A large population-based study in Sweden found that even a single course of antibiotics can leave a measurable imprint on the gut microbiome for years. Impacts were detectable up to four to eight years after treatment. Researchers analyzed stool samples and national drug registries for nearly 15,000 adults. The research compared people who had taken oral antibiotics within the previous eight years to those who had not. The number of antibiotic courses tracked with reduced microbial diversity, and exposures years in the past were still linked to how a person’s gut bacteria look today.
Bacterial diversity rebounded most quickly in the first two years after antibiotic use. It did not return to a pre-exposure state within the eight-year window studied. Certain commonly prescribed drugs were associated with especially persistent imbalances. Others had comparatively minor, short-lived effects.
Clindamycin stood out
Among the antibiotics examined, clindamycin stood out for strong and long-lasting disruption. Each course was linked to an average of 47 fewer detected bacterial species, and the signal could persist for as long as four to eight years. Courses of fluoroquinolones and flucloxacillin were each linked to about 20 fewer species on average. Fluoroquinolones were associated with changes in 172 species, and flucloxacillin with changes in 203 species. By contrast, penicillin V—commonly prescribed in Sweden—was associated with smaller and shorter-lived changes to gut bacteria.
The analysis drew on prescription records going back eight years. The authors noted that an even longer follow-up might yield more precise estimates of recovery and long-term effects. The scale of the Swedish analysis underscores how rare it is to capture the long arc of microbiome recovery and change after antibiotic exposure. The data suggest that many individuals carry a microbial “signature” of past treatments years later. The pronounced and durable effects observed for clindamycin, fluoroquinolones, and flucloxacillin stand in contrast to the relatively modest disruptions linked to penicillin V, a difference that may matter when equivalent alternatives are available.
In the study, people who had taken clindamycin, fluoroquinolones, and flucloxacillin showed a greater abundance of bacterial species associated with higher body mass index, elevated serum triglycerides, and increased risk of type 2 diabetes. These patterns mirror broader epidemiological links between antibiotic use and risks of type 2 diabetes and cardiovascular disease. The results align with observations that antibiotic courses can select for resistant “bad” bacteria while killing beneficial “good” bacteria. They may help inform future prescribing decisions when clinicians face a choice between two equally effective drugs with different microbiome impacts, according to ANSA.
“There’s just no evidence that probiotics are the answer” for microbiome recovery after antibiotic use, said Jotham Suez, citing a review he co-authored that found a lack of supporting evidence, according to Scientific American.