Long-Lasting Effects of Medications on Gut Microbiome Revealed
Recent research indicates that many commonly prescribed medications can cause significant, lasting changes in the gut microbiome. Researchers analyzed stool samples and prescription data from over 2,500 individuals in the Estonian Biobank and the Estonian Microbiome cohort. They aimed to determine if medication use correlated with alterations in gut bacteria and other microorganisms living in the digestive system.
The findings revealed that most medications studied were linked to changes in the gut microbiome, and these changes were detectable years after discontinuing the drugs. These associations were not confined to antibiotics, widely known to affect gut bacteria. Antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines also left distinctive microbial signatures in the gut.
Dr. Oliver Aasmets, 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.” This insight suggests that microbiome research might need to consider a person’s medication history when assessing links between the microbiome and diseases.
Impact on Vulnerable Groups
Dr. Lucy Hooper, a general practitioner, noted that specific groups could be more susceptible to long-lasting microbiome changes. Young children, whose gut microbiomes are still developing, may experience more significant effects. Early antibiotic use in children has been associated with conditions like asthma, obesity, and type 2 diabetes. Older adults might also face increased risks due to declining microbiome diversity with age and frequent medication use.
Benzodiazepines’ Notable Impact
One significant discovery involved benzodiazepines, often prescribed for anxiety. Their impact on the gut microbiome mirrored that of broad-spectrum antibiotics, known to substantially alter gut bacteria. Interestingly, drugs within the same class, such as diazepam and alprazolam, displayed varied effects on gut microbes. This implies that studies should evaluate individual drugs instead of grouping them by class.
Researchers also examined follow-up stool samples from a smaller participant group. They confirmed persistent microbiome effects from proton pump inhibitors, selective serotonin reuptake inhibitors (SSRIs), and certain antibiotics. Lifestyle factors, like low dietary fiber intake, could influence the microbiome’s resilience post-medication, Hooper mentioned.
Importance of Medication History
The study suggests that a person’s gut microbiome reflects past medication use, along with current diet, lifestyle, and health. This means that some microbiome changes linked to diseases could be related to medications used previously. Hooper emphasized the need for more research to clarify whether medication-induced microbiome changes directly affect health.
Dr. Hooper advised against stopping prescribed medications due to microbiome concerns. “No one should stop medication because they are worried about their microbiome, but it is always sensible to regularly review medicines,” she added.
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