A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences
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 wa...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/1/216 |
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| author | Ivan M. Pchelin Pavel V. Tkachev Daniil V. Azarov Andrey N. Gorshkov Daria O. Drachko Vasily V. Zlatogursky Alexander V. Dmitriev Artemiy E. Goncharov |
| author_facet | Ivan M. Pchelin Pavel V. Tkachev Daniil V. Azarov Andrey N. Gorshkov Daria O. Drachko Vasily V. Zlatogursky Alexander V. Dmitriev Artemiy E. Goncharov |
| author_sort | Ivan M. Pchelin |
| collection | DOAJ |
| description | 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 <i>Enterococcus faecalis</i> 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 <i>Enterococcus</i> spp. |
| first_indexed | 2024-03-09T11:02:21Z |
| format | Article |
| id | doaj.art-8f3cafcdb1744987872503ed8fb32d49 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T11:02:21Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-8f3cafcdb1744987872503ed8fb32d492023-12-01T01:13:06ZengMDPI AGViruses1999-49152023-01-0115121610.3390/v15010216A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter SequencesIvan M. Pchelin0Pavel V. Tkachev1Daniil V. Azarov2Andrey N. Gorshkov3Daria O. Drachko4Vasily V. Zlatogursky5Alexander V. Dmitriev6Artemiy E. Goncharov7Scientific 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, RussiaScientific 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, RussiaScientific 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, RussiaSmorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation, 197376 Saint Petersburg, RussiaLaboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, 199034 Saint Petersburg, RussiaDepartment of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 199034 Saint Petersburg, RussiaScientific 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, RussiaScientific 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, RussiaIn 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 <i>Enterococcus faecalis</i> 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 <i>Enterococcus</i> spp.https://www.mdpi.com/1999-4915/15/1/216bacteriophage<i>Enterococcus</i>siphovirusphylogenysequence space |
| spellingShingle | Ivan M. Pchelin Pavel V. Tkachev Daniil V. Azarov Andrey N. Gorshkov Daria O. Drachko Vasily V. Zlatogursky Alexander V. Dmitriev Artemiy E. Goncharov A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences Viruses bacteriophage <i>Enterococcus</i> siphovirus phylogeny sequence space |
| title | A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences |
| title_full | A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences |
| title_fullStr | A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences |
| title_full_unstemmed | A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences |
| title_short | A Genome of Temperate <i>Enterococcus</i> Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences |
| title_sort | genome of temperate i enterococcus i bacteriophage placed in a space of pooled viral dark matter sequences |
| topic | bacteriophage <i>Enterococcus</i> siphovirus phylogeny sequence space |
| url | https://www.mdpi.com/1999-4915/15/1/216 |
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