Drugs taken years—even decades—ago can leave lasting imprints on the gut microbiome, reshaping the community of microbes long after treatment stops. Scientists analyzing over 2,500 Estonian Biobank samples discovered that antibiotics aren’t the only culprits—antidepressants, beta-blockers, and anxiety medications also disrupt gut ecosystems. Some drugs from the same class even have different microbial effects.
FULL STORY
Researchers found that many common medications, from antidepressants to heart drugs, can alter gut microbes for years after use. Credit: Shutterstock
Medications a person took years ago can still influence the community of microbes living in their gut, according to a large study conducted by the University of Tartu Institute of Genomics.
By examining stool samples and prescription data from more than 2,500 participants in the Estonian Biobank’s Microbiome cohort, scientists discovered that most drugs they analyzed were associated with measurable changes in the gut microbiome. Many of these changes persisted long after people stopped taking the medications. The lasting impact was not limited to antibiotics: antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines also left distinct microbial “fingerprints.
"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," said Dr. Oliver Aasmets, lead author of the study. The findings underscore the importance of considering a person’s medication history when exploring connections between gut microbes and disease.
Interestingly, benzodiazepines -- commonly prescribed for anxiety -- produced microbiome alterations similar to those seen with broad-spectrum antibiotics. The study also revealed that drugs within the same category, such as diazepam and alprazolam, can vary in how much they disturb gut microbial balance.
Follow-up samples from a smaller group of participants showed that starting or discontinuing specific medications led to predictable shifts in gut microbes, supporting a likely cause-and-effect relationship. Although this second phase involved fewer samples, the researchers confirmed persistent effects from proton pump inhibitors, selective serotonin reuptake inhibitors, and several antibiotics, including penicillins in combination and macrolides.
"This is a comprehensive systematic evaluation of long-term medication effects on the microbiome using real-world medical health records," said Professor Elin Org, the study’s corresponding author. "We hope this encourages researchers and clinicians to factor in medication history when interpreting microbiome data."
Story Source:
Materials provided by Estonian Research Council. Note: Content may be edited for style and length.
Journal Reference:
Oliver Aasmets, Nele Taba, Kertu Liis Krigul, Reidar Andreson, Elin Org, Mait Metspalu, Andres Metspalu, Lili Milani, Tõnu Esko. A hidden confounder for microbiome studies: medications used years before sample collection. mSystems, 2025; DOI: 10.1128/msystems.00541-25[1]
Cite This Page:
Estonian Research Council. "Common medications may secretly rewire your gut for years." ScienceDaily. ScienceDaily, 9 October 2025. <www.sciencedaily.com/releases/2025/10/251008030953.htm>.
Estonian Research Council. (2025, October 9). Common medications may secretly rewire your gut for years. ScienceDaily. Retrieved October 9, 2025 from www.sciencedaily.com/releases/2025/10/251008030953.htm
Estonian Research Council. "Common medications may secretly rewire your gut for years." ScienceDaily. www.sciencedaily.com/releases/2025/10/251008030953.htm (accessed October 9, 2025).
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Dec. 22, 2022 Researchers have discovered a new mode of vertical mother-to-infant microbiome transmission, where microbes in the maternal gut shared genes with microbes in the infant gut during the perinatal ...
Nov. 4, 2022 Fecal microbial transplants have been given to alter a recipient's metabolism to reduce obesity or alter immunity to fight cancer, and in those transplants recipients are not given suppressive ...
Mar. 15, 2021 Depression was not more common in patients who used beta-blockers. The rate of discontinuing medications due to depression was the same for people taking beta-blockers compared to people taking other ...
Drugs taken years—even decades—ago can leave lasting imprints on the gut microbiome, reshaping the community of microbes long after treatment stops. Scientists analyzing over 2,500 Estonian Biobank samples discovered that antibiotics aren’t the only culprits—antidepressants, beta-blockers, and anxiety medications also disrupt gut ecosystems. Some drugs from the same class even have different microbial effects.
