Antibiotics are designed to wipe out infection-causing bacteria, but even a single course can leave lasting marks 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 prescription drug registry to compare the gut microbiomes of people who had taken antibiotics at some point in the previous eight years with those who had not — an “impressive” scope, said Jotham Suez, a microbiome researcher at the Johns Hopkins Bloomberg School of Public Health, who was not involved in the study. The newspaper was published today in Natural medicine.
On average, people who had not taken any antibiotics in the past eight years had about 350 unique species of bacteria 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 species detected, as well as changes in abundance for nearly 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 approx. 20 fewer species. (Flucloxacillin is not available in the US) 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 cardiometabolic health.
Previous research has linked lower gut diversity to obesity, type 2 diabetes and inflammatory bowel disease, but some evidence suggests that 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 effect of antibiotics was strongest when they were taken in the year immediately before the stool sample. In general, the more courses of antibiotics people took, the greater the change in microbial diversity. But even a single course of one of these three drugs, 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 nearly 300 bacterial species. In comparison, penicillin V – one of the most prescribed antibiotics in Sweden – was linked to changes in only 29 species.
The analysis showed that bacterial diversity recovered most rapidly during the first two years after people took antibiotics; the rate of recovery slowed after that point. “It seems like you don’t fully recover,” says Tove Fall, a molecular epidemiologist at Uppsala University in Sweden and the study’s senior author. The finding is consistent with other smaller and shorter studies.
Clindamycin and fluoroquinolones are “broad-spectrum” antibiotics — they target a wider range of bacteria — and they reach high concentrations in the colon, which may explain their big effects, Fall says. But flucloxacillin, a “narrow-spectrum” penicillin, was a surprise, she says; the effect may be related to its variable bioavailability and only partial biliary excretion, meaning more of it ends up in the colon. Suez says these findings may not be related to the US population. In Sweden, where the use of antibiotics is less frequent, “perhaps the microbiome is also more sensitive”, he says. The flucloxacillin results “may be a blip” that requires further investigation, he adds.
Studies have linked the use of 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 drug exposure is also debated. “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 restoring the microbiome after taking antibiotics. The new study did not examine the effect of probiotics on bacterial diversity.
Fall hopes the data will be useful to policymakers, but also worries it will be misinterpreted. If people use these findings as a reason not to take antibiotics when they’re needed, “that could be a very bad consequence,” she says. Suez agrees. “Antibiotics are nothing short of a miracle drug,” he says. “They are absolutely necessary in some cases.”
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