Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
Adv Sci (Weinh). 2024 Apr;11(13):e2305818. doi: 10.1002/advs.202305818. Epub 2024 Jan 19.
Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
目前的宏基因组组装的人类肠道噬菌体目录主要包含碎片化的基因组。在这里,开发了一种全面的肠道病毒组检测程序,包括从约 500g 粪便中富集病毒样颗粒(VLP),以及短读长和长读长测序的组合。应用于 135 个样本,组装了一个包含 21499 个非冗余病毒分类操作单元(vOTUs)的中国肠道病毒组目录(CHGV),这些 vOTUs 明显长于短读长测序获得的 vOTUs,并且包含约 35%(7675 个)完整基因组,是肠道病毒组数据库(GVD,约 4%,1443 个)的约九倍。有趣的是,CHGV vOTUs 的大多数(约 60%,13356 个)是通过长读长或混合组装获得的,与仅通过短读长数据组装的 vOTUs 几乎没有重叠。有了这个数据集,阐明了肠道病毒组的巨大多样性,包括与公共肠道病毒组数据库相比,鉴定了 32%(6962 个)新的 vOTUs,数十种比 crAssphages 和/或 Gubaphages 更普遍的噬菌体,以及几个比这两种更多样化的病毒进化枝。最后,还对 CHGV 编码蛋白的功能能力进行了表征,并构建了一个病毒-宿主相互作用网络,以促进未来的研究和应用。