The Germs That Make Us Us.

            There is a fascinating article by Michael Specter entitled "Germs Are Us," in the Oct 22 issue of New Yorker Magazine.  Specter says that medical thinking is beginning to change about germs, and about the relationship between microbes and the humans who carry them. In 1982, Barry Marshall and J. Robin Warren discovered that Helicobacter Pylori, and not stress, was the principle cause of peptic ulcers. For this discovery, they later shared a Nobel Prize.  By the 1990s, doctors began to seriously consider an effort to eradicate this organism, which would be quite a project.  H. Pylori has been around over 200,000 years and inhabits half the stomachs on earth.  But, they reasoned, "This microbe is clearly bad for us. Besides causing ulcers, it raises the risk of stomach cancer. So why not get rid of it totally?"  In 1997, one prominent microbiologist wrote, "The only good H. Pylori is a dead H.Pylori!"

            But by 1998,  it became clear that H. Pylori is completely harmless to most people, and may play a positive role.  In fact, of the thousands of species of bacteria which humans carry, many if not most may have some positive role,  perhaps even a role necessary to the long term survival of the human species. When a baby leaves the womb, it is free of all bacteria.  But as it passes through the birth canal, it picks up some of its mother's microbes.  When exposed to air, it picks up more. And by the time it's old enough to crawl, it is carrying a hundred trillion foreign bacteria, viruses, yeast, and fungi. An adult human may carry 10,000 different bacterial species.  These foreign cells may weigh a total of over three pounds and outnumber our own cells by ten to one.    We call this our microbiome.  We have coevolved with these organisms, and we depend on them to help digest our food, make some of our vitamins, ward off gut infections, and help develop our immune systems.

            But the typical human biome is not as diverse as it once was. Since the introduction of antibiotics, most individuals have lost cultures of gut bacteria which never returned. And this gradual loss of various kinds of gut bacteria may be contributing to the rise of many diseases, including Crohn's disease, asthma, and obesity. Unfortunately, the decline of biome diversity will be cumulative from generation to generation, since we cannot pass on to our children those bacterial cultures which we have already lost.  In 2007, after the completion of the Human Genome Project, the NIH instituted a project to map the DNA of the human microbiome. Since then, one study of only 124 people found about 1,000 species of gut bacteria. But the average for each individual was only about 160 species.  David Relman, of Stanford Medical School, says that our biome is vast, complex, and poorly understood. He says we must stop seeing medicine as a war between our bodies and invading pathogens, and start seeing an individual human body and its biome as a whole system--a system that needs to be managed.  A lab in Germany has discovered that human biomes can be placed into three categories, which are unrelated to age, race, or gender. Just as there are four blood types, there are three gut types. 

            Antibiotics have been a profound benefit to mankind. They are one of the main reasons that a child born in America today can expect to live 20 years longer than one born in 1930.  But by age 18,  an American has received 10 to 20 courses of antibiotics, and every time they are used, there is collateral damage.  A hundred years ago, nearly all humans carried H. Pylori.  Today, only 5% of American children do.  While H. Pylori can be harmful to some adults, it is rarely harmful to children and may be necessary to normal development. The article says that studies now show that children without H. Pylori are much more likely to develop asthma. And they are also more likely to become obese. Besides antibiotics, there are many other causes for the decline in biome diversity.  Improved sanitation has helped. And the rise of c-sections means that fewer babies will receive microbes from their mothers while passing through the birth canal.             While there are many ways to lose microbes, there may also be many ways to gain them.  The article tells of a man who had a chronic ear infection in one ear.  Several kinds of anti-fungal drops were tried, and several antibiotics, but nothing worked. Then, he cured himself--by transferring a bit of ear wax from his good ear to the infected one.

            About 10% of the population carries Clostridium difficile in their gut, which normally causes no trouble because it is held in check by other bacteria. But when a course of antibiotics wipes out nearly all other enteric bacteria, a nasty C. diff infection can result. For some patients, their microbiome is never successfully restored, and C. diff becomes chronic and untreatable. One of the more radical treatments now being tried is the fecal transplant. A sample of fecal material is obtained from a healthy donor, usually a close relative. Then [after being lab screened for parasites and other harmful pathogens] it is placed into the bowel of the patient, to re-establish a normal colony of beneficial bacteria. So far, the limited trials seem encouraging. In one study, all 34 patients were completely cured, and all were patients for whom all other approaches had failed. Ten years ago, this procedure would have been considered outrageous by most physicians. But the fact that this procedure is being tried in mainstream clinics indicates just how radically our ideas about germs have changed.

            We are still in our infancy in our understanding of our microbiome and the complex interactions between the thousands of species of germs with each other and with us.  But the new paradigm will not be that of an invading army needing to be slaughtered by chemical warfare, but that of a garden in need of a careful gardener.  To me, the human body is like a coral reef--a collection of cells which constitute a separate organism, yet host an entire ecosystem.  And if the ecosystem is healthy, the coral is healthy. 
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