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Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

Author

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  • Yongfei Hu

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Xi Yang

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Junjie Qin

    (BGI-Shenzhen)

  • Na Lu

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Gong Cheng

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Na Wu

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Yuanlong Pan

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Jing Li

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Liying Zhu

    (State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences)

  • Xin Wang

    (State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences)

  • Zhiqi Meng

    (State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences)

  • Fangqing Zhao

    (Computational Genomics Laboratory, Beijing Institutes of Life Science, Chinese Academy of Sciences)

  • Di Liu

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Juncai Ma

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

  • Nan Qin

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University)

  • Chunsheng Xiang

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University)

  • Yonghong Xiao

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University)

  • Lanjuan Li

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University)

  • Huanming Yang

    (BGI-Shenzhen)

  • Jian Wang

    (BGI-Shenzhen)

  • Ruifu Yang

    (State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology)

  • George F. Gao

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences
    Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences)

  • Jun Wang

    (BGI-Shenzhen)

  • Baoli Zhu

    (CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences)

Abstract

The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota.

Suggested Citation

  • Yongfei Hu & Xi Yang & Junjie Qin & Na Lu & Gong Cheng & Na Wu & Yuanlong Pan & Jing Li & Liying Zhu & Xin Wang & Zhiqi Meng & Fangqing Zhao & Di Liu & Juncai Ma & Nan Qin & Chunsheng Xiang & Yonghong, 2013. "Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota," Nature Communications, Nature, vol. 4(1), pages 1-7, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3151
    DOI: 10.1038/ncomms3151
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    Cited by:

    1. Samuel C. Forster & Junyan Liu & Nitin Kumar & Emily L. Gulliver & Jodee A. Gould & Alejandra Escobar-Zepeda & Tapoka Mkandawire & Lindsay J. Pike & Yan Shao & Mark D. Stares & Hilary P. Browne & B. A, 2022. "Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Zhenyan Zhang & Qi Zhang & Tingzhang Wang & Nuohan Xu & Tao Lu & Wenjie Hong & Josep Penuelas & Michael Gillings & Meixia Wang & Wenwen Gao & Haifeng Qian, 2022. "Assessment of global health risk of antibiotic resistance genes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Xuanji Li & Asker Brejnrod & Jonathan Thorsen & Trine Zachariasen & Urvish Trivedi & Jakob Russel & Gisle Alberg Vestergaard & Jakob Stokholm & Morten Arendt Rasmussen & Søren Johannes Sørensen, 2023. "Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Victoria T. Chu & Alexandra Tsitsiklis & Eran Mick & Lilliam Ambroggio & Katrina L. Kalantar & Abigail Glascock & Christina M. Osborne & Brandie D. Wagner & Michael A. Matthay & Joseph L. DeRisi & Car, 2024. "The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Peter J. Diebold & Matthew W. Rhee & Qiaojuan Shi & Nguyen Vinh Trung & Fayaz Umrani & Sheraz Ahmed & Vandana Kulkarni & Prasad Deshpande & Mallika Alexander & Ngo Hoa & Nicholas A. Christakis & Najee, 2023. "Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Laura Nies & Susheel Bhanu Busi & Mina Tsenkova & Rashi Halder & Elisabeth Letellier & Paul Wilmes, 2022. "Evolution of the murine gut resistome following broad-spectrum antibiotic treatment," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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