State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou, China.
State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, China.
NPJ Biofilms Microbiomes. 2024 Aug 29;10(1):76. doi: 10.1038/s41522-024-00554-0.
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.
猪肠道病毒组在猪肠道微生物生态系统中起着至关重要的作用。然而，目前人们对其多样性缺乏全面的了解，也缺乏病毒组的参考数据库。为了解决这一差距，我们使用名为“metav”的管道，从 4650 个公开的肠道宏基因组样本中建立了一个包含 5566804 条病毒连续序列的猪病毒组数据库（PVD）。通过对序列进行聚类，我们鉴定出了 48299 个至少具有中等质量的病毒分类操作单元（vOTUs）基因组，其中 92.83%的病毒在现有的主要数据库中没有发现。大多数 vOTUs 被鉴定为长尾病毒科（Caudoviricetes）（72.21%）。PVD 数据库包含了上述中等质量 vOTUs 基因组中总共 2362631 个编码蛋白的基因，这些基因可用于探索猪肠道病毒组的功能潜力。这些发现突显了猪肠道病毒的广泛多样性，并为即将到来的猪肠道病毒组研究提供了关键的参考数据集。
