Taking Antibiotics? Here’s How To Prevent Tummy Trouble

Katie Mui
Katie Mui is on the Research Team at GoodRx.
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Antibiotics are one of the wonders of modern medicine — they can purge the human body of infections that just a few decades ago would’ve been fatal. And they get used — a lot. Over 250 million prescriptions for antibiotics are written every year in the U.S., nearly one prescription for every American. What’s more, today’s antibiotics, such as Amoxil (amoxicillin, $4), Cipro (ciprofloxacin, $4), and Macrobid (nitrofurantoin, $19.61), used to treat most uncomplicated infections are affordable.

But antibiotics don’t just kill bad bacteria — they take out a lot of good bacteria as well, especially the bacteria in our gut. These bacteria help keep us healthy; they supply essential nutrients, digest cellulose, produce essential vitamins, and detox harmful substances. They are part of the ecosystem within our bodies, called the microbiome.

And it’s not just antibiotics; other medications can also harm these good microbes, including antacids like Prilosec (opremazole) and Nexium (esomeprazole), and the diabetes drug Glucophage (metformin). When your microbiome gets out of balance, you’ll likely suffer gastrointestinal issues such as upset stomach, indigestion, and diarrhea.

Beyond tummy trouble, an unhealthy microbiome is bad because it may make you more susceptible to health problems and diseases like cancer and obesity. So, if you’ve taken any of the above meds — or if you just want to help boost your immunity — here are some foods that can help rebalance the diversity of your microbiome. They are also perfectly fine to do even if you’re currently on those bacteria-depleting treatments.

Fiber-rich foods

High fiber foods can reduce inflammation in your gastrointestinal system, and can also positively affect your microbiome. You can get a lot of fiber from leafy greens like kale, beans, legumes, oatmeal and fruit. An easy way to incorporate more fiber into your diet is to sprinkle flax or chia seeds into your breakfast cereal or mix them into a yogurt or smoothie.

Cultured or fermented foods

Whether it’s kimchi, sauerkraut, miso, nattō (fermented soybeans), buttermilk, or kombucha, fermented foods provide enzymes that aid better digestion and rebuild gut flora. Pickled vegetables, yogurt, and cheese may also help — but check their labels to ensure they were made with live cultures or “active cultures” of microorganisms (which are also found in probiotic supplements, listed below). Examples include strains of Lactobacillus and Bifidobacteria, both of which can be found in yogurt.


It doesn’t just ward off vampires, but bad microbes as well. A study in the journal Phytomedicine shows that garlic hurts some of the bad bacteria in our guts and may boost the growth of good bacteria. For more ideas on adding garlic to your diet, check out these recipes.

Dark chocolate

Recent research has shown that the bacteria in our gut actually ferment the cocoa in chocolate to create anti-inflammatory compounds. Cocoa powder contains a small amount of dietary fiber and several antioxidant compounds (catechin and epicatechin) that don’t get absorbed well. But when they reach the colon, the good microbes take over and do their work.

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Probiotic supplements

These products, increasingly found in grocery stores in pill form or in beverages, usually include various strains of Lactobacillus, the same bacteria found in yogurt. But the quality of these supplements can vary widely, and they can be expensive. It’s easy to get confused by all the hype and claims around which probiotic supplements can actually do for you. The bottom line, though: Taking probiotics to avoid or reduce diarrhea associated with antibiotics has been found effective in numerous studies.

Prices shown are average GoodRx discounted prices as of Dec 21, 2017. Local results may vary.

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