Doctors Reveal the Number-1 Medication That Affects Your Gut

Here's what to do (and what not to do) to stay healthy.

Published on Mar. 2, 2026

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Ongoing research has revealed that some medications may have unexpected effects on the body, particularly on the gut microbiome. Gastroenterologists say the number-one medication that impacts the gut the most is antibiotics, which can kill not only the pathogenic bacteria they were prescribed to treat, but also the population of normal commensal bacteria that live in the gut. Other medications that can affect the gut include proton pump inhibitors, certain laxatives, nonsteroidal anti-inflammatory drugs (NSAIDs), and certain cardiac medications.

Why it matters

The changes these medications can make in your gut may persist for years after you stop taking them, so it's important to understand the potential impact on your gut health.

The details

Antibiotics are relatively broad in their action and can disrupt the normal gut microbiome. While antibiotics may be damaging, they aren't the only medication that can impact your gut - proton pump inhibitors, certain laxatives, nonsteroidal anti-inflammatory drugs (NSAIDs), and certain cardiac medications can also affect the gut. Unfortunately, there is no data to suggest that anything protects your microbiome from changes incurred by antibiotics, and probiotics have not been studied enough to determine if they offer any protection.

  • A new study published in the journal mSystems found that the changes these medications can make in your gut may persist for years after you stop taking the medication.

The players

John Nathanson, M.D.

A gastroenterologist at NewYork-Presbyterian/Columbia University Irving Medical Center.

Pratima Dibba, M.D.

A gastroenterologist with Medical Offices of Manhattan.

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What they’re saying

“Antibiotics are relatively broad in their action. They can kill not only the pathogenic bacteria they were prescribed to treat, but also the population of normal commensal bacteria that live in our gut.”

— John Nathanson, M.D., Gastroenterologist (Prevention)

“There is no data to suggest that anything protects your microbiome from changes incurred by antibiotics.”

— Pratima Dibba, M.D., Gastroenterologist (Prevention)

What’s next

If you're prescribed medication that can alter your gut microbiome, such as an antibiotic, taking steps to support your gut health, like eating fiber-rich foods, may help.

The takeaway

While medications like antibiotics can have a disruptive effect on the gut microbiome, it's important to take them as directed by your doctor. Supporting your gut health through diet and other means may help mitigate the impact, but more research is needed on effective strategies.