通过宏基因组学发现病毒世界的新维度。
New dimensions of the virus world discovered through metagenomics.
机构信息
Stowers Institute of Medical Research, Kansas City, MO 64110, USA.
出版信息
Trends Microbiol. 2010 Jan;18(1):11-9. doi: 10.1016/j.tim.2009.11.003. Epub 2009 Nov 26.
Abstract
Metagenomic analysis of viruses suggests novel patterns of evolution, changes the existing ideas of the composition of the virus world and reveals novel groups of viruses and virus-like agents. The gene composition of the marine DNA virome is dramatically different from that of known bacteriophages. The virome is dominated by rare genes, many of which might be contained within virus-like entities such as gene transfer agents. Analysis of marine metagenomes thought to consist mostly of bacterial genes revealed a variety of sequences homologous to conserved genes of eukaryotic nucleocytoplasmic large DNA viruses, resulting in the discovery of diverse members of previously undersampled groups and suggesting the existence of new classes of virus-like agents. Unexpectedly, metagenomics of marine RNA viruses showed that representatives of only one superfamily of eukaryotic viruses, the picorna-like viruses, dominate the RNA virome.
摘要
病毒的宏基因组分析表明了新的进化模式，改变了病毒世界组成的现有观念，并揭示了新的病毒和类病毒群体。海洋 DNA 病毒组的基因组成与已知的噬菌体有很大的不同。病毒组主要由稀有基因组成，其中许多可能包含在基因转移剂等类似病毒的实体中。对被认为主要由细菌基因组成的海洋宏基因组的分析揭示了多种与真核核质大 DNA 病毒保守基因同源的序列，从而发现了以前采样不足的群体的多种成员，并表明存在新的类病毒群体。出乎意料的是，海洋 RNA 病毒的宏基因组学表明，只有真核病毒的一个大家族，即微小 RNA 病毒，主宰着 RNA 病毒组。
相似文献
1
New dimensions of the virus world discovered through metagenomics.通过宏基因组学发现病毒世界的新维度。
Trends Microbiol. 2010 Jan;18(1):11-9. doi: 10.1016/j.tim.2009.11.003. Epub 2009 Nov 26.
2
Diverse and unique viruses discovered in the surface water of the East China Sea.在中国东海的地表水发现了多样且独特的病毒。
BMC Genomics. 2020 Jun 26;21(1):441. doi: 10.1186/s12864-020-06861-y.
3
Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer.宏基因组学通过揭示广泛的水平病毒转移，改变了 RNA 病毒进化的概念。
Virus Res. 2018 Jan 15;244:36-52. doi: 10.1016/j.virusres.2017.10.020. Epub 2017 Nov 8.
4
Metagenomic Characterization of the Viral Community of the South Scotia Ridge.南斯科舍海脊病毒群落的宏基因组特征分析
Viruses. 2019 Jan 24;11(2):95. doi: 10.3390/v11020095.
5
Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton. shotgun 宏基因组学表明，新型 A 家族 DNA 聚合酶在海洋病毒浮游生物中占主导地位。
ISME J. 2014 Jan;8(1):103-14. doi: 10.1038/ismej.2013.124. Epub 2013 Aug 29.
6
Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences.宏基因组分析小麦病毒组鉴定新型植物和真菌相关病毒序列。
Viruses. 2021 Dec 7;13(12):2457. doi: 10.3390/v13122457.
7
Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals.宏基因组时间序列揭示了一个以具有强烈季节性信号的成员为主导的西英吉利海峡病毒群落。
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae216.
8
VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.VirusSeeker，一种用于病毒发现和病毒群落组成分析的计算流程。
Virology. 2017 Mar;503:21-30. doi: 10.1016/j.virol.2017.01.005. Epub 2017 Jan 18.
9
The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics.利用靶向PCR和宏基因组学对热带海水中的RNA病毒进行表征。
mBio. 2014 Jun 17;5(3):e01210-14. doi: 10.1128/mBio.01210-14.
10
Construction and characterization of DNA libraries from cultured phages and environmental viromes.从培养噬菌体和环境病毒组中构建和表征 DNA 文库。
Appl Environ Microbiol. 2024 Oct 23;90(10):e0117124. doi: 10.1128/aem.01171-24. Epub 2024 Sep 24.
引用本文的文献
1
Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.解读冰川补给的恒河综合微生物群落及其功能方面：对“同一健康”的启示
Microbiol Spectr. 2025 Aug 5;13(8):e0172024. doi: 10.1128/spectrum.01720-24. Epub 2025 Jul 7.
2
Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.泥炭藓宏基因组中共享病毒序列的鉴定揭示了可能的泥炭藓核心病毒组的元素。
Environ Microbiome. 2025 Jun 5;20(1):62. doi: 10.1186/s40793-025-00719-0.
