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A metagenomic catalog of the early-life human gut virome.

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Zeng, Shuqin 
Li, Shiping 
Ying, Junjie 
Wang, Hua 


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.


Acknowledgements: This work was supported by the National Natural Science Foundation of China (82100590 and 82241036 to S.W., 81971433 and 82271749 to D.M., 81971428 to Y.Q., and 82201905 to J.Y.), the National Key Research and Development Program (2021YFC2701704 and 2021YFC2701700 to D.M.), the Department of Science and Technology of Sichuan Province (2023NSFSC0579 to S.W., 2023NSFSC0544 to S.L.), and the Fundamental Research Funds for the Central University (SCU2023D006). A.A. is supported by a Career Development Award from the Medical Research Council (MR/W016184/1).


Adult, Infant, Child, Humans, Metagenome, Virome, Viruses, Microbiota, Gastrointestinal Microbiome

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Nat Commun

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Springer Science and Business Media LLC
National Natural Science Foundation of China (National Science Foundation of China) (82100590, 82241036)