Massive expansion of the pig gut virome based on global metagenomic mining.

IF 7.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

npj Biofilms and Microbiomes Pub Date : 2024-08-29 DOI:10.1038/s41522-024-00554-0

Jiandui Mi, Xiaoping Jing, Chouxian Ma, Yiwen Yang, Yong Li, Yu Zhang, Ruijun Long, Haixue Zheng

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Abstract

The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.

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基于全球元基因组挖掘的猪肠道病毒组的大规模扩展。

猪肠道病毒组在猪的肠道微生物生态系统中发挥着至关重要的作用。然而，目前还缺乏对其多样性的全面了解和病毒组的参考数据库。为了填补这一空白，我们利用名为 "metav "的管道建立了猪病毒组数据库（PVD），该数据库由 5,566,804 个病毒序列组成，这些序列来自 4650 个公开的肠道元基因组样本。通过对序列进行聚类，我们确定了 48,299 个至少中等质量的病毒操作分类单元（vOTUs）基因组，其中 92.83% 的基因组在现有的主要数据库中找不到。大多数 vOTUs 被鉴定为 Caudoviricetes（72.21%）。PVD 数据库包含上述中等质量 vOTU 基因组中总共 2,362,631 个蛋白质编码基因，可用于探索猪肠道病毒组的功能潜力。这些发现凸显了猪肠道病毒的广泛多样性，为即将开展的猪肠道病毒组研究提供了重要的参考数据集。

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来源期刊

npj Biofilms and Microbiomes Immunology and Microbiology-Microbiology

CiteScore

12.10

自引率

3.30%

发文量

审稿时长

9 weeks

期刊介绍： npj Biofilms and Microbiomes is a comprehensive platform that promotes research on biofilms and microbiomes across various scientific disciplines. The journal facilitates cross-disciplinary discussions to enhance our understanding of the biology, ecology, and communal functions of biofilms, populations, and communities. It also focuses on applications in the medical, environmental, and engineering domains. The scope of the journal encompasses all aspects of the field, ranging from cell-cell communication and single cell interactions to the microbiomes of humans, animals, plants, and natural and built environments. The journal also welcomes research on the virome, phageome, mycome, and fungome. It publishes both applied science and theoretical work. As an open access and interdisciplinary journal, its primary goal is to publish significant scientific advancements in microbial biofilms and microbiomes. The journal enables discussions that span multiple disciplines and contributes to our understanding of the social behavior of microbial biofilm populations and communities, and their impact on life, human health, and the environment.