Some Antibiotic Drugs Can Alter Your Gut Microbiome for Up to Eight Years, New Research Suggests

Just a single course of treatment can leave a lasting impression, according to a study of nearly 15,000 people in Sweden

Sara Hashemi | Daily Correspondent

March 18, 2026

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Antibiotics save millions of lives each year. But the bacterial infection-fighting drugs can also disrupt the digestive tract in ways that scientists are only beginning to understand. The medications can make yearslong changes to your gut microbiome, according to a study that examined nearly 15,000 adults in Sweden. The findings were published March 11 in the journal Nature Medicine.

“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. Even a single course of treatment with certain types of antibiotics leaves traces,” says study co-author Gabriel Baldanzi, a molecular epidemiologist who conducted the research while at Uppsala University in Sweden, in a statement.

Past studies have hinted that long-term use of antibiotics might be linked with an increased risk of obesity, Type 2 diabetes, cardiovascular disease and other health issues. Researchers suspect that the associations, in part, are a result of the medications disrupting the good bacteria that live in people’s guts as part of their microbiomes.

So Baldanzi and his colleagues examined stool sample data from 14,979 adults living in Sweden collected as part of three different studies. Comparing the participants’ microbial makeup with the country’s prescription registry revealed that people who had taken certain antibiotics—even just one treatment regimen—within the past eight years often had less bacterial diversity in their guts than individuals who hadn’t taken such drugs in that time frame.

Those without recent antibiotic use had around 350 different species residing in their digestive tracts. But in people who were prescribed clindamycin—given for skin, lung and dental infections—each course taken less than one year before fecal sampling was associated with 47 fewer detected bacterial species and with abundance changes in nearly 300 of the 1,340 analyzed species. Each regimen of fluoroquinolones, usually prescribed for urinary tract and respiratory infections, and flucloxacillin, generally for skin and respiratory infections and not available in the United States, taken within a year before sampling was associated with an average of about 20 fewer species and altered abundances of around 200 species.

Just a single course of clindamycin, flucloxacillin or fluoroquinolones taken between four and eight years prior to stool sampling was associated with different abundances of 196, 148 and 80 bacterial species, respectively, compared with those who did not take antibiotics. Across all antibiotic users, bacterial diversity began to bounce back rapidly within two years of ending treatment, but it slowed after that, the researchers found.

“It seems like you don’t recover completely,” study co-author Tove Fall, a molecular epidemiologist at Uppsala University, tells Lori Youmshajekian at Scientific American.

Still, the findings might not be applicable to people in the United States, where antibiotic use is more popular, Jotham Suez, a microbiome researcher at the Johns Hopkins Bloomberg School of Public Health who was not involved in the work, tells the outlet. In Swedish people, “maybe the microbiome is also more sensitive.”

The team wants to know whether the impact of antibiotics is observable beyond eight years, a limit imposed because of the timing of two of the studies that collected fecal samples. That knowledge might help patients and doctors choose treatments that leave a shorter mark on the gut microbiome.

“We are currently collecting a second sample from almost half of the participants,” Fall says in the statement. “This will enable us to gain an even better understanding of the recovery time and identify which gut microbiomes are more susceptible to disruption following antibiotic treatment.”

Sara Hashemi | Read More

Sara Hashemi is a science writer and fact-checker currently based in New York City. Her work has appeared in Sierra, The Body, Maisonneuve magazine and more.