Submit to Viruses Review for Viruses Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Bacteriophage Diversity

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Related Special Issue
Published Papers

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

Deadline for manuscript submissions: closed (30 November 2024) | Viewed by 14235

Share This Special Issue

Special Issue Editor

Prof. Dr. Bert Ely

E-Mail Website
Guest Editor

Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
Interests: bacterial genetics; bacteriophage genomes; bacterial genome evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Numerous metagenomic analyses have provided new evidence that bacteriophages are abundant, ubiquitous and extremely diverse. In addition, the dramatically lower cost of nucleotide sequencing has enabled researchers to identify evolutionary relationships among collections of closely related bacteriophages isolated from specific environments. As a result, there has been a resurgence in the number of laboratories studying recently isolated bacteriophages.

As additional phages are isolated and the nucleotide sequence of their genomes is determined, new genera are being identified, and within-genera comparisons can identify evolutionary trends that lead to the diversification of bacteriophage genomes.

To highlight this renewed interest in bacteriophage diversity, the journal Viruses will devote a Special Issue to the topic of bacteriophage diversity that is intended to showcase research papers that investigate the diversity present in collections of bacteriophages that have been isolated from natural environments.

Prof. Dr. Bert Ely
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. 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 2600 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

bacteriophages
phage diversity
genome evolution
new genera
phage–host interactions

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Bacteriophage Diversity, 2nd Edition in Viruses

Published Papers (10 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

7 pages, 12704 KiB

Open AccessArticle

Caulobacter Strains Code for Novel Restriction Endonucleases That Protect Them from Bacteriophage Infections

by Ian Sisto and Bert Ely

Viruses 2025, 17(3), 311; https://doi.org/10.3390/v17030311 - 25 Feb 2025

Viewed by 431

Abstract

Bacteriophages grown on Caulobacter vibrioides strain CB15 have reduced plating efficiency on other Caulobacter strains. To determine the cause of this reduced plating efficiency, we performed a series of experiments that demonstrated that the reduced plating efficiency is due to a novel set of restriction and modification (RM) enzymes that are present in most of the Caulobacter strains that we tested. We then demonstrated that one of these RM systems recognizes the nucleotide sequence 5′-ATNNAT-3′. A careful inspection of the genome nucleotide sequences of each of the strains revealed that the genes coding for these RM enzymes have not been annotated or identified, suggesting that the proteins may differ from the common types of bacterial restriction and modification enzymes. In addition, the host strain NA1000 contains a 26 kb mobile element that provides resistance to incoming phages. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

23 pages, 10436 KiB

Open AccessArticle

Genomic Analysis of 96 Paenibacillus larvae Bacteriophages Including 26 from Aotearoa, New Zealand

by Danielle N. Kok, Sophia P. Gosselin, Brenham Howard, Steven G. Cresawn, Philippos K. Tsourkas and Heather L. Hendrickson

Viruses 2025, 17(2), 137; https://doi.org/10.3390/v17020137 - 21 Jan 2025

Viewed by 889

Abstract

The bacterium Paenibacillus larvae is responsible for the devastating honey bee (Apis mellifera) disease American Foulbrood. Research into bacteriophages that infect P. larvae is growing rapidly due to increasing antibiotic resistance and restrictions on antibiotic use in beehives in some countries. In this study, we present the sequenced and annotated genomes of 26 novel P. larvae phages recently isolated in New Zealand, which brings the total number of sequenced and annotated P. larvae phages to 96. The 26 novel phages belong to the pre-existing Vegas or Harrison clusters. We performed a comprehensive genomic analysis of all 96 phage genomes, grouping them into five divergent clusters and two singletons. The majority of these phages are temperate, with the possible exception of three phages that may be lytic. All 96 of these phages encode an N-acteylmuramoyl-L-alanine amidase that serves as their lysin. The amidases are from two divergent clusters, both of which show a high degree of intra-cluster similarity. Six phages and a prophage contain the Plx1 P. larvae toxin gene, which we suggest may be mobilizable. This study expands our knowledge of P. larvae phages from around the world. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

18 pages, 4160 KiB

Open AccessArticle

Expanding the Diversity of Actinobacterial Tectiviridae: A Novel Genus from Microbacterium

by Jacqueline M. Washington, Holly Basta, Angela Bryanne De Jesus, Madison G. Bendele, Steven G. Cresawn and Emily K. Ginser

Viruses 2025, 17(1), 113; https://doi.org/10.3390/v17010113 - 15 Jan 2025

Viewed by 849

Abstract

Six novel Microbacterium phages belonging to the Tectiviridae family were isolated using Microbacterium testaceum as a host. Phages MuffinTheCat, Badulia, DesireeRose, Bee17, SCoupsA, and LuzDeMundo were purified from environmental samples by students participating in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program at Alliance University, New York. The phages have linear dsDNA genomes 15,438–15,636 bp with 112–120 bp inverted terminal repeats. Transmission electron microscopy (TEM) imaging analysis revealed that the six novel phages have six-sided icosahedral double-layered capsids with an internal lipid membrane that occasionally forms protruding nanotubules. Annotation analysis determined that the novel Microbacterium phages all have 32–34 protein-coding genes and no tRNAs. Like other Tectiviridae, the phage genomes are arranged into two segments and include three highly conserved family genes that encode a DNA polymerase, double jelly-roll major capsid protein, and packaging ATPase. Although the novel bacteriophages have 91.6 to 97.5% nucleotide sequence similarity to each other, they are at most 58% similar to previously characterized Tectiviridae genera. Consequently, these novel Microbacterium phages expand the diversity of the Tectiviridae family, and we propose they form the sixth genus, Zetatectivirus. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

