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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 (20 October 2023) | Viewed by 29898

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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

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Keywords

bacteriophage
comparative genomics
recombination
phylogeny
horizontal gene transfer

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Published Papers (10 papers)

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Editorial

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4 pages, 204 KiB

Open AccessEditorial

Special Issue “Bacteriophage Genomics”: Editorial

by Igor V. Babkin and Nina V. Tikunova

Microorganisms 2023, 11(3), 693; https://doi.org/10.3390/microorganisms11030693 - 8 Mar 2023

Viewed by 1701

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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12 pages, 3393 KiB

Open AccessArticle

Isolation, Characterization and Genomic Analysis of a Novel Jumbo Phage, AerS_266, That Infects Aeromonas salmonicida

by Vera Morozova, Igor Babkin, Yuliya Kozlova, Artem Tikunov, Tatiana Ushakova, Alevtina Bardasheva, Valeria Fedorets, Elena Zhirakovskaya and Nina Tikunova

Microorganisms 2023, 11(11), 2649; https://doi.org/10.3390/microorganisms11112649 - 28 Oct 2023

Cited by 3 | Viewed by 1728

Abstract

Aeromonas salmonicida is the causative agent of septicemia in fish, and it is associated with significant economic losses in the aquaculture industry. While piscine Aeromonas infections are mainly treated with antibiotics, the emergence of resistance in bacterial populations requires the development of alternative methods of treatment. The use of phages can be one of them. A novel A. salmonicida jumbo phage, AerS_266, was isolated and characterized. This phage infects only mesophilic A. salmonicida strains and demonstrates a slow lytic life cycle. Its genome contains 243,674 bp and 253 putative genes: 84 encode proteins with predicted functions, and 3 correspond to tRNAs. Genes encoding two multisubunit RNA polymerases, chimallin and PhuZ, were identified, and AerS_266 was thus defined as a phiKZ-like phage. While similar phages with genomes >200 kb specific to Aeromonas hydrophila and Aeromonas veronii have been previously described, AerS_266 is the first phiKZ-like phage found to infect A. salmonicida. Full article

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

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13 pages, 2568 KiB

Open AccessArticle

Prevalence and Genetic Diversity of Cross-Assembly Phages in Wastewater Treatment Plants in Riyadh, Saudi Arabia

by Riyadh Alotaibi, Saleh Eifan, Atif Hanif, Islam Nour and Abdulrahman Alkathiri

Microorganisms 2023, 11(9), 2167; https://doi.org/10.3390/microorganisms11092167 - 27 Aug 2023

Viewed by 1876

Abstract

The most common DNA virus found in wastewaters globally is the cross-assembly phage (crAssphage). King Saud University wastewater treatment plant (KSU-WWTP); Manfoha wastewater treatment plant (MN-WWTP); and the Embassy wastewater treatment plant (EMB-WWTP) in Riyadh, Saudi Arabia were selected, and 36 untreated sewage water samples during the year 2022 were used in the current study. The meteorological impact on crAssphage prevalence was investigated. CrAssphage prevalence was recorded using PCR and Sanger sequencing. The molecular diversity of crAssphage sequences was studied for viral gene segments from the major capsid protein (MCP) and membrane protein containing the peptidoglycan-binding domain (MP-PBD). KSU-WWTP and EMB-WWTP showed a higher prevalence of crAssphage (83.3%) than MN-WWTP (75%). Phylogenetic analysis of MCP and MP-PBD segments depicted a close relationship to the Japanese isolates. The MCP gene from the current study’s isolate WW/2M/SA/2022 depicted zero evolutionary divergence from 3057_98020, 2683_104905, and 4238_99953 isolates (d = 0.000) from Japan. A significant influence of temporal variations on the prevalence of crAssphage was detected in the three WWTPs. CrAssphage displayed the highest prevalence at high temperatures (33–44 °C), low relative humidity (6–14%), and moderate wind speed (16–21 Km/h). The findings provided pioneering insights into crAssphage prevalence and its genetic diversity in WWTPs in Riyadh, Saudi Arabia. Full article

