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Taking Antibiotics? You Should Protect Your Gut Bacteria

Antibiotics can kill good bacteria with the bad. Here’s what to do about it.


There’s no question that antibiotics are lifesavers: They kill the harmful bacteria that cause infection. But antibiotics don’t discriminate. They can also attack good bacteria, like the kind that live in your intestines. According to a study, the effects of taking certain antibiotics can last from a few weeks up to a year. 

Why is it so important to keep friendly bacteria around? Because when your gut’s bacterial community—which consists of trillions of bacteria—is healthy, it plays a role with everything from digesting nutrients to supporting your immune system to affecting the hormones that help you think and feel better. Killing off the good bacteria in your gut can mess all that up. When your bacteria levels get out of balance, you can develop acid reflux or intestinal issues like diarrhea. Emerging evidence shows that an imbalance of your gut bacteria may even play a role in the development of allergies, diabetes, and obesity.

Bottom line: It’s important to keep your gastrointestinal tract’s bacteria—called the gut microbiota—diverse, balanced, and healthy, which can be a challenge when you’re taking antibiotics. Of course, you shouldn’t avoid antibiotics if your doctor says you need them, so use these easy ways to keep your microbiome robust during and after a course of meds:

  • Take a probiotic supplement. Not only can a daily probiotic supplement help ward off antibiotic-related diarrhea, but it may help with some intestinal infections and vaginal and urinary tract infections. Not all probiotic supplements contain the same bacteria, and different bacteria have different functions. Because different probiotics have different benefits, make sure you look for a product that supports the benefit you want. You can buy probiotics that are shelf-stable (they’re freeze-dried so the heat- and moisture-sensitive bacteria can survive) or refrigerated (just make sure to keep them cold). Ask your doctor to recommend a trusted brand, or visit, an independent lab that tests supplements to see if they contain what they claim on their label.
  • Go easy on sugar and fats. Bad bacteria love to feed on sugar and fat, so depriving them of their preferred diet can help keep the bad bugs from overtaking the good ones. And you can support good bacteria with fruits and vegetables, which have complex carbs that helpful bacteria thrive on. For your next meal, hit the salad bar, and skip the burger and shake.
  • Focus on fiber-rich foods. Bifidobacterium, a family of good bacteria, love fiber, especially inulin and FOS (fructooligosaccharide), both of which are found in onions, Jerusalem artichokes, asparagus, leeks, and garlic. Inulin and FOS fibers are prebiotics, carbs that probiotics feed on. By providing the gut’s good bacteria with food, you encourage healthier members of microbiota to grow and metabolize foods.
  • Eat fermented foods. Yogurt and kefir naturally contain live, active cultures (you need live cultures in fermented foods to reap the gut-healthy benefits). Look for the words “live and active cultures” on the label—it’s a voluntary seal that manufacturers participate in to indicate that their yogurts contain at least 100 million cultures per gram. Other fermented foods like miso, tempeh, and kimchi often contain live cultures, too. But when you’re doing your shopping, keep in mind that heat and filtration can kill or remove active cultures, so check the labels carefully and do your research before you hit the grocery store.