Common medications may secretly rewire your intestines for years

Medications a person took years ago can still affect the community of microbes living in their gut, according to a large study by the Institute of Genomics at the University of Tartu.

By examining stool samples and prescription data from more than 2,500 participants in the Estonian Biobank’s Microbiome Cohort, the scientists discovered that most of the drugs they analyzed were associated with measurable changes in the gut microbiome. Many of these changes persist long after people stop taking medications. The lasting impact was not limited to antibiotics: antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines also left distinct microbial fingerprints.

Dr Oliver Asmets, lead author of the study, said: ‘Most microbiome studies only consider current medications, but our results show that past drug use can be just as important as a surprisingly powerful factor in explaining individual microbiome differences.’ The results underscore the importance of considering a person’s medication history when exploring links between gut microbes and disease.

Interestingly, benzodiazepines—commonly prescribed for anxiety—produced microbiome changes similar to those seen with broad-spectrum antibiotics. The study also revealed that drugs in the same class, such as diazepam and alprazolam, can differ in the extent to which they disrupt intestinal microbial balance.

Follow-up samples from a smaller group of participants showed that starting or stopping certain medications led to predictable shifts in the gut microbiome, supporting a possible cause-and-effect relationship. Although this second phase involved fewer samples, researchers confirmed persistent effects of proton pump inhibitors, selective serotonin reuptake inhibitors, and several antibiotics, including combined penicillins and macrolides.

Professor Eileen Orge, corresponding author of the study, said: “This is a comprehensive systematic evaluation of the long-term effects of a drug on the microbiome using real-world medical health records.” “We hope this will encourage researchers and clinicians to take medication history into account when interpreting microbiome data.”