According to Gail Cresci, dietitian and researcher at the Medical College of Georgia healthy eating with high-quality protein, fiber, healthy fats and fresh fruits and vegetables is the best way to keep the good bacteria in your gut healthy.
Poor diets are hurting the bacteria in many of us and the overuse of antibiotics is taking its toll as well, particularly the common, broad-spectrum antibiotics that wipe out anything in their path, good and bad bacteria included.
According to scientists at Sweden's Karolinska Institute, eating a fatty diet actually changes genes by altering the function of DNA in certain cells. The fat they studied was a saturated fatty acid called palmitic acid, one of the two most common saturated fatty acids. It may raise both good HDL and bad LDL cholesterol, even when eaten in moderation.
There is even mounting evidence that a healthy gut microbiota helps maintain a healthy weight. Reports show that microbial populations in the gut are different between obese and lean people, and that when the obese people lost weight their microflora reverted back to that observed in a lean person, suggesting that obesity may have a microbial component. Also, when bacteria from a genetically fat mouse are placed in a lean germ-free mouse, it gains weight without changing its food intake.
If you eat a lot of processed foods, rely on mostly cooked foods or foods high in sugar, the balance of bacteria in your digestive tract will have a hard time staying optimal. Sugar, by the way, is also an incredibly efficient fertilizer for growing bad bacteria and yeast in your gut. Also, stress, pollution and taking antibiotics can further upset your gut bacteria balance in a negative way.
Eating fermented foods such as: Natto, Miso, Kimchee, Tempeh, Kefir, Yogurt, Olives, Sauerkraut, Pickles and/or taking a high-quality probiotic is recommended for getting the proper ratio between the good/bad bacteria as well. source