MSK
Search
- Page Path
- HOME > Search
Review
- Metaviromics coupled with phage-host identification to open the viral ‘black box’
- Kira Moon , Jang-Cheon Cho
- J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021
- DOI: https://doi.org/10.1007/s12275-021-1016-9
- 58 View
- 0 Download
- 9 Web of Science
- 9 Crossref
-
Abstract
- Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium- based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture- independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.
-
Citations
Citations to this article as recorded by
- Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
Joanna Warwick-Dugdale, Funing Tian, Michelle L. Michelsen, Dylan R. Cronin, Karen Moore, Audrey Farbos, Lauren Chittick, Ashley Bell, Ahmed A. Zayed, Holger H. Buchholz, Luis M. Bolanos, Rachel J. Parsons, Michael J. Allen, Matthew B. Sullivan, Ben Tempe
Nature Communications.2024;[Epub] CrossRef - Tools and methodology to in silico phage discovery in freshwater environments
Carlos Willian Dias Dantas, David Tavares Martins, Wylerson Guimarães Nogueira, Oscar Victor Cardenas Alegria, Rommel Thiago Jucá Ramos
Frontiers in Microbiology.2024;[Epub] CrossRef - A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae
Zhenyu Liu, Wenhui Jiang, Cholsong Kim, Xiaoya Peng, Cong Fan, Yingliang Wu, Zhixiong Xie, Fang Peng
International Journal of Molecular Sciences.2023; 24(8): 7662. CrossRef - Evaluation of the ABL NGS assay for HIV-1 drug resistance testing
Thomas Lhossein, Karine Sylvain, Véronique Descamps, Virginie Morel, Baptiste Demey, Etienne Brochot
Heliyon.2023; 9(11): e22210. CrossRef - Human virome: Implications in cancer
Rafael Tamayo-Trujillo, Patricia Guevara-Ramírez, Santiago Cadena-Ullauri, Elius Paz-Cruz, Viviana A. Ruiz-Pozo, Ana Karina Zambrano
Heliyon.2023; 9(3): e14086. CrossRef - Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii
Georgios E. Premetis, Nikolaos D. Georgakis, Angeliki Stathi, Nikolaos E. Labrou
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics.2023; 1871(4): 140918. CrossRef - Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining
Kang Du, Feng Yang, Jun-Tao Zhang, Rong-Cheng Yu, Ziqing Deng, Wei-Fang Li, Yuxing Chen, Qiong Li, Cong-Zhao Zhou
Microbiome.2022;[Epub] CrossRef - Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing
Harilanto Felana Andrianjakarivony, Yvan Bettarel, Fabrice Armougom, Christelle Desnues
Viruses.2022; 15(1): 76. CrossRef - Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef
- Long-read powered viral metagenomics in the oligotrophic Sargasso Sea
First
Prev
TOP
