Antibiotics Linked to Gut Microbiome Disruptions for Up to 8 Years

Antibiotics can disrupt the human gut microbiome for up to eight years after a single course of treatment, according to a study of nearly 15,000 people published in Nature Medicine. The research, conducted by scientists at Uppsala University in Sweden, linked antibiotic prescriptions to lasting changes in the composition of gut bacteria.

The study analyzed data from three population-based cohorts, connecting information from the Swedish Prescribed Drug Register with fecal metagenomes from adults over an eight-year period. Researchers found the most significant disturbances to gut species occurred within the first year of antibiotic apply, but some alterations persisted for much longer. Certain antibiotics, including clindamycin, fluoroquinolones and flucloxacillin, had the most pronounced and enduring effects, the study showed.

“Our study provides the strongest evidence so far of these effects and gives clinicians a reference when addressing patient concerns,” said Gabriel Baldanzi, MD, PhD, a research assistant at Uppsala University, according to reporting by Healio.

The research indicated that antibiotic use could alter the gut microbiome by 10% to 15% in the four to eight years following treatment. Although fluoroquinolones and clindamycin were linked to an increased risk of Clostridioides difficile infection, antibiotics like penicillin V, extended-spectrum penicillins, and nitrofurantoin caused less disruption to beneficial gut bacteria.

The study did not specifically compare the impact of narrow-spectrum versus broad-spectrum antibiotics, Baldanzi noted. “Although antibiotics are often referred to as narrow-spectrum or broad-spectrum, we did not group them this way in our analysis. We were interested in looking at each antibiotic class separately,” he said.

Researchers acknowledged that the mechanisms behind microbiome recovery remain unclear, stating that while partial recovery often occurs within weeks, a full restoration could take years. The study also suggests a potential link between antibiotic-induced microbiome disruptions and chronic health conditions like type 2 diabetes and cardiovascular disease, though researchers emphasized that evidence of a causal relationship is currently lacking.

Paul Feuerstadt, MD, FACG, AGAF, of Yale University School of Medicine, wrote in a perspective accompanying the study’s publication that the findings reinforce the importance of antimicrobial stewardship. “Antimicrobials were a game-changer in the field of medicine, but at what cost?” Feuerstadt wrote. “Studies like this should craft clinicians think about the risks and benefits of every treatment.”

The primary reason for judicious antibiotic use, Baldanzi emphasized, remains the growing threat of antimicrobial resistance. SLACK Incorporated, the parent company of Healio, publishes journals covering medical specialties and provides subscription rates for its publications, as detailed in a 2026 rates booklet.