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

Ran Li, Yongming Wang, Han Hu, Yan Tan and Yingfei Ma ()
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Ran Li: 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

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-35735-y

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