HQ Team
March 17, 2026: High antibiotic use may have a long-term effect on a person’s gut microbiome, and certain antibiotics can cause changes in the community of bacteria living in the gut for up to eight years, a Swedish study reveals.
An international research team led by scientists at Sweden’s Uppsala University found strong links between a person’s history of antibiotic use and the composition of their gut microbiome, including the diversity of bacterial species.
“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,” says Gabriel Baldanzi, the first author of the study and a former doctoral student at Uppsala University.
Human bodies consist of trillions of microorganisms (also called microbiota or microbes) of thousands of different species. These include not only bacteria but also fungi, parasites, and viruses.
In a healthy person, these ‘bugs’ coexist peacefully, with the largest numbers found in the small and large intestines, and throughout the body. The microbiome is even labelled a supporting organ because it plays many key roles in promoting daily operations.
Helpful, harmful
Each person has a unique microbiota network determined by one’s DNA. A person is first exposed to microorganisms as an infant, during delivery in the birth canal and through the mother’s breast milk. Exactly which microorganisms the infant is exposed to depends solely on the species found in the mother, according to the T.H. Chan School of Public Health, Harvard University
Environmental exposures and diet can change one’s microbiome to be either beneficial to health or place one at greater risk for disease.
The microbiome consists of microbes that are both helpful and potentially harmful. Most are symbiotic (where both the human body and microbiota benefit), and some, in smaller numbers, are pathogenic (promoting disease).
In a healthy body, pathogenic and symbiotic microbiota coexist without problems. But if there is a disturbance in that balance—brought on by infectious illnesses, certain diets, or the prolonged use of antibiotics or other bacteria-destroying medications—dysbiosis occurs, stopping these normal interactions. As a result, the body may become more susceptible to disease.
Antibiotics can be life-saving in serious infections. Epidemiological studies have also indicated links between high antibiotic use and an increased risk of certain health conditions, such as type 2 diabetes and gastrointestinal infections.
The reasons for these observations are not fully understood, but changes in the gut microbiome are thought to play a role. It is well known that antibiotics have a major short-term impact on the gut microbiome, but how long these changes persist has been unclear until now, the Swedish researchers wrote.
Fluoroquinolones, flucloxacillin
The researchers analysed drug register data alongside a detailed mapping of the gut microbiome of 14,979 adults living in Sweden. The gut microbiome was compared between participants who had received different types of antibiotics and those who had not received any at all during the period.
The study was made possible by Sweden’s comprehensive prescribed drug register, which contains information on all antibiotics dispensed at pharmacies. The researchers were then able to link this data to Swedish biobanks at Uppsala and Lund University containing gut microbiome data.
The researchers found that the results differed substantially depending on the type of antibiotic used.
The strongest associations were observed for clindamycin, fluoroquinolones and flucloxacillin. By contrast, penicillin V, the most commonly prescribed antibiotic for treating infections outside hospitals in Sweden, was linked to small, short-lived microbiome changes.
‘Second sample’
“The strong link between the narrow-spectrum flucloxacillin and the gut microbiome was unexpected, and we would like to see this finding confirmed in other studies,” said Tove Fall, Professor of Molecular Epidemiology at Uppsala University and principal investigator of the study.
“However, we believe that the findings of our study may help inform future recommendations on antibiotic use, especially when choosing between two equally effective antibiotics, one of which has a weaker impact on the gut microbiome.”
Fluoroquinolones (ciprofloxacin, levofloxacin) and flucloxacillin are distinct classes of antibiotics often used to treat bacterial infections, including staphylococcal bone and skin infections. Some studies suggest they are frequently used together for severe cases, according to PubMed Central (PMC).
Both are noted for their strong, long-lasting, and potentially negative impact on the gut microbiome, according to Inside Precision Medicine, which can last for years.
The Swedish researchers stated that the study covered only prescriptions from the previous eight years and that a longer follow-up period could provide further insights. Another aspect is that the gut microbiome was sampled only once per participant.
“We are currently collecting a second sample from almost half of the participants,” says Fall. “This will enable us to gain an even better understanding of the recovery time and identify which gut microbiomes are more susceptible to disruption following antibiotic treatment.”
The findings were published in the scientific journal Nature Medicine.