12 pages, 2555 KiB

Open AccessArticle

Isolation and Antibiofilm Activity of Bacteriophages against Cutibacterium acnes from Patients with Periprosthetic Joint Infection

by Baixing Chen, Marco Chittò, Siyuan Tao, Jeroen Wagemans, Rob Lavigne, R. Geoff Richards, Willem-Jan Metsemakers and T. Fintan Moriarty

Viruses 2024, 16(10), 1592; https://doi.org/10.3390/v16101592 - 10 Oct 2024

Cited by 1 | Viewed by 1444

Abstract

Background: Infections following shoulder surgery, particularly periprosthetic joint infection (PJI), are challenging to treat. Cutibacterium acnes is the causative pathogen in 39% to 76% of these cases. This study explores the efficacy of bacteriophage therapy as an alternative to conventional antibiotics for treating such infections. Methods: Nine phages with lytic activity were isolated from the skin of humans using C. acnes ATCC 6919 as the indicator host. These phages were tested individually or in combination to assess host range and antibiofilm activity against clinical strains of C. acnes associated with PJIs. The phage cocktail was optimized for broad-spectrum activity and tested in vitro against biofilms formed on titanium discs to mimic the prosthetic environment. Results: The isolated phages displayed lytic activity against a range of C. acnes clinical isolates. The phage cocktail significantly reduced the bacterial load of C. acnes strains 183, 184, and GG2A, as compared with untreated controls (p < 0.05). Individual phages, particularly CaJIE7 and CaJIE3, also demonstrated significant reductions in bacterial load with respect to specific strains. Moreover, phages notably disrupted the biofilm structure and reduced biofilm biomass, confirming the potential of phage therapy in targeting biofilm-associated infections. Conclusions: Our preclinical findings support the potential of phage therapy as a viable adjunct to traditional antibiotics for treating C. acnes infections in orthopedic device-related infections. The ability of phages to disrupt biofilms may be particularly beneficial for managing infections associated with prosthetic implants. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

18 pages, 30996 KiB

Open AccessArticle

The First Pseudomonas Phage vB_PseuGesM_254 Active against Proteolytic Pseudomonas gessardii Strains

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

Viruses 2024, 16(10), 1561; https://doi.org/10.3390/v16101561 - 30 Sep 2024

Viewed by 1483

Abstract

Bacteria of the Pseudomonas genus, including the Pseudomonas gessardii subgroup, play an important role in the environmental microbial communities. Psychrotolerant isolates of P. gessardii can produce thermostable proteases and lipases. When contaminating refrigerated raw milk, these bacteria spoil it by producing enzymes resistant to pasteurization. One possible way to prevent spoilage of raw milk is to use Pseudomonas lytic phages specific to undesirable P. gessardii isolates. The first phage, Pseudomonas vB_PseuGesM_254, was isolated and characterized, which is active against several proteolytic P. gessardii strains. This lytic myophage can infect and lyse its host strain at 24 °C and at low temperature (8 °C); so, it has the potential to prevent contamination of raw milk. The vB_PseuGesM_254 genome, 95,072 bp, shows a low level of intergenomic similarity with the genomes of known phages. Comparative proteomic ViPTree analysis indicated that vB_PseuGesM_254 is associated with a large group of Pseudomonas phages that are members of the Skurskavirinae and Gorskivirinae subfamilies and the Nankokuvirus genus. The alignment constructed using ViPTree shows that the vB_PseuGesM_254 genome has a large inversion between ~53,100 and ~70,700 bp, which is possibly a distinctive feature of a new taxonomic unit within this large group of Pseudomonas phages. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

15 pages, 3851 KiB

Open AccessArticle

New Viruses Infecting Hyperthermophilic Bacterium Thermus thermophilus

by Matvey Kolesnik, Constantine Pavlov, Alina Demkina, Aleksei Samolygo, Karyna Karneyeva, Anna Trofimova, Olga S. Sokolova, Andrei V. Moiseenko, Maria Kirsanova and Konstantin Severinov

