Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults

Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery. [Display omitted] •The microbiome recovers lost diversity after short courses of antibiotics•Azithromycin delays recovery and increases net compositional differences•Altered diversity, resistance, and composition redefine “antibiotic scarring”•Healthy microbiomes end compositionally similar to ICU microbiomes How are robust microbiomes affected by antibiotics? Anthony et al. characterize “antibiotic scarring” in healthy volunteers, identifying universal compositional changes and treatment-specific effects on resistance burden and time to recovery of diversity. Three low-diversity microbiomes end compositionally similar to ICU patient microbiomes, highlighting the need for antibiotic stewardship in medicine.