New research highlights that many commonly prescribed medications leave long-lasting changes in gut bacteria. Researchers analyzed stool samples from over 2,500 individuals in the Estonian Biobank. They compared these samples with participants’ prescription records and data from the Estonian Microbiome cohort.
The aim was to explore if medication use correlates with gut microbiome variations. The researchers discovered that most medications studied were linked to microbiome differences. These differences were detectable even years after stopping medication.
Significant impacts were observed with various drugs such as antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines. Each type left a unique microbial signature on the gut. Dr. Oliver Aasmets, the 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 finding impacts future microbiome research. If past medications affect the microbiome, researchers need to consider medication history when studying microbiome and disease links.
Dr. Lucy Hooper, a general practitioner and co-founder of Coyne Medical in London, added insights on vulnerability to microbiome changes. Babies and young children, whose gut microbiomes are still developing, could face significant impacts from disruptions. Previous studies have connected early antibiotic use to conditions like asthma, obesity, and type 2 diabetes. Older adults might also be at risk, as their microbiome diversity declines with age, alongside more frequent medication use.
Benzodiazepines Stand Out
A noteworthy finding involved benzodiazepines, drugs commonly prescribed for anxiety. Their gut microbiome impact was comparable to broad-spectrum antibiotics, known for significant microbial changes. The study revealed that medications in the same class might affect the microbiome differently. For instance, diazepam and alprazolam, both benzodiazepines, showed differing impacts on gut microbes.
Researchers concluded that microbiome studies should evaluate individual drugs separately rather than grouping them by class. Follow-up stool samples from participants showed predictable microbial shifts over time, suggesting medication as a cause. Persistent effects were noted with PPIs, selective serotonin reuptake inhibitors (SSRIs), and certain antibiotics.
Lifestyle factors, like low dietary fiber intake, may influence microbiome recovery post-medication, according to Hooper. Such individuals might face slower recovery.
Impact of Past Medication Use
The study suggests the gut microbiome might reflect not only diet, lifestyle, and health but also past medication use. This insight urges researchers and clinicians to consider medication history when analyzing microbiome data. Some disease-related microbiome changes might link to past medications rather than the disease itself.
Hooper emphasized the need for more research to determine if medication-induced microbiome changes cause health effects. 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 also advised against stopping prescribed medications due to microbiome concerns, recommending regular medicine reviews instead.
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.
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