FULL STORY
Researchers found that many common medications, from antidepressants to heart drugs, can alter gut microbes for years after use. Credit: Shutterstock
Medications a person took years ago can still influence the community of microbes living in their gut, according to a large study conducted by the University of Tartu Institute of Genomics.
By examining stool samples and prescription data from more than 2,500 participants in the Estonian Biobank’s Microbiome cohort, scientists discovered that most drugs they analyzed were associated with measurable changes in the gut microbiome. Many of these changes persisted long after people stopped taking the medications. The lasting impact was not limited to antibiotics: antidepressants, beta-blockers, proton pump inhibitors, and benzodiazepines also left distinct microbial “fingerprints.
"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," said Dr. Oliver Aasmets, lead author of the study. The findings underscore the importance of considering a person’s medication history when exploring connections between gut microbes and disease.
Interestingly, benzodiazepines -- commonly prescribed for anxiety -- produced microbiome alterations similar to those seen with broad-spectrum antibiotics. The study also revealed that drugs within the same category, such as diazepam and alprazolam, can vary in how much they disturb gut microbial balance.
Follow-up samples from a smaller group of participants showed that starting or discontinuing specific medications led to predictable shifts in gut microbes, supporting a likely cause-and-effect relationship. Although this second phase involved fewer samples, the researchers confirmed persistent effects from proton pump inhibitors, selective serotonin reuptake inhibitors, and several antibiotics, including penicillins in combination and macrolides.
"This is a comprehensive systematic evaluation of long-term medication effects on the microbiome using real-world medical health records," said Professor Elin Org, the study’s corresponding author. "We hope this encourages researchers and clinicians to factor in medication history when interpreting microbiome data."
Story Source:
Materials provided by Estonian Research Council. Note: Content may be edited for style and length.
Journal Reference:
Oliver Aasmets, Nele Taba, Kertu Liis Krigul, Reidar Andreson, Elin Org, Mait Metspalu, Andres Metspalu, Lili Milani, Tõnu Esko. A hidden confounder for microbiome studies: medications used years before sample collection. mSystems, 2025; DOI: 10.1128/msystems.00541-25[1]
Cite This Page:
Estonian Research Council. "Common medications may secretly rewire your gut for years." ScienceDaily. ScienceDaily, 9 October 2025. <www.sciencedaily.com/releases/2025/10/251008030953.htm>.
Estonian Research Council. (2025, October 9). Common medications may secretly rewire your gut for years. ScienceDaily. Retrieved October 9, 2025 from www.sciencedaily.com/releases/2025/10/251008030953.htm
Estonian Research Council. "Common medications may secretly rewire your gut for years." ScienceDaily. www.sciencedaily.com/releases/2025/10/251008030953.htm (accessed October 9, 2025).
Aug. 30, 2024 The appropriate duration of beta-blocker treatment after a heart attack (a myocardial infarction [MI]) is unknown in patients who do not need to take beta-blockers for another reason. In the ABYSS ...
Aug. 29, 2024 Microbes are part of the food we eat and can influence our own microbiome, but we know very little about the microbes in our foods. Now, researchers have developed a database of the 'food ...
Aug. 17, 2023 Early social and environmental exposures can have large and lasting effects on child development and adult health. One of the systems that is vulnerable to external influence is the gut microbiome. A ...
Dec. 22, 2022 Researchers have discovered a new mode of vertical mother-to-infant microbiome transmission, where microbes in the maternal gut shared genes with microbes in the infant gut during the perinatal ...
Nov. 4, 2022 Fecal microbial transplants have been given to alter a recipient's metabolism to reduce obesity or alter immunity to fight cancer, and in those transplants recipients are not given suppressive ...
Mar. 15, 2021 Depression was not more common in patients who used beta-blockers. The rate of discontinuing medications due to depression was the same for people taking beta-blockers compared to people taking other ...
