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Special Issue "Bacteriophage Genomes and Genomics: News from the Wild"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: 30 April 2018

Special Issue Editor

Guest Editor
Dr. Marie-Agnès Petit

Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
Website | E-Mail
Interests: molecular aspects of phage evolution: genome organization and rearrangements, mosaicism in temperate phage, phage recombination and mutagenesis; phage genome evolution in various ecological niches like the murine gastro-intestinal tract; emerging methods for phage genome annotation and analysis

Special Issue Information

Dear Colleagues,

In the jungle of the phage world, genomes analyses have started to bring some order: Genomics becomes a reliable tool to classify phages, and ICTV has recently begun implementing taxonomic classifications, based primarily on genomic data. The raising interest in phage therapy has launched phage discoveries for a variety of bacterial species, allowing to reduce the over-representation of model phage-like coliphages in databases, and to reach a more equilibrated view on the phage world. Teaching on its side has opened an unprecedented view on mycophages, and new teaching projects now tackle other genera, such as Bacilli or Streptomycetes. Finally, (meta)viromics and single whole genome amplification are also bringing to the shore a wealth of new genomes. As such, the time is ready to collect the most striking features of the recent discoveries into a single issue.

This wealth of data has also led to forge new tools dedicated to phage genome analyses, so that bio-informatics oriented manuscripts are also welcome in the special issue. Important questions are raised by some of the tools developed for virome analysis, such as the relevance of virome assemblies, the phage host or life style prediction issues. Benchmarking papers, or critical analyses on the state-of-the-art in this field will also be considered for publication in this Special Issue.

Dr. Marie-Agnès Petit
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • phage genomics
  • viromics
  • classification
  • prediction tools

Published Papers (6 papers)

