We are vastly, ridiculously, hopelessly, humblingly outnumbered: For every one human cell, there are an estimated 10 single-cell microbes in us or on us, at least 100 trillion in all, nestled in our guts and in our urogenital tracts, lying on our skin and happily ensconced in our mouths and noses—entire civilizations of fungi and protozoa and (mostly) bacteria that eat and breathe, evolve and reproduce and die.

Before you reach in horror for the hand sanitizer or industrial-strength mouthwash, you might want to keep something in mind. A profusion of research in just the past five years is showing that our microbial hitchhikers, collectively called the “human microbiota” and so small they account for only 1 or 2 percent of our weight, play a key role in maintaining our health. And we disrupt them at our peril. “It’s not possible to understand human health and disease without exploring the massive community of microorganisms we carry around with us,” says Professor George Weinstock of Washington University in St. Louis. Knowing which microbes live in healthy people “allows us to better investigate what goes awry in diseases that are thought to have a microbial link, like Crohn’s and obesity.”

The microbes in our body—especially some of the 10,000 or so species of bacteria in and on us—have indeed been implicated in disorders as diverse as obesity and Crohn’s, and also in asthma, heart disease, sinusitis, and possibly even mood disorders. They influence how big our appetite is and, possibly, even what foods we crave. They synthesize vitamins and affect how quickly we metabolize drugs such as acetaminophen (Tylenol), they protect against esophageal reflux and they churn out many of the same neurochemicals as our own brains. Given this job description, it’s hardly surprising that when perturbed, scientists are discovering, the microbiota can tip us into poor health or outright illness.

Exactly how our bacterial companions affect our health is the subject of ongoing research in labs around the world, but one thing is clear: Our decades-long war on germs is looking seriously wrongheaded. In an effort to obliterate disease-causing microbes through antibiotics and anti-microbials—from the pills we down for a cold (against which antibiotics are useless) to the meat we eat to the hand-sanitizer-dispensers everywhere you look—we are carpet-bombing our microbiota. And that war on germs takes a huge toll on beneficial bugs, too.

One example: The bacterium Helicobacter pylori causes ulcers and has been linked to stomach cancers. Although it was once in almost everyone’s gut, it is now found in just 6 percent of U.S. children, Science magazine reported in 2011, probably due to the widespread use of antibiotics and anti-microbials. That should mean fewer ulcers, but there’s a dark lining to that silver cloud: H. pylori may ward off asthma. Scientists led by Dr. Martin Blaser of New York University Langone Medical Center found that those without H. pylori are more likely to have had childhood asthma than those with it. Coincidence? In 2011 scientists in Switzerland infected half of a colony of mice with the bacteria and left the other half germ-free. They showered all the mice with dust mites and other allergens. Mice with H. pylori were fine; those without suffered airway inflammation, the hallmark of asthma.

Exactly how H. pylori might ward off asthma is still a mystery, but researchers have made progress understanding the link between our microbiota and other diseases.

The field of microbiota and health took off in 2006, when scientists led by Jeffrey Gordon of Washington University in St. Louis noticed something: Fat mice and svelte mice have very different gut microbes. Could different microbes actually cause obesity? To find out, Gordon transferred gut bacteria called Firmicutes from obese mice into thin ones. The thin mice ate no more than they used to, but they quickly started packing on the pounds (okay, ounces). Firmicutes, it turns out, are really good at liberating calories from food, much better than the common gut bugs called Bacteroidetes. That finding offers a hint of why your friend can scarf down calories and remain slim while you have merely to walk past a bakery window to gain weight. “Some microbes change how efficiently we metabolize food,” says biologist Rob Knight of the University of Colorado, who studies the genetics of the microbiota, called the microbiome.

It seems Firmicutes are quite adept at digesting fats and carbs, allowing you to absorb many more of, say, the 1,200 calories in half of a Domino’s bacon-cheeseburger pizza than if you have fewer Firmicutes and more Bacteroidetes. “Obesity depends not just on calories ingested but also on the microbiome,” says Dr. Yang-Xin Fu of the University of Chicago Medicine. And, yes, like mice, obese people tend to have more Firmicutes and fewer Bacteroidetes than slim people.

At this point everyone asks, how can I get my slim friend’s menagerie of gut microbes? Short answer: Scientists don’t know yet. But they have some clues. For instance, Bacteroidetes—the microbes linked to slimness—proliferate in the presence of fructans, a form of fructose found in asparagus, artichokes, garlic, and onions, among other foods, notes microbiologist Andrew Gewirtz of Georgia State University. A diet high in fructans might support a good crop of slimming Bacteroidetes. On the other hand, he notes, stress decreases the abundance of Bacteroidetes, suggesting one more way stress causes obesity.

