TY - JOUR
T1 - Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults
AU - Anthony, Winston E.
AU - Wang, Bin
AU - Sukhum, Kimberley V.
AU - D'Souza, Alaric W.
AU - Hink, Tiffany
AU - Cass, Candice
AU - Seiler, Sondra
AU - Reske, Kimberly A.
AU - Coon, Christopher
AU - Dubberke, Erik R.
AU - Burnham, Carey Ann D.
AU - Dantas, Gautam
AU - Kwon, Jennie H.
N1 - Funding Information:
This work was supported in part by a US Agency for International Development award (award no. 3220–29047) to C.-A.D.B. and G.D. W.E.A. was supported by a T32 NIH Ruth L. Kirschstein National Research Training Grant Fellowship (5T32GM007067-44). K.V.S. was supported by the Society for Healthcare Epidemiology of America Research Scholar Award . A.W.D. was supported by the Institutional Program Unifying Population and Laboratory-Based Sciences Burroughs Welcome Fund grant to Washington University . This work is supported by the Centers for Disease Control and Prevention (OADS BAA 2016-N-17812) contract no. 200-2016-90962 to J.H.K. J.H.K. is also supported by 1K23AI137321-01A1 from the National Institute of Allergy and Infectious Diseases . The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. The authors thank members of the Dantas lab for helpful comments on the manuscript. The authors thank the Edison Family Center for Genome Sciences & Systems Biology at Washington University School of Medicine in St. Louis staff (Eric Martin, Brian Koebbe, Jessica Hoisington-López, and MariaLynn Crosby) for technical support in high-throughput sequencing and computing.
Publisher Copyright:
© 2022 The Author(s)
PY - 2022/4/12
Y1 - 2022/4/12
N2 - 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.
AB - 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.
KW - CP: Microbiology
KW - antibiotic resistance
KW - host-microbe dynamics
KW - microbial pathogenesis
KW - microbiome
KW - population dynamics
KW - therapeutics
UR - http://www.scopus.com/inward/record.url?scp=85128144868&partnerID=8YFLogxK
U2 - 10.1016/j.celrep.2022.110649
DO - 10.1016/j.celrep.2022.110649
M3 - Article
C2 - 35417701
AN - SCOPUS:85128144868
SN - 2211-1247
VL - 39
JO - Cell Reports
JF - Cell Reports
IS - 2
M1 - 110649
ER -