Common Medications Found to Impact Gut Microbiome

Study shows many drugs can alter gut bacteria for up to a decade

Published on Feb. 3, 2026

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A new study has found that common medications like antibiotics, antidepressants, and proton pump inhibitors can significantly impact a person's gut microbiome, with changes often persisting for years after the medication is stopped. Researchers analyzed stool samples and prescription data from over 2,500 participants, discovering that most drugs affected gut bacteria diversity and composition in predictable ways.

Why it matters

The gut microbiome plays a crucial role in overall health, influencing metabolism, immune function, and disease risk. Disruptions to the gut ecosystem from medications may have far-reaching consequences, potentially impacting how the body responds to other drugs in the future and contributing to rising rates of conditions like mental disorders and colon cancer at younger ages.

The details

The study, published in the journal mSystems, found that in addition to antibiotics, medications like antidepressants, antipsychotics, beta-blockers, proton pump inhibitors, and benzodiazepines all had significant impacts on gut bacteria. Benzodiazepines, used for anxiety, created microbiome changes similar to those seen with antibiotics. Researchers say these medication-driven shifts in gut bacteria may reduce diversity, boost certain bacterial groups, and change the overall ecosystem, with effects lasting for years.

  • The study was published in February 2026.

The players

Elin Org, Ph.D.

A study co-author and head of the Micobiome Research Group at the University of Tartu.

Rudolph Bedford, M.D.

A gastroenterologist at Providence Saint John's Health Center in Santa Monica, California.

Martin Blaser, M.D.

Chair of the Henry Rutgers Chair of the Human Microbiome at the Rutgers Robert Wood Johnson Medical School.

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What they’re saying

“Such medications may reduce or boost certain bacterial groups and change the overall diversity of the gut ecosystem.”

— Elin Org, Ph.D., Study co-author and head of the Micobiome Research Group at the University of Tartu (mSystems)

“We're trying to figure out why we're seeing much more mental disorders and more colon cancers at younger ages. One of the theories is that the gut microbiomes have been changed.”

— Rudolph Bedford, M.D., Gastroenterologist at Providence Saint John's Health Center (Prevention)

“It may or may not matter—depends which bugs are changed, how much, how long—this should be a major area of study.”

— Martin Blaser, M.D. (Prevention)

What’s next

Doctors stress the importance of taking medications as prescribed to minimize disruptions to the gut microbiome. Researchers also say more study is needed to fully understand the long-term impacts of medication-driven changes to gut bacteria.

The takeaway

This research highlights how common medications, from antibiotics to antidepressants, can have lasting effects on the delicate balance of the gut microbiome. Understanding these impacts is crucial, as disruptions to gut health may contribute to a range of serious health issues down the line.