Common drugs alter gut microbiome for years, study finds
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- University of Tartu Institute of Genomics researchers analyzed stool samples and prescription records from more than 2,500 Estonian Biobank participants, finding most medications examined were associated with differences in the gut microbiome.
- Drug-related microbial changes persisted for years after patients stopped taking the medications, affecting not just antibiotics but also antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines.
- Benzodiazepines — commonly prescribed for anxiety — produced gut microbiome associations comparable in magnitude to those of broad-spectrum antibiotics, a particularly striking finding.
- Individual drugs within the same class affected the microbiome differently — for instance, diazepam and alprazolam differed in how strongly they appeared to disrupt gut microbes — suggesting medications should not be lumped together by drug class in microbiome research.
- Follow-up stool samples from a smaller subgroup confirmed predictable microbial shifts when people started or stopped proton pump inhibitors, SSRIs, penicillins, and macrolides.
- Lead author Dr. Oliver Aasmets said past drug use is 'a surprisingly strong factor' in explaining individual microbiome differences, and Professor Elin Org urged researchers and clinicians to factor in medication history when interpreting microbiome data.
Why it matters: With confirmation across follow-up samples and a 2,500-person cohort, the study gives microbiome researchers a concrete reason to track not just current but past prescriptions — otherwise disease-microbiome links could be distorted by medication history masquerading as biology, misattributing drug-driven microbial changes to illness itself.
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