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Open AccessArticle Genomic Characterization of Sixteen Yersinia enterocolitica-Infecting Podoviruses of Pig Origin
Viruses 2018, 10(4), 174; doi:10.3390/v10040174
Received: 15 December 2017 / Revised: 23 March 2018 / Accepted: 29 March 2018 / Published: 3 April 2018
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Abstract
Yersinia enterocolitica causes enteric infections in humans and animals. Human infections are often caused by contaminated pork meat. Y. enterocolitica colonizes pig tonsils and pigs secrete both the human pathogen and its specific bacteriophages into the stools. In this work, sixteen Y. enterocolitica
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Yersinia enterocolitica causes enteric infections in humans and animals. Human infections are often caused by contaminated pork meat. Y. enterocolitica colonizes pig tonsils and pigs secrete both the human pathogen and its specific bacteriophages into the stools. In this work, sixteen Y. enterocolitica—infecting lytic bacteriophages isolated from pig stools originating from several pig farms were characterized. All phages belong to the Podoviridae family and their genomes range between 38,391–40,451 bp in size. The overall genome organization of all the phages resembled that of T7-like phages, having 3–6 host RNA polymerase (RNAP)-specific promoters at the beginning of the genomes and 11–13 phage RNAP-specific promoters as well as 3–5 rho-independent terminators, scattered throughout the genomes. Using a ligation-based approach, the physical termini of the genomes containing direct terminal repeats of 190–224 bp were established. No genes associated with lysogeny nor any toxin, virulence factor or antibiotic resistance genes were present in the genomes. Even though the phages had been isolated from different pig farms the nucleotide sequences of their genomes were 90–97% identical suggesting that the phages were undergoing microevolution within and between the farms. Lipopolysaccharide was found to be the surface receptor of all but one of the phages. The phages are classified as new species within the T7virus genus of Autographivirinae subfamily. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Open AccessArticle Deciphering the Human Virome with Single-Virus Genomics and Metagenomics
Viruses 2018, 10(3), 113; doi:10.3390/v10030113
Received: 31 January 2018 / Revised: 28 February 2018 / Accepted: 1 March 2018 / Published: 6 March 2018
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Abstract
Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities.
[...] Read more.
Single-cell genomics has unveiled the metabolic potential of dominant microbes inhabiting different environments, including the human body. The lack of genomic information for predominant microbes of the human body, such as bacteriophages, hinders our ability to answer fundamental questions about our viral communities. Here, we applied single-virus genomics (SVGs) to natural human salivary samples in combination with viral metagenomics to gain some insights into the viral community structure of the oral cavity. Saliva samples were processed for viral metagenomics (n = 15) and SVGs (n = 3). A total of 1328 uncultured single viruses were sorted by fluorescence-activated virus sorting followed by whole genome amplification. Sequencing of 24 viral single amplified genomes (vSAGs) showed that half of the vSAGs contained viral hallmark genes. Among those bona fide viruses, the uncultured single virus 92-C13 putatively infecting oral Streptococcus-like species was within the top ≈10 most abundant viruses in the oral virome. Viral gene network and viral metagenomics analyses of 439 oral viruses from cultures, metagenomics, and SVGs revealed that salivary viruses were tentatively structured into ≈200 major viral clusters, corresponding to approximately genus-level groupings. Data showed that none of the publicly available viral isolates, excepting an Actinomyces phage, were significantly abundant in the oral viromes. In addition, none of the obtained viral contigs and vSAGs from this study were present in all viromes. Overall, the data demonstrates that most viral isolates are not naturally abundant in saliva, and furthermore, the predominant viruses in the oral cavity are yet uncharacterized. Results suggest a variable, complex, and interpersonal viral profile. Finally, we demonstrated the power of SVGs in combination with viral metagenomics to unveil the genetic information of the uncultured viruses of the human virome. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Open AccessArticle Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making
Viruses 2018, 10(1), 39; doi:10.3390/v10010039
Received: 14 November 2017 / Revised: 5 January 2018 / Accepted: 12 January 2018 / Published: 16 January 2018
Cited by 2 | PDF Full-text (6542 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because
[...] Read more.
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid. Transmission electron microscopy revealed tail-less icosahedral particles with a diameter of ~78 nm. The linear double-stranded DNA genome of GC1 (16,523 base pairs) contains terminal inverted repeats and carries 36 open reading frames, only a handful of which could be functionally annotated. These encode for the key proteins involved in DNA replication (protein-primed family B DNA polymerase) as well as in virion structure and assembly (major capsid protein, genome packaging ATPase (adenosine triphosphatase) and several minor capsid proteins). GC1 is the first tectivirus infecting an alphaproteobacterial host and is thus far the only temperate tectivirus of gram-negative bacteria. Based on distinctive sequence and life-style features, we propose that GC1 represents a new genus within the Tectiviridae, which we tentatively named “Gammatectivirus”. Furthermore, GC1 helps to bridge the gap in the sequence space between alphatectiviruses and betatectiviruses. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Open AccessArticle Comparative Analysis of 37 Acinetobacter Bacteriophages
Viruses 2018, 10(1), 5; doi:10.3390/v10010005
Received: 4 December 2017 / Revised: 21 December 2017 / Accepted: 22 December 2017 / Published: 24 December 2017
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Abstract
Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy
[...] Read more.
Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Open AccessArticle Metagenomic Analysis of Therapeutic PYO Phage Cocktails from 1997 to 2014
Viruses 2017, 9(11), 328; doi:10.3390/v9110328
Received: 13 October 2017 / Revised: 31 October 2017 / Accepted: 2 November 2017 / Published: 3 November 2017
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Abstract
Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory
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Phage therapy has regained interest in recent years due to the alarming spread of antibiotic resistance. Whilst phage cocktails are commonly sold in pharmacies in countries such as Georgia and Russia, this is not the case in western countries due to western regulatory agencies requiring a thorough characterization of the drug. Here, DNA sequencing of constituent biological entities constitutes a first step. The pyophage (PYO) cocktail is one of the main commercial products of the Georgian Eliava Institute of Bacteriophage, Microbiology and Virology and is used to cure skin infections. Since its first production in the 1930s, the composition of the cocktail has been periodically modified to add phages effective against emerging pathogenic strains. In this paper, we compared the composition of three PYO cocktails from 1997 (PYO97), 2000 (PYO2000) and 2014 (PYO2014). Based on next generation sequencing, de novo assembly and binning of contigs into draft genomes based on tetranucleotide distance, thirty and twenty-nine phage draft genomes were predicted in PYO97 and PYO2014, respectively. Of these, thirteen and fifteen shared high similarity to known phages. Eleven draft genomes were found to be common in the two cocktails. One of these showed no similarity to publicly available phage genomes. Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. aeruginosa and S. aureus were found in both cocktails. Finally, we estimated larger overlap of the PYO2000 cocktail to PYO97 compared to PYO2014. Using next generation sequencing and metagenomics analysis, we were able to characterize and compare the content of PYO cocktails separated by 17 years in time. Even though the cocktail composition is upgraded every six months, we found it to remain relatively stable over the years. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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Open AccessConference Report “French Phage Network”—Third Meeting Report
Viruses 2018, 10(3), 123; doi:10.3390/v10030123
Received: 5 March 2018 / Revised: 6 March 2018 / Accepted: 8 March 2018 / Published: 10 March 2018
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Abstract
In its third year of existence, the French Phage Network (Phages.fr) is pursuing its expansion. With more than 25 groups, mostly based in France, working on the various aspects of phage research, the network has increased its visibility, interactivity, and activity. The third
[...] Read more.
In its third year of existence, the French Phage Network (Phages.fr) is pursuing its expansion. With more than 25 groups, mostly based in France, working on the various aspects of phage research, the network has increased its visibility, interactivity, and activity. The third meeting of the Phages.fr network, held on November 2017 at the Gif-sur-Yvette Centre National de la Recherche Scientifique (CNRS) campus, was a great opportunity for many young scientists to present their work and interact with more senior scientists, amongst which several were invited from abroad. Here we provide a summary of the work presented at this occasion during the oral presentations and poster sessions. Full article
(This article belongs to the Special Issue Bacteriophage Genomes and Genomics: News from the Wild)
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