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Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut

Author

Listed:
  • Ran Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yongming Wang

    (Chinese Academy of Sciences)

  • Han Hu

    (Tsinghua High-Tech Park)

  • Yan Tan

    (Tsinghua High-Tech Park)

  • Yingfei Ma

    (Chinese Academy of Sciences)

Abstract

The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.

Suggested Citation

  • Ran Li & Yongming Wang & Han Hu & Yan Tan & Yingfei Ma, 2022. "Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-35735-y
    DOI: 10.1038/s41467-022-35735-y
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    References listed on IDEAS

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    1. Peter J. Turnbaugh & Ruth E. Ley & Micah Hamady & Claire M. Fraser-Liggett & Rob Knight & Jeffrey I. Gordon, 2007. "The Human Microbiome Project," Nature, Nature, vol. 449(7164), pages 804-810, October.
    2. Janina Rahlff & Victoria Turzynski & Sarah P. Esser & Indra Monsees & Till L. V. Bornemann & Perla Abigail Figueroa-Gonzalez & Frederik Schulz & Tanja Woyke & Andreas Klingl & Cristina Moraru & Alexan, 2021. "Lytic archaeal viruses infect abundant primary producers in Earth’s crust," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. César Díez-Villaseñor & Francisco Rodriguez-Valera, 2019. "CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
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    Cited by:

    1. Jiandui Mi & Xiaoping Jing & Chouxian Ma & Fuyu Shi & Ze Cao & Xin Yang & Yiwen Yang & Apurva Kakade & Weiwei Wang & Ruijun Long, 2024. "A metagenomic catalogue of the ruminant gut archaeome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Shuqin Zeng & Alexandre Almeida & Shiping Li & Junjie Ying & Hua Wang & Yi Qu & R. Paul Ross & Catherine Stanton & Zhemin Zhou & Xiaoyu Niu & Dezhi Mu & Shaopu Wang, 2024. "A metagenomic catalog of the early-life human gut virome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    3. Diana P. Baquero & Sofia Medvedeva & Camille Martin-Gallausiaux & Nika Pende & Anna Sartori-Rupp & Stéphane Tachon & Thierry Pedron & Laurent Debarbieux & Guillaume Borrel & Simonetta Gribaldo & Mart , 2024. "Stable coexistence between an archaeal virus and the dominant methanogen of the human gut," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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