Do Antibiotics Durably Disrupt Our Gut Flora Even Years After Taking Them?
A large study involving nearly 15,000 adults reveals that taking antibiotics can alter the composition of the gut microbiome for several years, well beyond the treatment period. These changes could have long-term health consequences.
Researchers analyzed antibiotic prescription data over eight years and compared it with stool samples to assess the impact on the diversity of gut bacteria. They observed that antibiotics taken less than one year before sampling most strongly reduced this diversity. However, even antibiotics taken one to four years, or even four to eight years earlier, continued to influence the microbiome composition. Certain antibiotics, such as clindamycin, fluoroquinolones, and flucloxacillin, had a more pronounced effect than others, affecting up to 15% of the bacterial species studied. In contrast, antibiotics like penicillin V or nitrofurantoin showed little impact.
Disruptions in the gut microbiome are already associated with increased risks of obesity, type 2 diabetes, cardiovascular diseases, and even certain cancers. This study confirms that antibiotics, by altering the balance of gut bacteria, could play a role in the development of these diseases. For example, a single course of antibiotics taken four to eight years before the analysis was sufficient to alter bacterial diversity and the abundance of certain species.
The gut microbiome is the collection of microorganisms that inhabit our digestive tract. It plays a key role in digestion, immunity, and even metabolic regulation. When it is unbalanced, this can promote the proliferation of potentially harmful bacteria or reduce the presence of beneficial bacteria. Fluoroquinolones and clindamycin, broad-spectrum antibiotics, were particularly linked to lasting changes, affecting bacteria from several different families. Flucloxacillin, which is more targeted, mainly affected specific bacteria such as those from the orders Lachnospirales and Oscillospirales.
The results also show that the recovery of the microbiome after a course of antibiotics is slow. While some bacteria return to normal within a few weeks or months, certain alterations can persist for years. This depends on the type of antibiotic used and individual sensitivity. In some people, the effects of treatment with ciprofloxacin, a fluoroquinolone, were observed up to two and a half years after taking the medication.
This study highlights the importance of the judicious use of antibiotics. Limiting their prescription to truly necessary cases could help preserve the balance of the microbiome and, consequently, reduce the risks of metabolic or inflammatory diseases. The observed differences according to age and sex also suggest that certain groups may be more vulnerable to these disruptions.
Researchers emphasize the need to better understand how the microbiome recovers after treatment. This could lead to more precise recommendations for choosing antibiotics that have less impact on gut bacteria, especially in already fragile patients. In the future, further studies could explore ways to accelerate microbiome recovery, such as the use of probiotics or a tailored diet.
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About This Study
DOI: https://doi.org/10.1038/s41591-026-04284-y
Title: Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals
Journal: Nature Medicine
Publisher: Springer Science and Business Media LLC
Authors: Gabriel Baldanzi; Anna Larsson; Sergi Sayols-Baixeras; Koen F. Dekkers; Ulf Hammar; Diem Nguyen; Tíscar Graells; Shafqat Ahmad; Camila Gazolla Volpiano; Guillaume Meric; Josef D. Järhult; Thomas Tängdén; Jonas F. Ludvigsson; Lars Lind; Johan Sundström; Karl Michaëlsson; Johan Ärnlöv; Beatrice Kennedy; Marju Orho-Melander; Tove Fall