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

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17 pages, 4025 KiB

Open AccessArticle

Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus

by Leise Riber, Alexander Byth Carstens, Peter Erdmann Dougherty, Chayan Roy, Katharina Willenbücher, Frank Hille, Charles M. A. P. Franz and Lars Hestbjerg Hansen

Microorganisms 2023, 11(7), 1831; https://doi.org/10.3390/microorganisms11071831 - 18 Jul 2023

Cited by 2 | Viewed by 1955

Abstract

Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages—particularly those targeting phyllosphere-associated bacteria—remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies. Full article

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

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18 pages, 8192 KiB

Open AccessArticle

Identification, Characterization, and Genome Analysis of Two Novel Temperate Pseudomonas protegens Phages PseuP_222 and PseuP_224

by Vera Morozova, Yuliya Kozlova, Artem Tikunov, Igor Babkin, Tatyana Ushakova, Alevtina Bardasheva, Ghadeer Jdeed, Elena Zhirakovskaya, Alina Mogileva, Sergei Netesov and Nina Tikunova

Microorganisms 2023, 11(6), 1456; https://doi.org/10.3390/microorganisms11061456 - 31 May 2023

Cited by 1 | Viewed by 2390

Abstract

Two novel P. protegens bacteriophages PseuP_222 and Pseu_224 and their host P. protegens CEMTC 4060 were isolated from the same sample (Inya river, Siberia). Both phages have siphovirus morphology and belong to lambdoid phages. Comparative genome analysis revealed a low nucleotide and amino acid sequence similarity of PseuP_222 and PseuP_224 between themselves, and between them and other lambdoid phages. Bioinformatics analysis indicated that PseuP_222 and PseuP_224 are members of a genetically diverse group of phages of environmental Pseudomonas spp.; this group is distant from a large group of P. aeruginosa phages. In phylogenetic trees, the positioning of the terminase large subunits, major capsid proteins, tail tape measure proteins, and CI-like repressors of PseuP_222 and PseuP_224 were remote and changed relative to those of the Escherichia lambda phage and lambdoid phages of Pseudomonas spp. However, the nucleoid-associated protein NdpA/YejK and P5-like structural protein from both phages showed high similarity and were not found in lambda phage and other lambdoid phages of Pseudomonas spp. Substantial divergences of the PseuP_222 and PseuP_224 genomes and proteomes indicated that the evolutionary history of these phages was mostly independent and they probably began to use one host only recently. Full article

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

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17 pages, 1838 KiB

Open AccessArticle

PHERI—Phage Host ExploRation Pipeline

by Andrej Baláž, Michal Kajsik, Jaroslav Budiš, Tomáš Szemes and Ján Turňa

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

Cited by 10 | Viewed by 2342

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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20 pages, 6529 KiB

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

by Amal Senevirathne, Jehee Lee, Mahanama De Zoysa and Chamilani Nikapitiya

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

Cited by 3 | Viewed by 3614

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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22 pages, 6644 KiB

Open AccessArticle

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

by Nikita Zrelovs, Juris Jansons, Andris Dislers and Andris Kazaks

Microorganisms 2022, 10(9), 1799; https://doi.org/10.3390/microorganisms10091799 - 7 Sep 2022

Cited by 6 | Viewed by 2931

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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14 pages, 1170 KiB

Open AccessReview

The Role of Temperate Phages in Bacterial Pathogenicity

by Vimathi S. Gummalla, Yujie Zhang, Yen-Te Liao and Vivian C. H. Wu

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

Cited by 30 | Viewed by 6535

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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Other

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8 pages, 1552 KiB

Open AccessBrief Report

Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions

by Mark Milhaven, Cyril J. Versoza, Aman Garg, Lindsey Cai, Sanjana Cherian, Kamalei Johnson, Kevin Salas Perez, Madison Blanco, Jackelyn Lobatos, Corinne Mitra, Maria Strasser and Susanne P. Pfeifer

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

Cited by 2 | Viewed by 3330

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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