Even when you think you’re alone, you’ve got a lot of company. Of the cells you carry around, only about half, it turns out, are human. The rest belong to micro-organisms — bacteria, fungi, protozoans and viruses — that are on and inside you. That may sound unsanitary, but most of them are either harmless or beneficial. Many researchers think that in our overzealousness to kill bad germs, we’ve knocked off some underappreciated good ones, depleting the diversity of our microbiota, whose collective genes are known as the human microbiome. According to one theory, this has contributed to the recent increase, in industrialized countries, of autoimmune diseases such as diabetes, multiple sclerosis and lupus. That’s led to a spate of new research on whether a better relationship with our fellow travelers could undo that rise, and whether some of our microbes could be deployed to make us even healthier.

The Situation

Scientific findings have come quickly, connecting human microbiota to infectious diseases such as HIV and hepatitis, non-communicable ones like heart disease and cancer, and even psychiatric disorders such as autism and depression. The discoveries have sparked an explosion of research by drug companies and academic labs into possible treatments and cures. The idea, usually, is to alter organisms in the gut, where about 99 percent of human microbiota live. Some of the most promising research involves fecal transplantation — the introduction through colonoscopy, endoscopy or enema of a donor stool. In early human trials, it’s shown potential as a superior treatment for recurrent infection with C. difficile, a pathogen often contracted in hospitals that causes diarrhea and kills about 30,000 people a year in the U.S. Obesity has been discussed as another tantalizing target. In experiments, fat mice transplanted with microbes from thin mice lost weight and vice versa.

The Background

Researchers connected to the Human Microbiome Project, an international effort led by the U.S. National Institutes of Health, have catalogued more than 10,000 microbial species among our companion germs. The average human gut contains about 38 trillion microbes, weighing about 0.2 kilograms (0.4 pounds). Compared with people in less-developed countries, those in industrialized states have significantly less diversity in the microorganisms that populate their bodies. An excessive use of antibiotics, both in medicine and agriculture, is thought to be a leading cause. Lower rates of natural childbirth and breast feeding are others: Those practices pass microbes from mother to child, perhaps explaining why cesarean section babies have higher rates of asthma and allergies, and formula-fed babies are at an elevated risk of obesity and diabetes. Less socializing, outdoor activity and exposure to animals may also deplete microbiota. Scientists for years have known that growing up with a dog lowers a child’s chance of having asthma — by 13 percent, according to one study — and microbial diversity has become the leading explanation. Family members, it seems, swap microbes by petting their dogs and being licked by them.

The Argument

Researchers stress that therapies based on microbiome science will take time to develop. Meanwhile, there’s widespread agreement among scientists that people in industrialized countries would do themselves a favor by going easy on antibiotics. Already blamed for breeding resistance in bacteria and thus creating superbugs, antibiotic overuse is now a suspect in killing off good as well as bad bacteria in the human gut. Physicians say they often prescribe unnecessary antibiotics for viral infections because their patients expect it and there’s no time to explain that a bacteria killer won’t destroy a virus. A public-information campaign in the U.S. aimed at reducing patient demand has corresponded with a decline in antibiotic prescriptions. U.S. farmers use antibiotics intensively on livestock both to treat and prevent disease. Usage is much lower in most countries in the European Union, which has banned dosing healthy animals since 2006. Another possibility for encouraging a better microbial balance is to take in “good” microbes, called probiotics. They can be found in food such as yogurt, miso and soy beverages or in dietary supplements. Some researchers see potential in probiotics, but the case for them requires more investigation, and there are no established protocols for how much or what strains to consume for various purposes.

The Reference Shelf

  • Microbiologist Martin Blaser’s book “Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues.” 
  • An article in the Journal of Cardiovascular Nursing details “20 Things You Didn’t Know About the Human Gut Microbiome.”
  • An article in Perspectives in Public Health suggests ways to restore the human microbiome and possibly reduce al
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