Modern humans are bacteria-killing machines. We assassinate microbes with hand soap, mouthwash and bathroom cleaners. It feels clean and right.

But some scientists say we're overdoing it. All this killing may actually cause diseases like eczema, irritable bowel syndrome and even diabetes. The answer, they say, is counterintuitive: Feed patients bacteria.

"Probiotics (pills containing bacteria) have resulted in complete elimination of eczema in 80 percent of the people we've treated," says Dr. Joseph E. Pizzorno Jr., a practicing physician and former member of the White House Commission on Complementary and Alternative Medicine Policy. Pizzorno says he's used probiotics to treat irritable bowel disease, acne and even premenstrual syndrome. "It's unusual for me to see a patient with a chronic disease that doesn't respond to probiotics."

Clinical trial data on probiotics is incomplete, but there are many indications that hacking the body's bacteria is beneficial.

In sheer numbers, bacterial cells in the body outnumber our own by a factor of 10, with 50 trillion bacteria living in the digestive system alone, where they've remained largely unstudied until the last decade. As scientists learn more about them, they're beginning to chart the complex symbiosis between the tiny bugs and our health.

"The microbes that live in the human body are quite ancient," says NYU Medical Center microbiologist Dr. Martin Blaser, a pioneer in gut microbe research. "They've been selected (through evolution) because they help us."

And it now appears that our daily antibacterial regimens are disrupting a balance that once protected humans from health problems, especially allergies and malfunctioning immune responses.

"After the Second World War, when our lifestyles changed dramatically, allergies increased. Autoimmune diseases like diabetes and inflammatory bowel disease are increasing," says Kaarina Kukkonen, a University of Helsinki allergy expert. "The theory behind (what causes) the diseases is the same: Lacking bacterial stimulation in our environments may cause this increase. I think this is the tip of the iceberg."

In a recent study, Kukkonen and her colleagues gave a probiotic containing four strains of gut bacteria to 461 infants labeled as high risk for developing allergic disorders. After two years, the children were 25 percent less likely than those given a placebo to develop eczema, a type of allergic skin inflammation. The study was published in the January issue of Journal of Allergy and Clinical Immunology.

Microbial exposures early in life, scientists believe, cause mild inflammation that calibrates the body's responses to other pathogens and contaminants later in life. Without exposure as infants, researchers say, people can end up with unbalanced immune systems.

"Many of the most difficult problems in medicine today are chronic inflammatory diseases," says Blaser. "These include rheumatoid arthritis, lupus, atherosclerosis, eczema and multiple sclerosis. One possibility is that they're autoimmune or genetic diseases. The other possibility is that they are physiological responses to changes in microbiota."

Blaser's specialty is Helicobacter pylori, a strain once common in every human stomach but now rare in the West. Its disappearance may have benefits: H. pylori-related inflammation is associated with peptic ulcers and some stomach cancers. However, H. pylori also reduces acid reflux, which in turn is associated with asthma and esophageal cancers.

H. pylori's decline, says Blaser, correlates with a rapid rise in those afflictions. H. pylori deficiency may also contribute to obesity, he says, because the bacteria help regulate production of two hormones, ghrelin and leptin, that affect metabolism and appetite.

Low levels of Bacteroidetes have also been linked to obesity. Studies indicate that bacterial imbalances are associated with irritable bowel syndrome, post-surgical infections and type 1 diabetes.

The health-food movement has moved ahead with probiotics without regard for clinical trial results. Women commonly use supplements like acidophilus to treat yeast infections. Other probiotics are making their way into products such as Kashi Vive cereal "to help you care for your digestive system" and Dannon's Activia yogurt, which in its first year boasted more than $100 million in sales. But scientists say over-the-counter probiotics are of inconsistent quality.

Pizzorno, for example, buys his probiotics from companies that sell directly to doctors. Consumer probiotics don't always contain medically recognized bacterial strains, he said, and often the bacteria they contain are dead.

"Most of the companies don't have any research ongoing at all," says Stig Bengmark, a University of London hepatologist. "They buy cheap bacteria from yogurt companies and say it's good, but it's never proven."

To more precisely hack the gut bacteria, Blaser calls for a Gut Genome Project, modeled after the Human Genome Project. It's a daunting task: The human genome, mapped to great fanfare but still dimly understood, contains a tenth of the genes believed to be in our gut bacteria. But though difficult, such research could prove vital.

"The world is very aware of the concept of global warming, which is a macro-ecological change," Blaser says. "I postulate that there are similar micro-ecological changes going on inside us."

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