03/12/2026
A single course of some antibiotics affected microbial diversity in the gut more than others, a new study found. And the effects can last for several years.
A recent study published in Nature Medicine indicates that certain antibiotics significantly disrupt gut microbial diversity, with effects persisting for four to eight years post-treatment. Broad-spectrum antibiotics, such as clindamycin and fluoroquinolones, cause the most severe, long-lasting damage by eliminating beneficial bacteria like Lactobacillus and Bifidobacterium.
Antibiotics like penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Enhanced antibiotics like Augmentin (amoxicillin-clavulanate) also significantly disrupt the gut microbiome for weeks to months after use.
Key Findings on Antibiotic Impact
• Long-Term Effects: While some gut bacteria recover within weeks, significant alterations in microbial composition can last for several years.
• High-Impact Antibiotics: Clindamycin, fluoroquinolones, and flucloxacillin are noted for causing severe, long-lasting disruptions.
• Consequences: Reduced diversity can lead to the growth of opportunistic pathogens like Klebsiella pneumoniae and Enterococcus faecium, as well as a higher risk of Clostridium difficile infections.
• Disease Association: The alteration of gut flora from high antibiotic use is associated with chronic inflammation, metabolic issues (like type 2 diabetes), obesity, colon cancer and gastrointestinal infections.
What You Can Do:
If you do have to use antibiotics to treat a bacterial infection, add daily probiotics of variable sources, with a variety of probiotic strains included, and continue this probiotic use for at least another two weeks after finishing antibiotics treatment.
Using individual-level data from the Swedish Prescribed Drug Register and f***l metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 years and gut microbiome and found evidence that antibiotics can have long-lasting impacts on the gut m...