3
Activation of bacterial programmed cell death by phage inhibitors of host immunity.宿主免疫噬菌体抑制剂对细菌程序性细胞死亡的激活作用。
Mol Cell. 2025 May 1;85(9):1838-1851.e10. doi: 10.1016/j.molcel.2025.04.010.
4
Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification.用于肠道微生物群和生物标志物识别的先进计算工具、人工智能和机器学习方法。
Front Med Technol. 2025 Apr 15;6:1434799. doi: 10.3389/fmedt.2024.1434799. eCollection 2024.
5
Expansion of the genomic and functional diversity of global ocean giant viruses.全球海洋巨型病毒的基因组和功能多样性扩展。
Npj Viruses. 2025 Apr 21;3(1):32. doi: 10.1038/s44298-025-00122-z.
6
Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth.全基因组筛选过表达分枝杆菌噬菌体阿梅莉亚基因可鉴定出多种分枝杆菌生长抑制剂。
G3 (Bethesda). 2025 Feb 5;15(2). doi: 10.1093/g3journal/jkae285.
7
Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals.宏基因组时间序列揭示了一个以具有强烈季节性信号的成员为主导的西英吉利海峡病毒群落。
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae216.
8
Detection, isolation and characterization of phage-host complexes using BONCAT and click chemistry.使用生物正交非天然氨基酸标记与点击化学技术检测、分离和表征噬菌体-宿主复合物
Front Microbiol. 2024 Sep 3;15:1434301. doi: 10.3389/fmicb.2024.1434301. eCollection 2024.
9
Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination.转录激活和反终止控制新月柄杆菌中的基因转移因子簇
Nat Commun. 2024 Jun 4;15(1):4749. doi: 10.1038/s41467-024-49114-2.
10
A novel and diverse family of filamentous DNA viruses associated with parasitic wasps.与寄生黄蜂相关的一个新颖多样的丝状DNA病毒家族。
Virus Evol. 2024 Mar 2;10(1):veae022. doi: 10.1093/ve/veae022. eCollection 2024.
本文引用的文献
1
Photosystem I gene cassettes are present in marine virus genomes.光系统I基因盒存在于海洋病毒基因组中。
Nature. 2009 Sep 10;461(7261):258-262. doi: 10.1038/nature08284. Epub 2009 Aug 26.
2
Compelling reasons why viruses are relevant for the origin of cells.病毒与细胞起源相关的令人信服的原因。
Nat Rev Microbiol. 2009 Aug;7(8):615; author reply 615. doi: 10.1038/nrmicro2108-c5.
3
Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin.植物病毒欧尔密病毒属的分子特征及病毒基因组片段跨界重配作为其可能起源途径的证据。
J Gen Virol. 2009 Oct;90(Pt 10):2525-2535. doi: 10.1099/vir.0.013086-0. Epub 2009 Jun 17.
4
Viruses manipulate the marine environment.病毒操控着海洋环境。
Nature. 2009 May 14;459(7244):207-12. doi: 10.1038/nature08060.
5
Laboratory procedures to generate viral metagenomes.生成病毒宏基因组的实验室程序。
Nat Protoc. 2009;4(4):470-83. doi: 10.1038/nprot.2009.10.
6
RNA viruses in the sea.海洋中的RNA病毒。
FEMS Microbiol Rev. 2009 Mar;33(2):295-323. doi: 10.1111/j.1574-6976.2008.00132.x.
7
Isolation and characterization of a single-stranded RNA virus infecting the bloom-forming diatom Chaetoceros socialis.一种感染形成水华的硅藻紧密角毛藻的单链RNA病毒的分离与鉴定
Appl Environ Microbiol. 2009 Apr;75(8):2375-81. doi: 10.1128/AEM.02580-08. Epub 2009 Feb 20.
8
Polydnaviruses of braconid wasps derive from an ancestral nudivirus.茧蜂的多分DNA病毒起源于一种原始的杆状病毒。
Science. 2009 Feb 13;323(5916):926-30. doi: 10.1126/science.1166788.
9
Estimating the size of the bacterial pan-genome.估算细菌泛基因组的大小。
Trends Genet. 2009 Mar;25(3):107-10. doi: 10.1016/j.tig.2008.12.004. Epub 2009 Jan 23.
10
Viral lysis of Phaeocystis pouchetii: implications for algal population dynamics and heterotrophic C, N and P cycling.波氏褐囊藻的病毒裂解：对藻类种群动态及异养碳、氮和磷循环的影响
ISME J. 2009 Apr;3(4):430-41. doi: 10.1038/ismej.2008.125. Epub 2009 Jan 8.
Zotero 插件