Photo: Levi Brown
Your belly is a popular place: As many as 100 trillion microbes call it home. Many of them are beneficial bacteria that process hard-to-digest foods, produce nutrients, and—as we're now learning—guard against disease. "Studies suggest that these bacteria may protect you not just from food-borne pathogens but also from cold-causing germs," says Justin Sonnenburg, PhD, assistant professor of microbiology and immunology at Stanford School of Medicine.

Yet your gut is also filled with "bad" bacteria that release toxins and are increasingly associated with a range of health problems. "If you have an autoimmune disorder, depression, allergies, or any number of other illnesses, the underlying cause may be an unhealthy balance of gut bugs," says Mark Hyman, MD, founder and medical director of the UltraWellness Center in Lenox, Massachusetts. Having the wrong mix of microbes may even contribute to obesity.

So how do you cultivate beneficial bacteria and force the harmful ones out? Here's where new research says to start.

Feed the good bugs.
Intestinal bacteria need to eat, and mounting evidence indicates that beneficial bugs prefer nutrients called prebiotics, which are primarily found in high-fiber foods including onions, garlic, bananas, artichokes, and many greens. Bad bacteria, on the other hand, prefer the sugars and fats found in processed foods. "There are indications that a low-fiber, high-fat diet results in more harmful gut microbes," says Hyman. A 2010 study compared a group of European children who had a diet high in fat, sugar, and starch, with tribal African children who ate high-fiber, plant-based foods, and found that the Africans had more health-promoting bacteria.

Pick the right probiotics.
You can also tilt your balance toward good bugs simply by eating more of them—in the form of probiotics, which are live bacteria contained in foods and supplements. But if you have a specific health goal in mind, check the bacteria a product contains. "There are different species, and different strains within species, and they all have different functions," says Mary Ellen Sanders, PhD, executive director of the International Scientific Association for Probiotics and Prebiotics. A 2010 Georgetown University study found that the strain Lactobacillus casei (available in the yogurt drink DanActive) reduced the frequency of ear infections and gastrointestinal infections in children, while a 2006 study found that Bifidobacterium infantis (available in the probiotic supplement Align) relieved the symptoms of irritable bowel syndrome.

Avoid bacteria-harming drugs.
The antibiotics we take to kill pathogens also lay waste to the bacteria in our digestive tract. Research from Stanford University published last September found that taking two courses of antibiotics, spaced six months apart, changed the composition of good and bad intestinal bugs, disrupting the overall balance. Hyman recommends avoiding antibiotics when you can—if you have a virus that antibiotics won't help, don't ask for a prescription anyway. He also suggests laying off heartburn pills; although less harmful to gut flora than antibiotics, they alter the proportions of intestinal bacteria as well. The upside is, if you're already getting the right prebiotics and probiotics, you may be less likely to need such meds in the first place.

Celeste Perron is a freelance writer and blogger in San Francisco.

More Digestive Health and Probiotics