Digestive System > Fundamental Physiology and Anatomy of the Digestive System

Microbial Life in the Digestive Tract

The gastrointestinal tract contains an immensely complex ecology of microorganisms. A typical person harbors more than 500 distinct species of bacteria, representing dozens of different lifestyles and capabilities. The composition and distribution of this menagerie varies with age, state of health and diet.

The number and type of bacteria in the gastrointestinal tract vary dramatically by region. In healthy individuals the stomach and proximal small intestine contain few microorganisms, largely a result of the bacteriocidal activity of gastric acid; those that are present are aerobes and facultative anaerobes. One interesting testimony to the ability of gastric acid to suppress bacterial populations is seen in patients with achlorhydria, a genetic condition which prevents secretion of gastric acid. Such patients, which are otherwise healthy, may have as many as 10,000 to 100,000,000 microorganisms per ml of stomach contents.

In sharp contrast to the stomach and small intestine, the contents of the colon literally teem with bacteria, predominantly strict anaerobes (bacteria that survive only in environments virtually devoid of oxygen). Between these two extremes is a transitional zone, usually in the ileum, where moderate numbers of both aerobic and anaerobic bacteria are found.

Microbial Populations in the Digestive Tract of Normal Humans

Stomach Jejunum Ileum Colon
Viable bacteria per gram
0 - 103
0 - 104
105 - 108
1010 - 1012

The gastrointestinal tract is sterile at birth, but colonization typically begins within a few hours of birth, starting in the small intestine and progressing caudally over a period of several days. In most circumstances, a "mature" microbial flora is established by 3 to 4 weeks of age.

It is also clear that microbial populations exert a profound effect on structure and function of the digestive tract. For example:

Finally, bacterial populations in the large intestine digest carbohydrates, proteins and lipids that escape digestion and absorption in small intestine. This fermentation, particularly of cellulose, is of critical importance to herbivores like cattle and horses which make a living by consuming plants. However, it seems that even species like humans and rodents derive significant benefit from the nutrients liberated by intestinal microorganisms.

Next Topic: Review of Food Chemistry >

Send comments to Richard.Bowen@colostate.edu