Bacteria, like the H. pylori show, seem to have co-evolved with humans to live inside our bodies. Some can have negative consequences, like ulcers, but others provide helpful functions like digesting food. (Image: Yutaka Tsutsumi, M.D. Professor Department of Pathology Fujita Health University School of Medicine)

The average human body contains ten times as many microbial cells, about 100 trillion, as it has human cells. Those microbes include thousands of different species, and collectively have millions of different protein-encoding genes compared to only 23,000 or so human genes. The Human Microbiome Project has found that healthy human individuals differ widely in the species that inhabit them; that each person is a unique island habitat for microbes.

Human microbes include bacteria, archea, fungi and a few other eukaryotic species, some of which are clearly parasites. Microbes inhabit the skin, the upper respiratory tract, the gastrointestinal tract and the vagina. The large intestine seems clearly to have evolved as a warm, moist incubator for bacteria that aid in completing digestion of our food, meanwhile supplying us with vitamins, trace nutrients, bile acids, polyamines, and some unusual lipids.

Some of our resident bacteria can be harmful. Nobel laureates Barry Marshall and Robin Warren famously proved that Helicobacter pylori cause gastritis and peptic ulcers. There were initially many doubters because it was believed that the low pH of the stomach, akin to battery acid, would prevent bacteria from thriving there. Apparently H. pylori survive by burrowing down into the mucus covering the stomach's epithelium. Thanks to Marshall and Warren, ulcers can now be cured with a short course of antibiotics. However, 50% of the human population is "infected" with H. pylori and most never suffer any ill effects. H. pylori co-evolved in Africa along with its human hosts and then hitched a ride to the rest of the world within our stomach linings as we emigrated.

Although humans and other animals can survive in an aseptic environment, they do not thrive. "Germ-free" animals suffer from deficiencies in digestion and in the development of their immune systems.

Much of the twentieth century progress in medicine was due to better sewage systems, better hygiene and the development of antibiotics to combat pathogenic microbes. There is some reason to believe that we have now upset the balance between our microbes and ourselves. The current epidemic of metabolic syndrome and resultant Type II diabetes may be caused, in part, by disturbances in the microbial ecosystem in the human gut. Mouse models of metabolic syndrome show reproducible changes in the composition of their microbiota and a low grade intestinal inflammation.

The particular species that inhabit a particular individual is relatively constant over time, and depends upon their diet, habits, immune system, and history of antibiotic use. However, there is a significant exception in the vagina of pregnant women. The dominant species of microbes change as pregnancy proceeds, according to the work of Kjersti Aagaard-Tillery and colleagues at the Baylor School of Medicine. One species that becomes dominant is Lactobacillus johnsonii, normally found in the gut where its enzymes aid in the digestion of milk. The implication is that this bacterium is acquired by the baby during its passage through the birth canal, preparing the child to digest breast milk.

The study of the human microbiome is likely to reveal many other unusual adaptations between ourselves and our microbial associates.