Some antibiotics change the composition of the gut microbiome for up to eight years

Antibiotic treatments can affect the composition of the bacterial community living in the gut, known as the gut microbiome, over a long period of time.

Antibiotic treatment can affect the composition of the community of bacteria living in the intestines, known as the gut microbiome, for a long time.New research shows that certain types of antibiotics can be associated with changes in the gut microbiome even four to eight years after treatment.The findings were published in the scientific journal Nature Medicine.

Antibiotics can be life-saving in serious infections.But epidemiological studies have also shown a link between high use of antibiotics 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 key role.This raises questions about the long-term imprint of antibiotics on the gut microbiome.It is well known that antibiotics have a large short-term impact on the gut microbiome.But so far it's unclear how long these changes will last.

A treatment also left a mark

An international research team led by researchers at Uppsala University has now found a link between a person's history of antibiotic use and the composition of their gut microbiota, including different types of bacteria.

From four to eight years ago, we can now see that antibiotic use is related to the composition of a person's gut microbiome.Even one treatment with some kind of antibiotic leaves traces."

Gabriele Baldanzi, first author of the study and former PhD student at Uppsala University

“Antibiotic use is taken very seriously in Sweden and the country already has strict antibiotic stewardship,” Baldansi adds."People should continue to follow their doctor's advice. However, 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.

Strong interaction with certain types of antibiotics

The researchers found that the results varied depending on the antibiotic used.The strongest association was observed with clindamycin, fluoroquinolones and flucloxacillin.In contrast, penicillin V, the antibiotic most commonly prescribed to treat infections outside the hospital in Sweden, is associated with small and long-lasting changes in the microbiome.

“The strong association between narrow-spectrum flucloxacillin and the gut microbiome was unexpected, and we would like to confirm this finding in other studies.However, we believe that the results of our study may help future recommendations on antibiotic use, especially when choosing between two equally effective antibiotics, one of which has a weaker effect on Molt-MU microbiomes.university and the principal investigator of the study.

A new sample was collected for follow-up

The researchers acknowledge that the study only included prescriptions from the past eight years and that a longer follow-up period may have provided more insight.Another aspect is that the gut microbiome was sampled only once per participant.

"We are collecting a second sample from half of the participants," Fall said."This will help us better understand the recovery period and identify which gut microbiomes are more susceptible to damage after antibiotic treatment."

Baldanji, G., et al(2026) Linking antibiotic use and gut microbiome composition from individual-level prescription data from 14,979 individuals.NaturopathyDOI: 10.1038/s41591-026-04284-y