Recovery of gut microbiota of healthy adults following antibiotics exposure

To minimize the impact of antibiotics the gut microbes harbor and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing based metagenomics, we analyzed partial eradication and subsequent regrowth of gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin.Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and depletion of Bifidobacterium spp. and butyrate producers. Still, subjects’ gut microbiota recovered to near-baseline composition by 1.5 months, although nine common species which were present in all subjects prior to the treatment, remained undetectable in most of the subjects after 180 days. Species harboring beta-lactam resistance genes were positively selected for during and after the intervention. Harboring glycopeptide or aminoglycoside resistance genes increased odds of de novo colonization, while the former also decreased odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention, and their antibiotics resistance gene carriage modulates their recovery processes.