儿童早期多生态位病毒组解析:未分类噬菌体多样性及其宿主特征

Early childhood multi-niche viromes: unclassified phage diversity and host features

摘要

目的 构建儿童早期多生态位病毒组数据集,解析该发育阶段病毒群落的结构特征及细菌宿主。 方法 整合公开的宏基因组数据,采用病毒样颗粒富集与从头组装策略,建立涵盖上呼吸道、血浆及粪便的病毒组资源库;结合成簇规律间隔短回文重复序列(clustered regularly interspaced short palindromic repeats, CRISPR)比对、基因共享网络等多维度生物信息学方法,实现噬菌体的分类学注释、生活方式预测及细菌宿主预测。 结果 构建了包含14 555个重叠群的病毒组数据集,其中完整病毒基因组(完整度≥90%)509个(3.50%)、高质量完整基因组(完整度≥95%)340个(2.34%)。共鉴别到6个真核病毒科和23个噬菌体科,其中71.70%的噬菌体无法归类至已知病毒科。宿主预测覆盖96.45%的噬菌体细菌宿主,关联到3 283个细菌物种,包括双歧杆菌(Bifidobacterium)、乳杆菌(Lactobacillus)等益生菌。 结论 儿童早期病毒组中存在大量未分类噬菌体,其与肠道益生菌形成了广泛的互作网络,提示该发育阶段的病毒群落具有高度的多样性、独特的结构及其在塑造早期微生态中的关键潜在作用。

Abstract

Objective To construct a multi-niche viromic dataset in early childhood and analyze the structural characteristics and bacterial hosts of the viral community at this developmental stage. Methods Integrating publicly available metagenomic data, a virome repository covering the upper respiratory tract, plasma, and feces was established using viral-like particle enrichment and de novo assembly strategies. Combined with multi-dimensional bioinformatics methods such as clustered regularly interspaced short palindromic repeats(CRISPR)comparison and gene sharing networks, taxonomic annotation of phages, prediction of lifestyle, and prediction of bacterial hosts were achieved. Results A virome dataset comprising 14,555 contigs was constructed, including 509 complete viral genomes(completeness ≥90%)and 340 high-quality complete genomes(completeness ≥95%). A total of six eukaryotic virus families and 23 phage families were identified, of which 71.70% of the phages could not be classified into known virus families. Host prediction covered 96.45% of the phage bacterial hosts, associated with 3,283 bacterial species, including probiotics such as Bifidobacterium and Lactobacillus. Conclusion There are a large number of unclassified phages in the early childhood virome, which form a extensive interaction network with intestinal probiotics, suggesting the high diversity, unique structure, and key potential role of the viral community at this developmental stage in shaping the early microecology.

关键词

婴幼儿 / 病毒 / 噬菌体 / 宏基因组 / 病毒组

Key words

Infants and young children / Virus / Bacteriophages / Metagenome / Virome

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