• Posted March 19, 2026

Gut Microbiome May Take Years to Recover From Antibiotic Use

Antibiotics are often hailed as miracle drugs for their ability to wipe out dangerous infections, but new research suggests they leave a more lasting footprint on our bodies than previously thought.

A study of nearly 15,000 adults found that certain antibiotics can alter the community of helpful bacteria in our digestive system for nearly a decade.

The research, led by a team at Uppsala University in Sweden and published March 11 in Nature Medicine, mapped the gut microbiome — the trillions of bacteria that live in our intestines — of close to 15,000 adults in Sweden.

A stool sample from each participant was analyzed and participants answered a detailed lifestyle and diet questionnaire. 

Then, using national drug registries, scientists could see exactly which medications people had taken years prior. They adjusted for other medication use and several characteristics known to affect the microbiome in order to see the effects of antibiotic use.

The results were surprising. For some antibiotics, even a single round of use was linked to decreases in bacterial diversity four to eight years later.

Overall, the worst effects were seen in the first year after using an antibiotic.

“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 first author Gabriel Baldanzi, a research assistant at Uppsala University. "Even a single course of treatment with certain types of antibiotics leaves traces."

This is significant because a healthy, diverse microbiome supports human health and wellness. It acts as a shield against infections, boosts immune system health and helps the body digest food for energy.

Not all antibiotics were equal, the study showed.

The damage seen in the gut depended on the type of antibiotic used. Clindamycin, fluoroquinolones and flucloxacillin had the most lasting negative effects on gut health.

On the other hand, penicillin V and some extended-spectrum penicillins, which were the most commonly prescribed antibiotics, were found to be much friendlier to the gut. Their impact was small and faded relatively quickly.

The balance of gut bacteria is important to human health. 

Previous research has linked high antibiotic use to an increased risk of type 2 diabetes, heart disease, obesity, serious gastrointestinal infections and even colon cancer, researchers noted. Scientists suspect these long-term microbiome changes might be the reason why.

“The findings of our study may help inform future recommendations on antibiotic use, especially when choosing between two equally effective antibiotics, one of which has a weaker impact on the gut microbiome,” said lead researcher Dr. Tove Fall, a professor of molecular epidemiology at Uppsala.

Despite these findings, researchers urge patients not to stop taking medications prescribed by their doctors. Instead, the goal is to encourage prescribing the right one when truly necessary to protect the body's internal ecosystem for the long haul.

More information

The National Institutes of Health provides a detailed guide on the role of the microbiome in human health.

SOURCES: Uppsala University, news release, March 11, 2026; Nature Medicine, March 11, 2026