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

Winston E. Anthony, Bin Wang, Kimberley V. Sukhum, Alaric W. D'Souza, Tiffany Hink, Candice Cass, Sondra Seiler, Kimberly A. Reske, Christopher Coon, Erik R. Dubberke, Carey Ann D. Burnham, Gautam Dantas, Jennie H. Kwon

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Article number110649
JournalCell Reports
Volume39
Issue number2
DOIs
StatePublished - Apr 12 2022

Keywords

  • CP: Microbiology
  • antibiotic resistance
  • host-microbe dynamics
  • microbial pathogenesis
  • microbiome
  • population dynamics
  • therapeutics

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