A study of 2,509 people from the Estonian Biobank found that antibiotics, antidepressants, beta-blockers, proton pump inhibitors and benzodiazepines leave measurable changes in the gut microbiome that persist for years after the last pill.
Of the 186 drugs the researchers screened, 42 percent were still tied to microbiome differences when they had been stopped more than a year earlier.
For most patients this is not a reason to stop a prescription. Lead author Oliver Aasmets, a computational biologist at the University of Tartu, put it bluntly. "People definitely should keep taking drugs as their doctor has prescribed," he said.
The practical step is simpler. Mention medications you took months or years ago when a new gut issue comes up, and feed the bacteria you have with a fiber-rich, plant-forward diet.
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What the Estonian data actually showed
The team, publishing in the journal mSystems, matched stool samples with digital prescription records. About 90 percent of medications a person was actively taking showed a microbiome signal.
Benzodiazepines produced disruption comparable to broad-spectrum antibiotics, a class not typically thought of as gut-active.
Lasting effects from proton pump inhibitors, selective serotonin reuptake inhibitors (SSRIs) and antibiotics were confirmed in a smaller subgroup whose stool samples were collected again years after the original round.
"Most microbiome studies only consider current medications, but our results show that past drug use can be just as important," Aasmets said.
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An antibiotic footprint that lasts nearly a decade
The Estonian findings echo separate work from Uppsala University published March 11, 2026 in the journal Nature Medicine.
That team mapped the gut microbiomes of 14,979 Swedish adults and found antibiotic exposure still detectable four to eight years later, most notably for clindamycin, fluoroquinolones and flucloxacillin.
"We can see that antibiotic use as far back as four to eight years ago is linked to the composition of a person's gut microbiome today," said Gabriel Baldanzi, first author on the Uppsala study.
Feeding the bacteria you have
The everyday step with the strongest backing is a diet that fuels helpful microbes.
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Harvard Health lists asparagus, artichokes, leeks, garlic, onions, oats, barley, beans, lentils, apples, bananas and berries as prebiotic foods that provide fiber your gut bacteria feed on.
"Following a plant-based diet not only helps increase your intake of prebiotics, but also helps cut down on unhealthy foods that support bad bacteria," said Teresa Fung, a registered dietitian at Harvard's T.H. Chan School of Public Health.
If you are on a long-term prescription such as an SSRI or a proton pump inhibitor, or recently finished a course of antibiotics, and notice new or persistent digestive symptoms, the study authors point to one concrete step. Bring a full medication history to the appointment, including drugs you have already stopped.
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This article is made and published by Jesper Bengtson, who may have used AI in the preparation.