Healthy eating, not supplements, is the best way to keep the good bacteria in your gut healthy, says a dietitian and researcher. As with vitamins, it's best to get the bacteria you need from healthy food rather than taking often expensive and potentially ineffective supplements, says Gail Cresci, Medical College of Georgia dietitian and researcher.

She equates the good bacterium in your gastrointestinal tract to another living being inside that helps keep you healthy. "If you do good by your bacteria, they will do good by you," Ms. Cresci says.

There is even mounting evidence that a healthy gut microbiota helps maintain a healthy weight. Studies have shown, for example, that when bacteria from a genetically fat mouse are placed in a lean germ-free mouse, it gains weight without changing its food intake.

Unfortunately poor diets are hurting the bacteria in many of us and the overuse of antibiotics is taking its toll as well, she says, particularly the common, broad spectrum antibiotics that wipe out anything in their path, good and bad bacteria included. She sites inadequate fiber and excess unhealthful fats as contributing to the problem, and states that a good daily diet has adequate high-quality protein, including dairy products.