A new study from the University of Tartu Institute of Genomics has found that medications taken years ago can continue to shape the human gut microbiome.
This groundbreaking research, published in the journal mSystems, used data from over 2,500 participants in the Estonian Microbiome cohort of the Estonian Biobank.
By analyzing stool samples and prescription records, researchers discovered that a majority of the drugs studied were associated with long-term microbiome changes—some detectable even years after patients had stopped taking them.
This impact extended beyond antibiotics and included commonly used drugs such as antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines.
“Most microbiome studies only consider current medications, but our results show that past drug use can be just as important,” said Dr. Oliver Aasmets, the study’s lead author. “It is a surprisingly strong factor in explaining individual microbiome differences.”
The study underscores the need to consider a patient’s complete medication history when examining the microbiome and its links to health and disease.
Interestingly, the research found that benzodiazepines, often prescribed for anxiety, had effects on the microbiome comparable to those caused by broad-spectrum antibiotics.
Moreover, different drugs within the same class—such as diazepam versus alprazolam—produced varying degrees of disruption.
To strengthen their findings, researchers examined follow-up samples from a subset of participants and confirmed that the introduction or discontinuation of certain medications caused predictable changes in microbial composition.
Long-term effects were especially noted with PPIs, selective serotonin reuptake inhibitors (SSRIs), and antibiotic classes like penicillins in combination and macrolides.
“This is a comprehensive systematic evaluation of long-term medication effects on the microbiome using real-world medical health records,” said Professor Elin Org, the study’s senior author. “We hope this encourages researchers and clinicians to factor in medication history when interpreting microbiome data.”
This research has major implications for future studies on the microbiome and could change how clinicians interpret stool sample analyses and patient gut health.
The study is published in mSystems.
Copyright © 2025 Knowridge Science Report. All rights reserved.
