Medications May Leave Long-Lasting Imprints on Gut Bacteria

New research indicates that many commonly prescribed medications could induce lasting changes in the gut’s bacterial makeup. The study analyzed stool samples from over 2,500 individuals in the Estonian Biobank, alongside prescription records and data from the Estonian Microbiome cohort. It aimed to assess whether medication use was associated with variations in the gut microbiome, which consists of bacteria and other microorganisms residing in the digestive tract.

Long-Lasting Effects of Medications

The research discovered that most medications studied were linked with differences in the gut microbiome. Notably, for numerous drugs, these differences were still identifiable years after the medication had been discontinued. This finding was not exclusive to antibiotics, which are already known to influence gut bacteria. Similar links appeared with antidepressants, beta-blockers, proton pump inhibitors (PPIs), and benzodiazepines. Each medication class was associated with a unique microbial “fingerprint” in the gut.

Dr. Oliver Aasmets, lead author, mentioned, “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 study’s findings may influence future microbiome research. If medications taken months or years prior continue to affect the gut microbiome, researchers examining the connections between the microbiome and diseases might need to consider a person’s medication history.

Impact on Vulnerable Groups

Dr. Lucy Hooper, a GP and co-founder of Coyne Medical in London, highlighted that certain groups, such as babies and young children, might be more susceptible to long-lasting microbiome changes. Their developing gut microbiome could face more significant disruptions. Prior research has linked early antibiotic use and microbiome changes in children to conditions like asthma, obesity, and type 2 diabetes. Hooper also mentioned that older adults are at increased risk due to microbiome diversity decline with age and the likelihood of more frequent or long-term medication use.

Benzodiazepines and Gut Microbiome

Among the study’s notable findings was the association of benzodiazepines with changes in the gut microbiome. This link was comparable to those seen with broad-spectrum antibiotics, which impact various bacteria and are known to cause substantial changes in gut microbes. Interestingly, different medications within the same class do not affect the microbiome equally. For instance, diazepam and alprazolam, two benzodiazepines often prescribed for similar issues, varied in their effects on gut microbes.

The authors point out the significance of considering individual drugs separately in microbiome studies, rather than grouping medications within a class. Researchers also examined follow-up stool samples from a smaller participant group. This allowed them to observe the impact of starting or stopping certain medications on gut microbes, revealing consistent shifts over time linked to the medications themselves.

Lifestyle and Microbiome Recovery

According to Hooper, lifestyle factors may affect the microbiome’s recovery after medication use. People consuming low dietary fiber amounts generally have a less resilient microbiome, complicating recovery after disruptions.

The Importance of Past Medication Use

The study suggests that a person’s gut microbiome may reflect more than just their current diet, lifestyle, health, and medication use. It could also show traces of past medications. Researchers argue that both scientists and clinicians should consider medication history when interpreting microbiome data. Some microbiome changes linked to diseases might actually relate to medications used months or years earlier.

Hooper emphasized the need for more research to determine if medication-induced microbiome changes directly cause health effects. She noted, “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.”

Additionally, she advised against discontinuing prescribed medications due to microbiome concerns, suggesting instead a regular review of medicines.

Source: 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