We Asked Gastroenterologists If Taking Probiotics During Antibiotics Really Helps—Here’s What They Said

Probiotics can support gut health during antibiotics, but they don’t work the same for everyone.

Reviewed by Dietitian Katey Davidson, M.Sc.FN, RD, CPT

Key Points

• Antibiotics can temporarily disrupt the balance of good bacteria in the gut.
• Probiotics may help reduce antibiotic-related diarrhea but aren’t helpful for everyone.
• A fiber-rich diet and fermented foods support overall gut health.

Antibiotics are essential for treating serious bacterial infections and can be life-saving. However, while they target harmful bacteria, they can also disrupt the balance of good bacteria in the gut microbiome—the unique ecosystem of microbes living in your gut.

Research shows that antibiotic use can temporarily alter the gut microbiome and, in some cases, may increase the risk of digestive issues such as antibiotic-associated diarrhea and irritable bowel syndrome.

As a result, many people consider taking probiotics to help support gut health during or after a course of antibiotics. To better understand how to use probiotics effectively—and whether they’re even necessary—we spoke with gastroenterologists about the do’s, don’ts and best practices for combining probiotics with antibiotics.

How Antibiotics Affect the Gut Microbiome

The majority of antibiotics are broad-spectrum, meaning they don’t discriminate between good and bad bacteria. “Although antibiotics can eliminate harmful bacteria in the body, they can also destroy beneficial bacteria in the digestive system,” says Peyton Berookim, M.D., FACG. This disruption can lead to an unbalanced microbiome, also known as gut dysbiosis.

“That is one reason diarrhea, bloating, cramping and stomach upset are so common during or after a course of antibiotics,” adds Jason Korenblit, MD.

Berookim and Korenblit also note that antibiotics can increase the risk of certain gut infections, such as Clostridioides difficile (C. diff)and that it often takes weeks or even months for the gut microbiome to recover from just one course of antibiotics.

How Probiotic Supplements May Help

The good news is that some negative side effects caused by antibiotics may be managed with probiotics. Korenblit points to research that suggests probiotics may help prevent antibiotic-associated diarrhea, as well as diarrhea related to C. diff infection, specifically in people taking antibiotics.

However, he also emphasizes that the research is still evolving and doesn’t guarantee effectiveness: “Probiotics may help some people, especially those who are prone to antibiotic-associated diarrhea, but they are not a cure-all and they do not fully ‘restore’ the microbiome.” More research is needed to determine which strains, doses and treatment duration are most effective (if any).

In other words, the benefits of taking a probiotic during or after antibiotic treatment can vary widely from person to person. This highlights the importance of individualized guidance from a health care provider.

How to Support a Healthy Gut During Antibiotic Treatment

While certain probiotic supplements may help some individuals, the foods you eat play a key role in supporting gut health. “While supplements can be helpful, diet is the key to gut health,” says Berookim.

Foods rich in prebiotics and probiotics are especially important. Prebiotics are plant fibers that act as “food” for beneficial gut bacteria, helping them grow and thrive. Probiotics, on the other hand, are live microorganisms found in certain foods and supplements that may offer health benefits. Getting your probiotics from whole-food sources instead of supplements is often best, shares Pratima Dibba, MD.

Gastroenterologists commonly recommend eating prebiotic fiber–rich foods, such as fruits, vegetables, nuts, seeds and whole grains. For probiotics, look for fermented foods such as yogurt with live active cultures, kefir, sauerkraut (unpasteurized and vinegar-free), kimchi, miso and pickles.

If you choose to take a probiotic supplement, timing may matter. Some research suggests starting within two days of your first antibiotic dose may be more beneficial than waiting.

“[Probiotics] should be taken at least one to two hours before [or after] the antibiotics so they are not killed off,” Berookim recommends. Still, this isn’t an exact rule. “I would avoid acting like there is one ‘magic spacing’ rule, such as exactly one hour, because the evidence is not that precise,” explains Korenblit. “The bigger message is to start early if you are going to use one, and separate it from the antibiotic dose.”

What to Look For in a Probiotic Supplement

Not all probiotic supplements are created equal, and one size doesn’t fit all. Here are some expert-backed tips to consider when choosing a probiotic:

• Look for Independent Testing. To ensure what’s on the label is what’s in the bottle, choose brands that undergo independent (third-party) testing.
• Pick the Right Strains. “You want to make sure that you understand the types of probiotic strains,” advises Rucha Shah, MD. Korenblit recommends choosing specific genera, species and strains that have been studied for the concern you’re trying to address. For example, Lactobacillus rhamnosus GG and Saccharomyces boulardii are among the most well-researched for antibiotic-associated diarrhea and dysbiosis.
• Consider Potency. “Follow storage instructions carefully, because these are live organisms and some products lose potency over time,” says Korenblit. He suggests choosing products that list colony-forming units (CFUs) at the end of shelf life rather than at the time of manufacture.
• More Isn’t Always Better. A higher number of strains or CFUs doesn’t necessarily mean a probiotic is more effective. “A supplement that promises 10 to 15 strains [may not] be as strong as one or two good-quality strains,” says Shah.
• Get Professional Advice. Talk to your health care provider before starting a probiotic to ensure it’s appropriate for your needs—especially if you have underlying health conditions or are experiencing side effects from antibiotics.

Our Expert Take

Antibiotics can disrupt the balance of bacteria in your gut. Certain probiotics may help reduce the risk of antibiotic-associated diarrhea, especially when started early in treatment and taken a few hours apart from the antibiotic dose.

That said, probiotic supplements aren’t necessary or helpful for everyone during or after antibiotic use. In many cases, eating a diet rich in prebiotics and fermented foods is a safe and effective way to support a healthy gut microbiome.

Probiotic supplements may help in some cases, but they’re not a substitute for a balanced diet and personalized medical advice.