Antibiotics are among the most important medical discoveries of the past century. They have transformed the treatment of bacterial infections, made routine surgery safer and saved millions of lives around the world.
For most people, however, taking antibiotics has always been viewed as a short-term intervention. Finish the prescription, recover from the infection and move on.
Research published in Nature Medicine suggests the story may be more complicated. A large population-based analysis found that the effects of certain antibiotics on the gut microbiome can persist for years, raising new questions about how antibiotics are prescribed and how the body’s microbial ecosystem recovers after treatment.
The international study, led by Giacomo Baldanzi and colleagues, examined how oral antibiotics influenced the gut microbiome over an unusually long period. Instead of focusing on changes immediately after treatment, the researchers investigated whether previous antibiotic use continued to shape the composition of gut bacteria years later.
To answer that question, the team combined prescription records with deep shotgun metagenomic sequencing data from 14,979 adults across three large Swedish population-based cohorts: the Swedish CArdioPulmonary bioImage Study (SCAPIS), the Swedish Infrastructure for Medical Population-based Life-course and Environmental Research (SIMPLER), and the Malmö Offspring Study. Participants’ antibiotic prescriptions covering the previous eight years were linked to detailed analyses of the bacterial species present in stool samples. Statistical models adjusted for age, sex, smoking, education, body mass index, existing medical conditions and medication use, allowing the researchers to isolate the relationship between antibiotics and long-term microbiome composition.
One finding stood out immediately.
As expected, people who had taken antibiotics within the previous year generally showed the greatest reduction in gut bacterial diversity. More surprising was that measurable changes remained visible among people whose antibiotic use had occurred one to four years earlier, and even four to eight years before their microbiome was analysed.
The effects also varied considerably depending on the type of antibiotic.
Among the 11 antibiotic classes evaluated, clindamycin, fluoroquinolones and flucloxacillin were associated with the largest and most persistent reductions in microbial diversity. By contrast, commonly prescribed narrow-spectrum antibiotics such as penicillin V appeared to have far more limited long-term effects. Even individuals who had received only a single course of certain antibiotics several years earlier continued to show differences in the abundance of specific bacterial species.
Why does this matter?
The gut microbiome has become one of the fastest-growing areas of medical research because it influences far more than digestion. Previous studies have linked microbial diversity to immune function, metabolism, cardiovascular health and the risk of several chronic diseases. Although this study does not prove that antibiotics directly cause these conditions, it strengthens the evidence that disrupting the microbiome may have consequences that extend well beyond the original infection.
The findings should not discourage people from taking antibiotics when they are genuinely needed.
Untreated bacterial infections can become serious very quickly, and antibiotics remain one of medicine’s most effective tools. Instead, the research reinforces a principle that infectious disease specialists have advocated for years: antibiotics should be prescribed carefully, selecting the narrowest effective treatment for the shortest appropriate duration whenever possible.
The study also highlights how medicine is changing.
Traditionally, healthcare has focused on eliminating harmful bacteria. Increasingly, clinicians are recognising that preserving beneficial bacteria is just as important. The goal is no longer simply to treat an infection, but to do so while minimising unnecessary disruption to the complex microbial ecosystem that supports human health.
This perspective is particularly relevant as antimicrobial resistance continues to rise globally. Efforts to reduce unnecessary antibiotic prescribing are often framed around preventing resistant bacteria. The evidence now suggests there may be another important benefit: protecting the long-term health of the microbiome itself.
The research stops short of suggesting that everyone needs microbiome testing after taking antibiotics. Much remains unknown about how individual microbiomes recover and whether interventions such as probiotics, dietary changes or microbiome-based therapies can accelerate that process. Those questions are now becoming major areas of medical research.
One thing is becoming increasingly clear, however. Antibiotics do far more than fight infection. They also influence one of the most complex ecosystems in the human body, and the effects of that interaction may last far longer than most people realise.
Source Information
Study Title: Antibiotic use and gut microbiome composition links from 14,979 population-based metagenomes
Authors: Giacomo Baldanzi, Erik Kristiansson and colleagues
Journal: Nature Medicine
Year: 2026
