A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences

Ivan M Pchelin; Pavel V Tkachev; Daniil V Azarov; Andrey N Gorshkov; Daria O Drachko; Vasily V Zlatogursky; Alexander V Dmitriev; Artemiy E Goncharov

doi:10.3390/v15010216

A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences

Viruses. 2023 Jan 12;15(1):216. doi: 10.3390/v15010216.

Authors

Ivan M Pchelin¹, Pavel V Tkachev¹, Daniil V Azarov¹, Andrey N Gorshkov^{2

3}, Daria O Drachko^{4

5}, Vasily V Zlatogursky⁵, Alexander V Dmitriev¹, Artemiy E Goncharov¹

Affiliations

¹ Scientific and Educational Center "Molecular Bases of Interaction of Microorganisms and Human" of the WCRC "Center for Personalized Medicine", Institute of Experimental Medicine, 197022 Saint Petersburg, Russia.
² Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, Russia.
³ Laboratory of Pathomorphology, Almazov National Research Centre, 197341 Saint Petersburg, Russia.
⁴ Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, 199034 Saint Petersburg, Russia.
⁵ Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 199034 Saint Petersburg, Russia.

Abstract

In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.

Keywords: Enterococcus; bacteriophage; phylogeny; sequence space; siphovirus.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages*
Enterococcus / genetics
Genome, Viral
Humans
Myoviridae / genetics
Phylogeny
Sequence Analysis, DNA

Grants and funding

The work was supported by the Ministry of Science and Higher Education of the Russian Federation, no. 075-15-2022-302, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine” (FSBSI “IEM”) Scientific and Educational Center “Molecular bases of interaction of microorganisms and human” of the World-Class Research Center “Center for Personalized Medicine” at FSBSI “IEM”.