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Special Issue "Bacteriophage Genomics 2.0"

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Systems Microbiology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 6782

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Dr. Igor V. Babkin

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Leading Researcher, Department of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk State University, Novosibirsk, Russia
Interests: virus evolution; human bocavirus; complete genome
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Bacteriophage Genomics”

Bacteriophages (or phages) are viruses of prokaryotes and are the most abundant biological entities known so far. The approximate size of the global phage population is more than 1031 phage particles, and recent studies have shown that bacteriophages play an important role in the biosphere. The natural genetic diversity of bacteriophage genomes is enormous, and their genome architectures are typically mosaic. This genetic diversity is first of all driven by the recombination between bacteriophage genomes and horizontal gene transfer from the host genomes. The evolution of bacteriophages is different for that of temperate and lytic phages and depends on the host and genetic structure of phages. Thus, the taxonomic classification of bacteriophages is a complex problem. At present, according to the International Committee on Taxonomy of Viruses (ICTV) and Bacterial and Archaeal Subcommittee (BAVS) within the ICTV, bacteriophages are classified by the type of nucleic acid, the structure of the virus capsid, etc. The number of bacteriophage families is constantly increasing as new objects are studied. Today, bacteriophages are classified into 3 orders (petitvirales, tubulavirales, and caudovirales) and 22 families. The vast majority of sequenced bacteriophage genomes belong to double-stranded DNA phages. The diversity of bacteriophage genomes is very large; genome sizes range from 4 to almost 700 kb.

This Special Issue of Microorganisms will be dedicated to the topic of bacteriophage genomics. This includes, but is not limited to, the following themes: bacteriophage comparative genomics and proteomics, phage genome evolution, phage rates of mutation and recombination, isolation and characterization of new phages, genomics approach for identifying host range determinants in bacteriophages, bacteriophage taxonomy, approaches to the artificial phage host range management, bacteriophage-mediated gene transfers, as well as other aspects of bacteriophage molecular biology.

Dr. Igor V. Babkin
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 submissions that pass pre-check are 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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

bacteriophage
comparative genomics
recombination
phylogeny
horizontal gene transfer

Published Papers (6 papers)

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Editorial

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Open AccessEditorial

Special Issue “Bacteriophage Genomics”: Editorial

Igor V. Babkin

and

Nina V. Tikunova

Microorganisms 2023, 11(3), 693; https://doi.org/10.3390/microorganisms11030693 - 08 Mar 2023

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Abstract

Virus genomics as a separate branch of biology has emerged relatively recently [...] Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

Research

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Open AccessArticle

PHERI—Phage Host ExploRation Pipeline

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Microorganisms 2023, 11(6), 1398; https://doi.org/10.3390/microorganisms11061398 - 26 May 2023

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Abstract

Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages’ host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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Open AccessArticle

Genome Characterization of Bacteriophage KPP-1, a Novel Member in the Subfamily Vequintavirinae, and Use of Its Endolysin for the Lysis of Multidrug-Resistant Klebsiella variicola In Vitro

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Microorganisms 2023, 11(1), 207; https://doi.org/10.3390/microorganisms11010207 - 13 Jan 2023

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Abstract

Multidrug-resistant members of the Klebsiella pneumoniae complex have become a threat to human lives and animals, including aquatic animals, owing to the limited choice of antimicrobial treatments. Bacteriophages are effective natural tools available to fight against multidrug-resistant bacteria. The bacteriophage KPP-1 was found to be strictly lytic against K. variicola, a multidrug-resistant isolate, producing clear plaques. The genome sequence analysis of KPP-1 revealed that it comprised 143,369 base pairs with 47% overall GC content. A total of 272 genes (forward 161, complementary 111) encode for 17 tRNAs and 255 open reading frames (ORFs). Among them, 32 ORFs could be functionally annotated using the National Center for Biotechnology Information (NCBI) Protein Basic Local Alignment Search Tool (BLASTp) algorithm while 223 were found to code for hypothetical proteins. Comparative genomic analysis revealed that the closest neighbor of KPP-1 can be found in the genus Mydovirus of the subfamily Vequintavirinae. KPP-1 not only markedly suppressed the growth of the host but also worked synergistically with ampicillin. Useful genes for pathogen control such as endolysin (locus tag: KPP_11591) were found to have activity against multidrug-resistant isolate of K. variicola. Further studies are necessary to develop a strategy to control the emerging pathogen K. variicola using bacteriophages such as KPP-1. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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Open AccessArticle

