Title |
Metaviromics coupled with phage-host identification to open the viral ‘black box’ |
Author |
Kira Moon1 and Jang-Cheon Cho2* |
Address |
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 Korea |
Bibliography |
Journal of Microbiology, 59(3),311–323, 2021,
|
DOI |
10.1007/s12275-021-1016-9
|
Key Words |
virome, metagenome, metaviromics, phage, aquatic,
viral ecology, cultivation |
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. |