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A metagenomic catalog of the early-life human gut virome

Author

Listed:
  • Shuqin Zeng

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Alexandre Almeida

    (University of Cambridge)

  • Shiping Li

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Junjie Ying

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Hua Wang

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Yi Qu

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • R. Paul Ross

    (APC Microbiome Ireland, University College Cork)

  • Catherine Stanton

    (APC Microbiome Ireland, University College Cork
    Teagasc Food Research Centre, Moorepark, Fermoy)

  • Zhemin Zhou

    (Pasteurien College, Medical College of Soochow University, Soochow University)

  • Xiaoyu Niu

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Dezhi Mu

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

  • Shaopu Wang

    (West China Second University Hospital, Sichuan University
    West China Second University Hospital, Sichuan University)

Abstract

Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as “virome”) remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45793-z
    DOI: 10.1038/s41467-024-45793-z
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