Popular medications could change your gut health for years, experts warn

17 Oct 2025 By foxnews

Some everyday medications could be impacting your gut health in the long term.

A large study from Estonia has found that the gut microbiome - or the ecosystem that lives in the intestines - can be reshaped by antibiotics, according to new research published in ASM Journals.

Other medicines - like antidepressants and cold medications - can also change the bacteria in your gut. These effects can build up over time and may even last for years after taking the drugs.

GROWING ANTIBIOTIC CRISIS COULD TURN BACTERIAL INFECTIONS DEADLY, EXPERTS WARN

The study analyzed stool samples from 2,509 individuals, linking their microbiome data with electronic health records containing up to five years of prescription history. A second stool sample was collected from a sub-cohort of 328 individuals about 4.4 years later.

The researchers investigated which drugs were associated with microbiome changes, whether the amount or duration of use strengthened these impacts, and what happened to a patient when a drug was started or discontinued.

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Of 186 drugs that were tested, 167, or 89.8%, were linked to at least one microbial effect.

Even when taken years before the study, many drugs still had an association with microbiome variation, including antibiotics, psycholeptics, antidepressants, proton pump inhibitors (PPIs), beta blockers and benzodiazepine derivatives, the researchers found.

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For some drugs, more frequent or longer past use was associated with a stronger disturbance in the microbiome, suggesting that these effects accumulate over time.

The study also found that starting and stopping certain medications - particularly PPIs, SSRIs and some antibiotics - could cause microbiome shifts.

Fox News senior medical analyst Dr. Marc Siegel shared with Fox News Digital the old saying, "You are what you eat."

"It may turn out that you are what medications you take, too," he said in regard to the new study.

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Siegel noted that these findings are "not surprising," since the gut flora is fragile and can be "easily altered by active chemicals."

"It can have short- and long-term implications for metabolic processes - and not only the health of the gastrointestinal system, but also the brain, because of direct links between the gut and brain via the vagus nerve," he said.

The doctor added, "This is a study with important implications that should lead to a lot more research, especially connecting altered gut flora from various medications to various diseases."

The study authors pointed out a few limitations in their research, including the fact that it only focused on prescription-based drugs and did not consider the effects of over-the-counter medications.

There was also the possibility that some people taking antibiotics had underlying health conditions that could have also affected gut health. Diet, lifestyle and other factors could have also played a role.

Additionally, electronic health record data could have been incomplete or unclear in some cases.

The researchers also only analyzed stool samples, which means microbial changes in some gut regions could have been missed.

"We highlight the importance of accounting for the history of drug usage when assessing disease-microbiome associations," the authors stated in the journal publication.

"Taken together, our results expand the understanding of drug effects on the microbiome, and we encourage researchers to focus on the long-term drug effects whenever feasible."