Medicines you took years ago may still be affecting your gut health today.
A major study by scientists at the University of Tartu’s Institute of Genomics has found that past medication use can change the community of microbes living in your gut—and these changes can last long after you’ve stopped taking the drugs.
The research team analyzed stool samples and prescription data from more than 2,500 people in the Estonian Biobank’s Microbiome cohort.
They found that most of the medications studied left behind measurable traces in the gut microbiome—the collection of bacteria and other microorganisms that help with digestion, immunity, and overall health.
What’s even more surprising is that these long-lasting changes weren’t just caused by antibiotics. Drugs used to treat anxiety, depression, heart conditions, and stomach acid—like benzodiazepines, antidepressants, beta-blockers, and proton pump inhibitors—also left their mark on the gut.
Dr. Oliver Aasmets, the study’s lead author, explained that most previous studies only look at the medicines people are currently taking.
But this new research shows that medication history can play just as big a role in shaping a person’s gut microbiome. These long-term effects may help explain why gut health varies so much from one person to another.
One especially interesting finding was that benzodiazepines—commonly prescribed for anxiety—had effects on the microbiome that were similar to those of strong antibiotics. Even among drugs in the same class, such as diazepam and alprazolam, the study found differences in how much they disrupted the balance of gut microbes.
To explore this further, the researchers collected follow-up samples from a smaller group of participants. They tracked how the gut microbiome changed when people started or stopped certain medications.
The results showed predictable shifts in gut bacteria after using drugs like proton pump inhibitors, SSRIs (a type of antidepressant), and common antibiotics such as penicillins and macrolides. This suggests a direct link between drug use and changes in gut health.
Professor Elin Org, the senior author of the study, said that this is one of the most detailed evaluations ever done on how medications affect the microbiome over time using real-world health records.
She hopes the findings will encourage doctors and researchers to consider a person’s full medication history—not just what they’re currently taking—when studying or treating gut-related conditions.
The research adds to a growing body of evidence showing that the gut microbiome plays a major role in overall health.
By understanding how drugs influence gut bacteria, scientists may one day find better ways to protect or restore the microbiome, especially in people dealing with long-term illness or complex treatment plans.
If you care about gut health, please read studies that your gut can help lower your blood pressure: here’s how and from shock to awe: a zap in the gut could be the new insulin for people with diabetes.
For more about gut health, please read studies about a surprising link between gut health and eye disease risk and Gut troubles could signal future Parkinson’s disease.
The study is published in mSystems.
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