and when lactose lies undigested, it increases the osmotic pressure in the gut, resulting in cramps, diarrhea, and intestinal distress. To complicate matters, the lactose can be digested by intestinal bacteria, which release gas and intestinal irritants. The recommended treatment for this deficiency is avoiding these foods or eating lactose-free substitutes.
