Antibiotics can have a lasting impact on the gut microbiome, with effects detectable for years after treatment, new research reveals.
Antibiotics, essential tools in modern medicine, can disrupt the delicate balance of bacteria in the gut for a surprisingly long time. A new study published March 11, 2026, demonstrates that changes to the gut microbiome can persist for as long as eight years after antibiotic use. This finding highlights the importance of understanding the long-term consequences of these widely prescribed medications.
Researchers at Uppsala University in Sweden analyzed data from 14,979 adults over an eight-year period. The study, detailed in Nature Medicine, linked antibiotic prescriptions – gathered from Swedish pharmacies – with detailed microbiome analyses from biobanks at Uppsala and Lund Universities.
The gut microbiome, comprised of trillions of microorganisms, primarily bacteria, plays a critical role in digestion, metabolism, and immune function. Antibiotics, while targeting harmful bacteria, similarly impact these beneficial microbes, disrupting the complex ecosystem within the gut.
Previous research has established that antibiotics cause short-term changes to the gut microbiome. However, the duration of these effects remained unclear until now. The Swedish study reveals that even a single course of antibiotics can leave lasting traces on gut health.
The research team examined eleven classes of antibiotics. They found that six of these were associated with reduced diversity of gut bacteria when taken in the year prior to sample collection. While the most significant impact occurred within the first year, antibiotic use four to eight years prior still correlated with alterations in the microbiome. The microbiome showed some initial recovery, but did not fully return to its original state, researchers noted.
“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,” said Gabriel Baldanzi, the study’s first author and a former doctoral student at Uppsala University, in a university press release.
Long-Term Disruption of the Microbiome
A diverse microbiome is considered a hallmark of a healthy gut. The study showed that bacterial diversity tended to decrease with each additional antibiotic treatment. However, the effects varied depending on the specific antibiotic used.
Penicillin V, commonly prescribed for strep throat and ear infections, showed minimal and short-lived changes. Other antibiotics had more pronounced effects. Tetracyclines, used to treat respiratory and urinary tract infections, were linked to long-term shifts in the microbiome.
The most substantial effects were observed with clindamycin, fluoroquinolones, and flucloxacillin, which were associated with changes in numerous bacterial species. These antibiotics are sometimes reserved for situations where other treatments have failed.
Researchers emphasize that antibiotics remain vital medications. They view their findings as a call for more targeted antibiotic use in the future.
“We believe that the results of our study can contribute to improving future recommendations for antibiotic use, especially when choosing between two equally effective antibiotics, one of which has a smaller impact on the gut microbiome,” explained Tove Fall, an epidemiologist and co-author of the study.
