Study Finds Certain Antibiotics Have Longer Impact on Gut Microbiome Than Others

Clindamycin, fluoroquinolones, and flucloxacillin were identified as having longer effects on bacterial diversity in the gut.
March 17, 2026
2 min read

A new study led by Swedish researchers indicated that “certain antibiotics may have a far longer impact on the gut microbiome” than others. CIDRAP has the news.

The study found that “people who took certain oral antibiotics had fewer bacterial species in their gut, and a lower abundance of individual species of gut bacteria, for four to eight years after taking them. The antibiotics most strongly associated with these long-lasting impacts were clindamycin, fluoroquinolones, and flucloxacillin.”

The study authors combined “individual-level data from the Swedish Prescribed Drug Register…with fecal metagenomic data collected from three population-based studies. Their aim was to assess how oral antibiotics used in the eight years before fecal sampling were associated with changes in gut microbiome composition.” Some previous studies had indicated that “microbiome differences can last as long as 1 or 1.5 years.”

Their analysis found that “use of six of 11 antibiotic classes a year before fecal sampling was associated with significant reductions in gut microbiome diversity compared with no antibiotic use.” The three antibiotics stood out repeatedly in different analyses. Gut microbiome diversity “recovered most quickly in the two years after antibiotic use, then more slowly in subsequent years. But use of clindamycin, fluoroquinolones, and flucloxacillin one to four years and four to eight years before fecal sampling was still significantly associated with reduced gut microbiome diversity.”

Previous observational studies had also found “associations between long-term antibiotic use and increased risk of obesity, type 2 diabetes, and cardiovascular disease. And their analysis found that use of clindamycin, fluoroquinolones, and flucloxacillin was associated with an increased abundance of certain gut microbiome species that have previously been linked to higher body mass index, higher serum triglyceride levels, and increased risk of type 2 diabetes.”

About the Author

Matt MacKenzie

Associate Editor

Matt is Associate Editor for Healthcare Purchasing News.

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