New research reveals that medications taken years-even decades-ago can leave lasting marks on the gut microbiome, reshaping the balance of microbes long after treatment stops. Scientists analyzing over 2,500 participants from the Estonian Biobank found that the effects are not limited to antibiotics.

Antidepressants, beta-blockers, proton pump inhibitors, and anxiety medications also disrupt gut ecosystems, sometimes in unexpected ways. Even drugs from the same class can have different impacts on microbial communities.

Study Highlights

Researchers at the University of Tartu Institute of Genomics examined stool samples and prescription records, discovering that most drugs analyzed were linked to measurable changes in the gut microbiome. Many of these changes persisted long after patients discontinued treatment. The study is published in mSystems, the journal of the American Society for Microbiology.

Benzodiazepines, commonly prescribed for anxiety, produced microbial alterations similar to broad-spectrum antibiotics. Other drugs, such as selective serotonin reuptake inhibitors (SSRIs) and proton pump inhibitors, also showed lasting effects. Follow-up testing confirmed predictable shifts in gut microbes when specific medications were started or stopped, suggesting a likely cause-and-effect relationship.

Why This Matters

“Most microbiome studies only consider current medications, but our results show that past drug use is a surprisingly strong factor in explaining individual microbiome differences,” said Dr. Oliver Aasmets, lead author.

Professor Elin Org, the study's corresponding author, emphasized that these findings encourage researchers and clinicians to consider a patient's medication history when studying the microbiome and its links to disease.

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