Recovery of gut microbiota of healthy adults following antibiotic exposure.
Level 4 - case-series / case-control
Small prospective uncontrolled before-and-after interventional study in healthy volunteers
PubMed 30349083 · doi:10.1038/s41564-018-0257-9
What was done
Twelve healthy men received a 4-day intervention with a cocktail of 3 antibiotics (meropenem, gentamicin, and vancomycin) and were followed for 6 months. Changes in gut microbiota composition, resistome dynamics, and eradication/regrowth patterns were analyzed using shotgun sequencing-based metagenomics.
What was found
Initial exposure led to blooms of enterobacteria and pathobionts (Enterococcus faecalis, Fusobacterium nucleatum) and depletion of Bifidobacterium species and butyrate producers. Microbiota composition returned to near-baseline within 1.5 months; however, 9 common species present in all subjects at baseline remained undetectable in most subjects after 180 days. Species harbouring β-lactam resistance genes were positively selected, while harbouring glycopeptide or aminoglycoside resistance genes increased odds of de novo colonization.
Why it matters
It demonstrates that while the healthy adult gut microbiome exhibits substantial resilience following heavy antibiotic perturbation, short-term exposure causes long-lasting depletion of specific commensal taxa and resistome selection.
Limits
The study is limited by a very small sample size (n=12), an exclusively male cohort, the lack of an unexposed parallel control group, and an aggressive three-drug antibiotic regimen that does not represent standard single-agent clinical therapy.
Cited by
- context Following antibiotic use, the gut microbiome shifts but generally bounces back to its baseline composition after cessation of the antibiotic.