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Genomic variation landscape of the human gut microbiome

Author

Listed:
  • Siegfried Schloissnig

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Manimozhiyan Arumugam

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Shinichi Sunagawa

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Makedonka Mitreva

    (The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

  • Julien Tap

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Ana Zhu

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Alison Waller

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Daniel R. Mende

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Jens Roat Kultima

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • John Martin

    (The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

  • Karthik Kota

    (The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

  • Shamil R. Sunyaev

    (Brigham & Women’s Hospital & Harvard Medical School)

  • George M. Weinstock

    (The Genome Institute, Washington University School of Medicine, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA)

  • Peer Bork

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Max Delbrück Centre for Molecular Medicine)

Abstract

Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.

Suggested Citation

  • Siegfried Schloissnig & Manimozhiyan Arumugam & Shinichi Sunagawa & Makedonka Mitreva & Julien Tap & Ana Zhu & Alison Waller & Daniel R. Mende & Jens Roat Kultima & John Martin & Karthik Kota & Shamil, 2013. "Genomic variation landscape of the human gut microbiome," Nature, Nature, vol. 493(7430), pages 45-50, January.
    • Handle: RePEc:nat:nature:v:493:y:2013:i:7430:d:10.1038_nature11711
    DOI: 10.1038/nature11711
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    Cited by:

    1. Xiaofan Jin & Feiqiao B. Yu & Jia Yan & Allison M. Weakley & Veronika Dubinkina & Xiandong Meng & Katherine S. Pollard, 2023. "Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Liang Chen & Na Zhao & Jiabao Cao & Xiaolin Liu & Jiayue Xu & Yue Ma & Ying Yu & Xuan Zhang & Wenhui Zhang & Xiangyu Guan & Xiaotong Yu & Zhipeng Liu & Yanqun Fan & Yang Wang & Fan Liang & Depeng Wang, 2022. "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Xiyang Dong & Yongyi Peng & Muhua Wang & Laura Woods & Wenxue Wu & Yong Wang & Xi Xiao & Jiwei Li & Kuntong Jia & Chris Greening & Zongze Shao & Casey R. J. Hubert, 2023. "Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Zhi-Ping Zhong & Jingjie Du & Stephan Köstlbacher & Petra Pjevac & Sandi Orlić & Matthew B. Sullivan, 2024. "Viral potential to modulate microbial methane metabolism varies by habitat," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Jingqiu Liao & Liat Shenhav & Julia A. Urban & Myrna Serrano & Bin Zhu & Gregory A. Buck & Tal Korem, 2023. "Microdiversity of the vaginal microbiome is associated with preterm birth," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    7. Xiyang Dong & Chuwen Zhang & Yongyi Peng & Hong-Xi Zhang & Ling-Dong Shi & Guangshan Wei & Casey R. J. Hubert & Yong Wang & Chris Greening, 2022. "Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    8. Kathrin Busch & Beate M. Slaby & Wolfgang Bach & Antje Boetius & Ina Clefsen & Ana Colaço & Marie Creemers & Javier Cristobo & Luisa Federwisch & Andre Franke & Asimenia Gavriilidou & Andrea Hethke & , 2022. "Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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