Morganella Phage Mecenats66 Utilizes an Evolutionarily Distinct Subtype of Headful Genome Packaging with a Preferred Packaging Initiation Site

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Microorganisms 2022, 10(9), 1799; https://doi.org/10.3390/microorganisms10091799 - 07 Sep 2022

Cited by 1 | Viewed by 1191

Abstract

Both recognized species from the genus Morganella (M. morganii and M. psychrotolerans) are Gram-negative facultative anaerobic rod-shaped bacteria that have been documented as sometimes being implicated in human disease. Complete genomes of seven Morganella-infecting phages are publicly available today. Here, we report on the genomic characterization of an insect associated Morganella sp. phage, which we named Mecenats66, isolated from dead worker honeybees. Phage Mecenats66 was propagated, purified, and subjected to whole-genome sequencing with subsequent complete genome annotation. After the genome de novo assembly, it was noted that Mecenats66 might employ a headful packaging with a preferred packaging initiation site, although its terminase amino acid sequence did not fall within any of the currently recognized headful packaging subtype employing phage (that had their packaging strategy experimentally verified) with clusters on a terminase sequence phylogenetic tree. The in silico predicted packaging strategy was verified experimentally, validating the packaging initiation site and suggesting that Mecenats66 represents an evolutionarily distinct headful genome packaging with a preferred packaging initiation site strategy subtype. These findings can possibly be attributed to several of the phages already found within the public biological sequence repositories and could aid newly isolated phage packaging strategy predictions in the future. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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Review

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Open AccessReview

The Role of Temperate Phages in Bacterial Pathogenicity

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Microorganisms 2023, 11(3), 541; https://doi.org/10.3390/microorganisms11030541 - 21 Feb 2023

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Abstract

Bacteriophages are viruses that infect bacteria and archaea and are classified as virulent or temperate phages based on their life cycles. A temperate phage, also known as a lysogenic phage, integrates its genomes into host bacterial chromosomes as a prophage. Previous studies have indicated that temperate phages are beneficial to their susceptible bacterial hosts by introducing additional genes to bacterial chromosomes, creating a mutually beneficial relationship. This article reviewed three primary ways temperate phages contribute to the bacterial pathogenicity of foodborne pathogens, including phage-mediated virulence gene transfer, antibiotic resistance gene mobilization, and biofilm formation. This study provides insights into mechanisms of phage–bacterium interactions in the context of foodborne pathogens and provokes new considerations for further research to avoid the potential of phage-mediated harmful gene transfer in agricultural environments. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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Open AccessBrief Report

Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions

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Microorganisms 2023, 11(1), 170; https://doi.org/10.3390/microorganisms11010170 - 10 Jan 2023

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Abstract

Bacteriophages are being widely harnessed as an alternative to antibiotics due to the global emergence of drug-resistant pathogens. To guide the usage of these bactericidal agents, characterization of their host specificity is vital—however, host range information remains limited for many bacteriophages. This is particularly the case for bacteriophages infecting the Microbacterium genus, despite their importance in agriculture, biomedicine, and biotechnology. Here, we elucidate the phylogenomic relationships between 125 Microbacterium cluster EA bacteriophages—including members from 11 sub-clusters (EA1 to EA11)—and infer their putative host ranges using insights from codon usage bias patterns as well as predictions from both exploratory and confirmatory computational methods. Our computational analyses suggest that cluster EA bacteriophages have a shared infection history across the Microbacterium clade. Interestingly, bacteriophages of all sub-clusters exhibit codon usage preference patterns that resemble those of bacterial strains different from ones used for isolation, suggesting that they might be able to infect additional hosts. Furthermore, host range predictions indicate that certain sub-clusters may be better suited in prospective biotechnological and medical applications such as phage therapy. Full article

(This article belongs to the Special Issue Bacteriophage Genomics 2.0)

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