Some antibiotics alter gut microbiome composition for up to eight years

Antibiotic treatments can affect the composition of the community of bacteria living in the gut, known as the gut microbiome, for a long time. A new study shows that certain types of antibiotics can be linked to changes in the gut microbiome as long as four to eight years after treatment. The findings have now been published in the scientific journal Nature Medicine.

Antibiotics can be life-saving in serious infections, but 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. This has raised questions about the long-term footprint of antibiotics on the gut microbiome. 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. 

Even a single course of treatment left traces

An international research team, led by scientists at Uppsala University, has now 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."

Gabriel Baldanzi, first author of the study and former doctoral student at Uppsala University

"Antibiotic use is taken very seriously in Sweden, and country already have a strict antibiotic stewardship," Baldanzi adds. "People should continue to follow their doctor's recommendations. Having said that, our findings help shed light on other long-term consequences of antibiotics that are rarely considered." 

In the study, 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. 

Stronger association with certain types of antibiotics

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 the treatment of infections outside hospitals in Sweden, was linked to small and short-lasting microbiome changes. 

"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. 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," says Tove Fall, Professor of Molecular Epidemiology at Uppsala University and principal investigator of the study. 

New samples collected for follow-up

The researchers acknowledge that the study only covered 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."