Anxiety medications may disrupt your gut health years after use, says study

That prescription you took years ago, the one you barely remember, might still be inside you, in a way you never imagined. A latest study from Estonia has revealed that common medications can reshape your gut’s microbial community long after you've stopped taking them. From antibiotics to anxiety pills, these drugs leave behind lasting impacts that could be influencing your digestion, immunity, and even mental health today.

You’ve probably heard antibiotics can mess with your gut bacteria, but what if your blood pressure tablets or antidepressants are doing the same? And not just for weeks, but for years? That’s the unsettling finding from a large-scale study led by the University of Tartu’s Institute of Genomics. By analysing over 2,500 stool samples from the Estonian Biobank, researchers uncovered clear links between long-past medication use and current gut microbiome profiles.

“Most studies only look at what people are taking now,” explains Dr Oliver Aasmets, lead author. “But we found that past drug use, even from years ago, plays a strong role in shaping a person’s gut bacteria.” That includes everyday medications like beta-blockers, antidepressants, and even acid-reducing drugs.

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Here’s how common medications may leave a long-term imprint on your gut:

• Antidepressants can alter gut microbes

Selective serotonin reuptake inhibitors (SSRIs) don’t just affect mood. The study found lasting microbial changes linked to these medications, well after patients had stopped using them.

• Anxiety drugs act like antibiotics

Benzodiazepines — such as diazepam or alprazolam — showed gut alterations similar to those caused by broad-spectrum antibiotics. “That was unexpected,” says Professor Elin Org, the study’s senior author.

• Not all drugs in the same class act the same

Interestingly, even medications from the same group had different effects. For example, diazepam and alprazolam — both benzos — varied in how much they disrupted gut balance.

• Proton pump inhibitors (PPIs) leave a mark

Used for heartburn and acid reflux, PPIs like omeprazole were also linked to significant shifts in microbial communities — some of which persisted long after stopping the drug.

• Beta-blockers and other common meds join the list

Drugs often prescribed for high blood pressure and heart disease also showed associations with changes in gut microbiota, highlighting how widespread the issue might be.

“These results change how we interpret gut microbiome studies,” says Professor Org. “A person’s medication history, not just their current prescriptions, must be considered when connecting gut health to disease.”

The team also observed that starting or stopping certain meds caused predictable microbial shifts, reinforcing the idea that these effects are not just coincidental.

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While the research doesn’t yet prove these changes cause disease, it raises questions about the long-term impact of modern medicine on our gut ecosystems, and, by extension, on our health.

It’s easy to forget a medication once you’ve finished the course. But your gut doesn’t. “We need to stop treating the gut as a blank slate,” Dr Aasmets told Moneycontrol. It’s a living, evolving ecosystem, and your medical history is part of its story. Whether you’re starting a new prescription or exploring unexplained digestive issues, your past pills may be playing a bigger role than you think.

Disclaimer: This article, including health and fitness advice, only provides generic information. Don’t treat it as a substitute for qualified medical opinion. Always consult a specialist for a specific health diagnosis