Recent research indicates that many commonly prescribed medications can lead to enduring changes in gut bacteria. The study analyzed stool samples from over 2,500 participants from the Estonian Biobank, comparing their prescription records with data from the Estonian Microbiome cohort. The researchers aimed to explore if medication usage influenced the gut microbiome, the community of bacteria and microorganisms in the digestive tract.
The study uncovered that most medications examined were linked to variations in the gut microbiome. Surprisingly, these changes persisted years after patients discontinued the medication. This effect was not limited to antibiotics, which are already known to impact gut bacteria, but included antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines. Each medication category presented a unique microbial ‘fingerprint’ in the gut.
Dr. Oliver Aasmets, the study’s lead author, stated, “Most microbiome studies only consider current medications, but our results show that past drug use can be just as important as it is a surprisingly strong factor in explaining individual microbiome differences.”
Such findings suggest new directions for future microbiome research. If past medication use continues to affect the gut microbiome, researchers will need to consider medication history when exploring links between the microbiome and disease.
Dr. Lucy Hooper, a GP and co-founder of Coyne Medical in London, explained to Newsweek that certain groups might be more susceptible to long-term microbiome alterations. Babies and young children, who are still developing their gut microbiome, face potential greater impacts from disruptions. Previous studies linked early antibiotic use and microbiome modifications in children to conditions such as asthma, obesity, and type 2 diabetes. Similarly, older adults, whose microbiome diversity generally declines with age, may be more susceptible due to frequent or prolonged medication use.
Benzodiazepines Stand Out in the Findings
The study highlighted significant findings related to benzodiazepines, a drug class often prescribed for anxiety and other disorders. The correlation between benzodiazepine use and changes in the gut microbiome was similar to that seen with broad-spectrum antibiotics, known for causing substantial alterations in gut microbes.
Notably, medications within the same class did not uniformly affect the microbiome. For instance, diazepam and alprazolam, although prescribed for similar conditions, showed varying degrees of impact on gut microbes. This finding is crucial as microbiome studies frequently group medications of the same class together, but these results suggest assessing individual drugs separately is necessary when considering their effects on the microbiome.
Follow-up stool sample analyses from a smaller participant group allowed observation of gut microbial changes following medication usage shifts. These findings provided evidence that the medications themselves contribute to certain microbiome differences observed.
Although based on a relatively small follow-up group, the researchers confirmed ongoing effects related to proton pump inhibitors, selective serotonin reuptake inhibitors (SSRIs), and specific antibiotics, such as combination penicillins and macrolides. Lifestyle factors might also affect microbiome recovery post-medication, according to Hooper. Low dietary fiber intake typically results in a less resilient microbiome, potentially complicating recovery after disruptions.
Why Past Medication Use Matters
The study suggests that a person’s gut microbiome reflects more than just their current diet, lifestyle, health, and medication use. Traces of past medications may still be detectable. The researchers urge scientists and clinicians to take medication history into account when analyzing microbiome data. Some microbiome changes that seem related to disease could instead be linked to drugs taken months or years earlier.
Hooper stated, “We have lots of studies showing correlation or patterns. But fewer studies show ‘causation.’ We need to track microbiome changes in more people over time to determine the true impact of medication.” She emphasized, “No one should stop medication because they are worried about their microbiome, but it is always sensible to regularly review medicines.”
Reference: Oliver Aasmets, et al. A hidden confounder for microbiome studies: medications used years before sample collection. mSystems, 2025; 10 (10) DOI: 10.1128/msystems.00541-25
Contact Newsweek editors on this story: Kara Dolman and Emma Lee-Sang.