Study: Common Medications May Alter the Gut Microbiome for Years After Use
A large Estonian study finds that many medications leave lasting traces in the gut microbiome long after people stop taking them. Researchers say past prescription history may be as important as current medication use in explaining individual microbiome differences.
Researchers at the University of Tartu Institute of Genomics have found that medications can shape the community of microbes living in the human gut for years after a person stops taking them. The team analyzed stool samples and prescription records from more than 2,500 participants in the Estonian Biobank's Microbiome cohort.
Most of the medications examined were linked to differences in the gut microbiome, and for a substantial number of drugs those differences remained detectable years after use had ended. This lasting effect was not limited to antibiotics, whose disruptive impact on gut bacteria is already well documented. Antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines were also tied to distinctive microbial signatures.
Anxiety medications show a surprisingly strong effect
One notable finding involved benzodiazepines, commonly prescribed for anxiety, whose association with the gut microbiome was comparable to that of broad-spectrum antibiotics. The study also revealed that drugs within the same class did not necessarily affect the microbiome in the same way — diazepam and alprazolam, for instance, though prescribed for similar conditions, differed in how strongly they appeared to disrupt gut microbes.
A smaller subset of participants provided follow-up stool samples, allowing researchers to track what happened when people started or stopped certain medications. These changes followed predictable patterns, supporting the idea that the medications themselves were responsible for at least some of the observed microbiome shifts. Persistent effects were confirmed for proton pump inhibitors, selective serotonin reuptake inhibitors, and certain antibiotics, including combined penicillins and macrolides.
The researchers noted that most microbiome studies only account for medications a person is currently taking, whereas their findings show past drug use can be an equally strong factor in explaining individual differences. They hope the results will encourage scientists and clinicians to factor in medication history when interpreting microbiome data, helping to better distinguish disease-related changes from those caused by previously taken drugs.
