Antibiotics are designed to wipe out infection-causing bacteria, but even a single course can leave a lasting mark on the gut microbiome, according to a new study of nearly 15,000 adults in Sweden.
The research cross-referenced stool samples with Sweden’s prescribed drug registry to compare the gut microbiomes of people who had taken antibiotics at some point in the previous eight years with those who hadn’t—an “impressive” scope, says Jotham Suez, a microbiome researcher at the Johns Hopkins Bloomberg School of Public Health, who was not involved in the study. The paper was published today in Nature Medicine.
On average, people who had not taken any antibiotics in the past eight years had about 350 unique bacterial species living in their gut, but those who had taken any antibiotics in that time frame had fewer. The level of microbial diversity also depended on which drug they had taken.
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Clindamycin, which is sometimes prescribed for skin and dental infections, was the most disruptive: each course taken in the year before stool sampling was linked to an average of 47 fewer detected species, as well as changes in abundance in almost 300 of the 1,340 species analyzed. Courses of fluoroquinolones, which are often prescribed for urinary tract infections and respiratory infections, and flucloxacillin, which is mainly prescribed for Staphylococcus aureus infections, both corresponded to an average of about 20 fewer species. (Flucloxacillin is not available in the U.S.) They were also linked to changes in the abundance of 172 and 203 species, respectively. Most of the other antibiotics analyzed in the study were linked to decreases in bacterial abundance, but some were linked to increases in bacteria that have been associated with poor cardiometabolichealth.
Previous research has linked lower gut diversity to obesity, type 2 diabetes and inflammatory bowel disease, but some evidence suggests specific bacterial species, rather than diversity alone, drive poor health. “High diversity is probably better,” Suez says, “but there’s not strong evidence.”
In the study, the antibiotics’ effects were strongest when they were taken in the year immediately before the stool sampling. In general, the more courses of antibiotics people took, the larger the change in microbial diversity was. But even a single course of one of these three medications, taken up to eight years earlier, had an effect. Clindamycin alone, taken in the year before sampling, was linked to changes in the abundance of almost 300 bacterial species. By comparison, penicillin V—one of the most commonly prescribed antibiotics in Sweden—was linked to changes in just 29 species.
The analysis showed bacterial diversity recovered the fastest in the first two years after people took antibiotics; the rate of recovery tapered off after that point. “It seems like you don’t recover completely,” however, says Tove Fall, a molecular epidemiologist at Uppsala University in Sweden and the study’s senior author. That finding is consistent with other smaller and shorter studies.
Clindamycin and fluoroquinolones are “broad-spectrum” antibiotics—they target a broader range of bacteria—and they reach high concentrations in the colon, which might explain their outsize effects, Fall says. But flucloxacillin, a “narrow-spectrum” penicillin, was a surprise, she says; its effect might be related to its variable bioavailability and only partial bile excretion, meaning more of it ends up in the large intestine. Suez says these findings might not relate to the U.S. population. In Sweden, where the use of antibiotics is less frequent, “maybe the microbiome is also more sensitive,” he says. The flucloxacillin results “could be a blip” that warrants further investigation, he adds.
Studies have linked using antibiotics to inflammatory bowel disease and cardiovascular disease, as well as an increased risk of Clostridioides difficile infection. Whether probiotics help the microbiome recover from exposure to medication is debated, too. “There’s just no evidence that probiotics are the answer,” says Suez, who co-authored a December 2024 review that found a lack of evidence to support the use of probiotics for microbiome recovery after taking antibiotics. The new study did not investigate the effect of probiotics on bacterial diversity.
Fall hopes the data will be useful for policymakers but also worries about them being misinterpreted. If people use these findings as a reason to not take antibiotics when they are necessary, “that could be a very bad consequence,” she says. Suez agrees. “Antibiotics are nothing less than a miracle drug,” he says. “They are absolutely needed in some cases.”
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