“Lots of people are exploring the possibility of using antibiotics or prebiotics or probiotics to treat obesity,” says Colorado’s Knight. Prebiotics are foods that promote the growth of some bacteria at the expense of others. Probiotics are live microorganisms such as the Lactobacillus in yogurt; the idea is to ingest beneficial ones. The strategy with antibiotics would be similar: Zap the obesity-promoting ones. These ideas are in their very earliest stages, so don’t go looking on your drugstore shelves for such products just yet.

Much clearer is the strong evidence that modern medicine’s penchant for antibiotics has a downside beyond the well-known problem of breeding antibiotic-resistant bugs. A study of 11,532 children found that, on average, those exposed to antibiotics for the usual childhood ills, such as ear infections, from birth to 5 months of age weighed more for their height than other kids. By 38 months, they had a 22 percent greater likelihood of being overweight, scientists reported last August. “The rise of obesity around the world is coincident with widespread antibiotic use,” says Blaser. “It is possible that early exposure to antibiotics primes children for obesity later in life.” That’s one reason farmers add antibiotics to animal feed: The drugs alter the gut bacteria in cattle, pigs, and others, substituting bacteria that are better at extracting maximum calories from feed and thereby making the animals pack on the pounds.

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The story, recounted in a 1911 book The Bacillus of Long Life, describes healthy bacteria now called probiotics. Today, probiotics—defined by the World Health Organization as live microbes that confer a health benefit—are one of the hottest consumer health products. Last year, according to research firm Euromonitor International, more than 63,000 tons of probiotic cultures were consumed worldwide.

Americans are turning to probiotics in part to counter the sanitizing effect of modern food processing, which minimizes risks of pathogens in food but also kills natural flora which some scientists believe have health benefits. Live bacteria, originally marketed mainly in yogurt and dietary supplements, are now being added to breakfast cereals, juices, sports drinks, muffins, chocolate, and even pizza. Potential health benefits range from better digestive health to prevention of colds and flus.

Consider Herald Hollingshed, a 44-year-old technical director for a computer-services company, who felt his digestion started “slowing” when he hit middle age. He was frequently uncomfortable and bloated, but found relief with a Procter & Gamble product, Align. The pill “helps everything flow as it should,” says Hollingshed, who also switched to a healthier diet. “I feel in my best shape ever.”

For Cheryl Richardson, a 67-year-old retired lab technician from Chestertown, Maryland, probiotics over the years have helped balance the negative effects of antibiotics. Several years ago, after becoming ill from restaurant food while on vacation in the British Isles, a doctor prescribed an antibiotic that seemed to throw her digestive system out of whack. High doses of probiotics put it back on track.

“This replaces all the bacteria and helps your system digest food properly,” says Richardson.

For consumers, it’s simultaneously a cornucopia of choice and a confusing cacophony of marketing messages. The consumer “goes into a supermarket and has no idea which product to buy,” says Gregor Reid, professor of microbiology at the University of Western Ontario’s Lawson Research Institute. Despite the potential for confusion, scientists say probiotics hold great promise for human health. The evidence lies, in part, with the beneficial effects of breast milk. Beneficial gut flora called bifidobacteria are higher in breast-fed infants than in those fed by formula, says Glenn R. Gibson, professor of food microbiology at University of Reading in England, adding that the breast-fed infants have lower incidence of asthma and eczema. Good bacteria drop after babies are weaned, then remain stable through adult life until they drop precipitously around age 60 to 65. “They don’t go away completely, but they decrease and make us more prone to infections,” Gibson says. Low levels of good gut bacteria, he says, is likely at least part of the reason why the elderly suffer most during food-poisoning outbreaks.

The theory of how probiotics help us has for years been simple: The good bacteria crowd out the bad, resulting in better health. In recent years, scientists have learned that probiotic bacteria also take on many more useful tasks, says Philip M. Sherman, a scientist at the Hospital for Sick Children in Toronto. For example, scientists believe some types of probiotic bacteria help boost production of a protective mucus which lines the gut. Others, he says, produce cellular messages that calm harmful inflammation.

A growing number of scientists believe that gut microbes can change overall health. Scientists are beginning to study the use of probiotics to treat depression and even obesity. Benefits have already been shown for the digestive system, immune modulation, and dental health. There is even talk of the potential to increase longevity. “It’s exciting and there’s great promise,” says Joan Salge Blake, a clinical associate professor of nutrition at Boston University and a spokeswoman for the nonprofit Academy of Nutrition and Dietetics.

Meet the Healthy Microbes: These microorganisms have been shown to boost health in published scientific studies. (Click image to enlarge chart.)

If you want the benefits of probiotics, you need to select carefully. “It’s not one size fits all,” says Salge Blake. “The one that may help with constipation is different from the one that may help with immune support. Make sure you are getting the right strain for what you want.”

For example, Dannon Activia yogurt and Procter & Gamble Co.’s probiotic capsule Align have shown in scientific studies to improve gastrointestinal health. In four published studies, Activia improved food’s transit time through the gut. Align, shown to be effective in a chronic condition called irritable bowel syndrome, is also helpful for milder digestion problems.

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