Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
Nat Commun. 2024 Feb 29;15(1):1864. doi: 10.1038/s41467-024-45793-z.
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.
早期人类肠道病毒组是肠道内稳态和婴儿健康的关键驱动因素。然而，病毒组（称为“病毒组”）在很大程度上仍未被探索。在这里，我们建立了早期肠道病毒组（ELGV），这是一个从生命的头三年中 8130 个富含肠道病毒样颗粒（VLPs）或大量宏基因组中富集或提取的 160478 个非冗余 DNA 和 RNA 病毒序列的目录。通过聚类，鉴定出 82141 种病毒物种，其中 68.3%的病毒物种不存在于主要基于成人构建的现有数据库中，分别有 64 种和 8 种基于 VLPs 富集和大量宏基因组的病毒物种具有作为区分婴儿和成人的生物标志物的潜力。通过 VLPs 富集或大量宏基因组测序对最大的纵向婴儿群体进行分析，我们追踪了早期人类肠道病毒组的固有不稳定性和时间发展，并鉴定出与多种临床因素相关的差异病毒。母婴共享病毒组以及肠道病毒组和细菌组之间的早期相互作用得到了进一步扩展。总的来说，ELGV 目录提供了最全面和完整的早期人类肠道病毒组的宏基因组蓝图，为未来发现儿科疾病-病毒组关联提供了便利。
