Metaviromics coupled with phage-host identification to open the viral ‘black box’

Kira Moon; Jang-Cheon Cho

doi:10.1007/s12275-021-1016-9

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Metaviromics coupled with phage-host identification to open the viral ‘black box’: Kira Moon ¹, Jang-Cheon Cho ²; Journal of Microbiology 2021;59(3):311-323.
DOI: https://doi.org/10.1007/s12275-021-1016-9
Published online: February 23, 2021

¹Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea, ²Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea¹Biological Resources Utilization Division, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea, ²Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea

Corresponding author: Jang-Cheon Cho , Tel: +82-32-860-7711,

Received: 11 January 2021 • Revised: 28 January 2021 • Accepted: 28 January 2021

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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.

Keywords: Archaea;Core gene;Phylogenomics;Phylogeny;Software;UACG

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Metaviromics coupled with phage-host identification to open the viral ‘black box’

J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021

DOI: https://doi.org/10.1007/s12275-021-1016-9

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