Our bodies house some 400 species of friendly bacteria, or “probiotics.” They cling to the walls of our stomachs and intestines. In the age of germphobia, it’s hard to imagine microbes as our allies. But mounting evidence suggests that these friendly flora aid digestion, ward off pathogens and help us process folic acid and other critical nutrients. When the complex balance of microbes is jilted by stress, alcohol, antibiotics or poor nutrition, the consequences can be most unpleasant–ranging from stomachaches to vaginal infections, vitamin deficiencies and chronic inflammation. Fortunately, a little fine-tuning can keep your system humming.

We are not born with probiotics; they come from our environment. Babies encounter their first friendly microbes in breast milk. Familiar sources include yogurt, buttermilk, fermented cheese, kefir (cultured milk) and miso (fermented soybeans). And because these microbes thrive on nondigested sugars called fructooligosaccharides (“prebiotics”), foods such as onions, asparagus, tomatoes, garlic, artichokes, honey and bananas can all help the bacteria thrive.

Scientists have long suspected a link between these microbes and overall health. Russian bacteriologist Elie Metchnikoff won a Nobel Prize in the early 1900s for linking yogurt consumption to longevity. But probiotics received little attention until the mid-1980s, when Drs. Sherwood Gorbach and Barry Goldin of Tufts University discovered lactobacillus, the bacteria used in the majority of today’s research. Today, says microbiologist Gerald Tannock of the University of Otago in Dunedin, New Zea-land, “we are experiencing a renaissance in [probiotics] research.”

Besides crowding out harmful bacteria, friendly flora maintain the acidic environment needed to control them, even releasing hydrogen peroxide to maim wayward bugs. And when there are fewer pathogens on hand, the immune system is less likely to get overwhelmed. Studies suggest that healthy bacteria can help ward off bladder infections, vaginal infections, even sexually transmitted diseases. Among hospitalized infants, those given formula enriched with bifidobacteria (the bacteria found in breast milk) are less likely to develop infectious diarrhea. People who take lactobacillus supplements for two weeks before receiving a typhoid vaccine exhibit a stronger immune response. And researchers will soon report evidence that lactobacillus can lower the risk of respiratory infections in children.

Healthy colonies of gut flora can also ease the inflammation caused by food allergies, Crohn’s disease, ulcerative colitis and irritable-bowel syndrome. These conditions arise when the body misidentifies harmless enteric bacteria as pathogens and mounts an immune response. Some doctors now use probiotic supplements as therapy for these conditions, hoping the friendly bacteria will displace the indigenous strains causing the inflammation. And researchers have recently begun testing genetically modified bacteria as treatments for various inflammatory disorders–a pursuit that could take the science of probiotics to a whole new level.

Does a healthy person need daily probiotic capsules? Gorbach doesn’t think so. But if you suffer from lactose intolerance, food allergies or traveler’s diarrhea–or you’ve spent the last three months popping penicillin–an extra hit of friendly bacteria is worth considering. Europeans have long championed yogurt and fermented milk as tonics for good health. But Americans consume fewer fermented dairy products than any other developed country. It may be no coincidence that 60 to 70 percent of us complain of digestive ills.

What is the best way to boost your bacterial intake? Food and drug companies now peddle probiotics in pills, powders and liquids. Probiotics normally take about three days to affect your system. They have almost no side effects, but as dietary supplements they aren’t subject to rigorous quality-inspection or labeling rules. “Many times the bug [advertised on the label] is not even there,” says Dr. Roger Clemens of California State Polytechnic University. Experts recommend buying a reputable brand, such as Dannon, Nature’s Way, Imodium or Culturelle. Look for a label that promises “live and active cultures,” and make sure it carries an expiration date. Most products need to be kept refrigerated and away from sunlight, though at least one supplement (Culturelle) comes freeze-dried and lasts up to two years.

You can also add probiotics naturally to your diet. Valio just launched a probiotic cheese in Europe. And milk enriched with acidophilus and bifidus now sits on my refrigerator shelf–right beside the mango-mandarin-orange yogurt. The thought of eating bugs may turn your stomach. Get over it. I know they’ve done wonders for mine.