A metagenomic catalog of the early-life human gut virome

Shuqin Zeng, Alexandre Almeida, Shiping Li, Junjie Ying, Hua Wang, Yi Qu, R. Paul Ross, Catherine Stanton, Zhemin Zhou, Xiaoyu Niu (), Dezhi Mu () and Shaopu Wang ()
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Shuqin Zeng: West China Second University Hospital, Sichuan University
Alexandre Almeida: University of Cambridge
Shiping Li: West China Second University Hospital, Sichuan University
Junjie Ying: West China Second University Hospital, Sichuan University
Hua Wang: West China Second University Hospital, Sichuan University
Yi Qu: West China Second University Hospital, Sichuan University
R. Paul Ross: APC Microbiome Ireland, University College Cork
Catherine Stanton: APC Microbiome Ireland, University College Cork
Zhemin Zhou: Pasteurien College, Medical College of Soochow University, Soochow University
Xiaoyu Niu: West China Second University Hospital, Sichuan University
Dezhi Mu: West China Second University Hospital, Sichuan University
Shaopu Wang: West China Second University Hospital, Sichuan University

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-45793-z

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