New research published in the journal Nature Medicine shows that antibiotic treatments can have long-lasting effects on the gut microbiome—the complex community of bacteria living in the human intestine—potentially lasting up to eight years after use.
A Long-Term Impact on Gut Bacteria
An international team led by scientists from Uppsala University in Sweden found a strong association between an individual’s history of antibiotic use and the composition of their gut microbiome, including bacterial diversity. The study analyzed prescription data from Sweden’s national drug registry and mapped the gut microbiomes of nearly 15,000 adults living in the country.
Researchers compared microbiome profiles among participants who had taken different classes of antibiotics with those who had not used any during the same time period. They discovered that the type of antibiotic mattered significantly: clindamycin, fluoroquinolones, and flucloxacillin showed the strongest links to lasting changes in gut bacteria. In contrast, penicillin V—the most commonly prescribed outpatient antibiotic in Sweden—was associated only with minor, short-term shifts.
Surprising Findings and Clinical Implications
Gabriel Bäckhed, the study’s lead author and former doctoral student at Uppsala University, noted: “We see that antibiotic use—even four to eight years ago—is linked to today’s gut microbiome composition. Even a single course of certain antibiotics leaves detectable traces.”
Tove Fall, senior researcher and Professor of Molecular Epidemiology at Uppsala University, described the strong connection between flucloxacillin and microbiome alterations as “unexpected.” She added: “We believe our findings could help shape future antibiotic prescribing guidelines—especially when choosing between two equally effective drugs, one of which may cause less disruption to the microbiome.”
Limitations and Next Steps
The study covered only prescriptions issued within the past eight years, and each participant’s gut microbiome was sampled just once. Researchers are now collecting a second stool sample from nearly half of the participants to better understand how—and how quickly—the microbiome recovers over time.