Recent research highlights that many commonly prescribed medications can cause enduring changes in the gut microbiome. A study analyzed stool samples from over 2,500 people at the Estonian Biobank, along with their prescription records and data from the Estonian Microbiome cohort. The study aimed to determine if medication use is linked to variations in the microbiome, the community of bacteria and microorganisms in the digestive tract.
Most examined medications were associated with microbiome changes, with effects lasting years after discontinuation. These findings weren’t limited to antibiotics, known for affecting gut bacteria. Similar associations were identified for antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines, each linked to unique microbial fingerprints 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.”
The implications for future microbiome research are significant. If medications taken long before continue to impact the microbiome, studies on microbiome-disease links might need to include a person’s medication history.
Dr. Lucy Hooper, a GP and co-founder of Coyne Medical in London, noted that certain groups could be more vulnerable to lasting microbiome changes. For instance, babies and young children, whose microbiomes are still developing, might experience greater impacts. Previous research connects early antibiotic use and microbiome alterations in children to asthma, obesity, and type 2 diabetes. Older adults also face increased risks due to declining microbiome diversity and frequent medication use.
Benzodiazepines Stand Out
A notable finding involved benzodiazepines, used for anxiety and other disorders. Changes in the microbiome linked to benzodiazepine use were as significant as those from broad-spectrum antibiotics, known to cause substantial microbiome shifts.
Importantly, drugs within the same class can affect the microbiome differently. For example, diazepam and alprazolam, both benzodiazepines, showed varied levels of microbiome disruption. This suggests that microbiome studies should consider individual drugs separately instead of grouping them.
Researchers also analyzed follow-up samples from some participants, monitoring the microbiome changes when medications were initiated or ceased. They observed expected microbial shifts over time, indicating medications might be responsible for some microbiome variations.
Despite a small follow-up group, persistent effects were linked to PPIs, selective serotonin reuptake inhibitors (SSRIs), and specific antibiotics like combination penicillins and macrolides.
Lifestyle factors can influence microbiome recovery after medication use. Hooper advised that low dietary fiber could lead to a less resilient microbiome, complicating recovery post-disruption.
Why Past Medication Use Matters
The study implies a person’s gut microbiome may reflect more than current diet, lifestyle, health, and medication use. It might retain traces of past medications. Researchers urge scientists and clinicians to include medication history when interpreting microbiome data.
Microbiome changes perceived as disease-related might, in fact, link to past medications. Hooper stressed the necessity of more research to determine if medication-induced microbiome alterations directly 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,” said Hooper.
However, she cautioned against abandoning prescribed medications over microbiome concerns. “No one should stop medication because they are worried about their microbiome, but it is always sensible to regularly review medicines,” Hooper advised.
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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