Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, Stephen; Páez-Espino, David; Call, Lee; Low, Soo Jen; Sberro, Hila; Ivanova, Natalia N.; Proal, Amy D.; Fischbach, Michael A.; Bhatt, Ami S.; Hugenholtz, Philip; Kyrpides, Nikos C.

doi:10.1038/s41564-021-00928-6

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Journal Article · Thu Jun 24 00:00:00 EDT 2021 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-021-00928-6· OSTI ID:1815925

^[1]; ^[2]; Call, Lee ^[2]; Low, Soo Jen ^[3]; Sberro, Hila ^[4]; ^[2]; Proal, Amy D. ^[5]; ^[6]; ^[7]; ^[3]; ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division; USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division; USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Univ. of Queensland, Brisbane, QLD (Australia). School of Chemistry and Molecular Biosciences. Australian Centre for Ecogenomics
Stanford Univ., CA (United States). Dept. of Medicine (Hematology); Stanford Univ., CA (United States). Dept. of Genetics
PolyBio Research Foundation, Kenmore, WA (United States)
Stanford Univ., CA (United States). Dept. of Bioengineering; Stanford Univ., CA (United States). Dept. of Microbiology and Immunology; Stanford Univ., CA (United States). ChEM-H Inst.; Chan Zuckerberg Biohub, San Francisco, CA (United States)
Stanford Univ., CA (United States). Dept. of Medicine (Hematology); Stanford Univ., CA (United States). Dept. of Genetics

Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.

View Accepted Manuscript (DOE)

Sponsoring Organization:: USDOE Office of Science (SC); Autoimmunity Research Foundation; Australian Research Council Laureate Fellowship; National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1815925

Journal Information:: Nature Microbiology, Journal Name: Nature Microbiology Journal Issue: 7 Vol. 6; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 1 of Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis Chen, Changming; Zhang, Yue; Yao, Xueming figshare https://doi.org/10.6084/m9.figshare.24633318.v1	dataset	January 2023
Additional file 1 of A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments Wu, Yingjian; Gao, Na; Sun, Chuqing figshare https://doi.org/10.6084/m9.figshare.25547037	dataset	January 2024
Additional file 1 of Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs Hu, Jun; Chen, Jianwei; Nie, Yangfan figshare https://doi.org/10.6084/m9.figshare.25980522.v1	dataset	January 2024

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