Viruses 2024, 16(9), 1410; https://doi.org/10.3390/v16091410 - 3 Sep 2024

Viewed by 1537

Abstract

Highly diverse phages infecting thermophilic bacteria of the Thermus genus have been isolated over the years from hot springs around the world. Many of these phages are unique, rely on highly unusual developmental strategies, and encode novel enzymes. The variety of Thermus phages is clearly undersampled, as evidenced, for example, by a paucity of phage-matching spacers in Thermus CRISPR arrays. Using water samples collected from hot springs in the Kunashir Island from the Kuril archipelago and from the Tsaishi and Nokalakevi districts in the Republic of Georgia, we isolated several distinct phages infecting laboratory strains of Thermus thermophilus. Genomic sequence analysis of 11 phages revealed both close relatives of previously described Thermus phages isolated from geographically distant sites, as well as phages with very limited similarity to earlier isolates. Comparative analysis allowed us to predict several accessory phage genes whose products may be involved in host defense/interviral warfare, including a putative Type V CRISPR-cas system. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

15 pages, 3331 KiB

Open AccessArticle

Phylogenetic Relationships and Evolution of the Genus Eganvirus (186-Type) Yersinia pestis Bacteriophages

by Jin Guo, Youhong Zhong, Yiting Wang, Pan Liu, Haixiao Jin, Yumeng Wang, Liyuan Shi, Peng Wang and Wei Li

Viruses 2024, 16(5), 748; https://doi.org/10.3390/v16050748 - 8 May 2024

Viewed by 1454

Abstract

Plague is an endemic infectious disease caused by Yersinia pestis. In this study, we isolated fourteen phages with similar sequence arrangements to phage 186; these phages exhibited different lytic abilities in Enterobacteriaceae strains. To illustrate the phylogenetic relationships and evolutionary relationships between previously designated 186-type phages, we analysed the complete sequences and important genes of the phages, including whole-genome average nucleotide identity (ANI) and collinearity comparison, evolutionary analysis of four conserved structural genes (V, T, R, and Q genes), and analysis of the regulatory genes (cI, apl, and cII) and integrase gene (int). Phylogenetic analysis revealed that thirteen of the newly isolated phages belong to the genus Eganvirus and one belongs to the genus Felsduovirus in the family Peduoviridae, and these Eganvirus phages can be roughly clustered into three subgroups. The topological relationships exhibited by the whole-genome and structural genes seemed similar and stable, while the regulatory genes presented different topological relationships with the structural genes, and these results indicated that there was some homologous recombination in the regulatory genes. These newly isolated 186-type phages were mostly isolated from dogs, suggesting that the resistance of Canidae to Y. pestis infection may be related to the wide distribution of phages with lytic capability. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

13 pages, 3752 KiB

Open AccessArticle

New Genera and Species of Caulobacter and Brevundimonas Bacteriophages Provide Insights into Phage Genome Evolution

by Bert Ely, Michael Hils, Aaron Clarke, Maegan Albert, Nadia Holness, Jacob Lenski and Tannaz Mohammadi

Viruses 2024, 16(4), 641; https://doi.org/10.3390/v16040641 - 20 Apr 2024

Cited by 2 | Viewed by 1679

Abstract

Previous studies have identified diverse bacteriophages that infect Caulobacter vibrioides strain CB15 ranging from small RNA phages to four genera of jumbo phages. In this study, we focus on 20 bacteriophages whose genomes range from 40 to 60 kb in length. Genome comparisons indicated that these diverse phages represent six Caulobacter phage genera and one additional genus that includes both Caulobacter and Brevundimonas phages. Within species, comparisons revealed that both single base changes and inserted or deleted genetic material cause the genomes of closely related phages to diverge. Among genera, the basic gene order and the orientation of key genes were retained with most of the observed variation occurring at ends of the genomes. We hypothesize that the nucleotide sequences of the ends of these phage genomes are less important than the need to maintain the size of the genome and the stability of the corresponding mRNAs. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

19 pages, 23754 KiB

Open AccessArticle

Genome Analysis of Epsilon CrAss-like Phages

by Igor V. Babkin, Artem Y. Tikunov, Ivan K. Baykov, Vera V. Morozova and Nina V. Tikunova

Viruses 2024, 16(4), 513; https://doi.org/10.3390/v16040513 - 27 Mar 2024

Cited by 1 | Viewed by 1899

Abstract

CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Figure 1

Review

Jump to: Research

15 pages, 577 KiB

Open AccessReview

Are You My Host? An Overview of Methods Used to Link Bacteriophages with Hosts

by Paul Hyman

Viruses 2025, 17(1), 65; https://doi.org/10.3390/v17010065 - 5 Jan 2025

Cited by 1 | Viewed by 1475

Abstract

Until recently, the only methods for finding out if a particular strain or species of bacteria could be a host for a particular bacteriophage was to see if the bacteriophage could infect that bacterium and kill it, releasing progeny phages. Establishing the host range of a bacteriophage thus meant infecting many different bacteria and seeing if the phage could kill each one. Detection of bacterial killing can be achieved on solid media (plaques, spots) or broth (culture clearing). More recently, additional methods to link phages and hosts have been developed. These include methods to show phage genome entry into host cells (e.g., PhageFISH); proximity of phage and host genomes (e.g., proximity ligation, polonies, viral tagging); and analysis of genomes and metagenomes (e.g., CRISPR spacer analysis, metagenomic co-occurrence). These methods have advantages and disadvantages. They also are not measuring the same interactions. Host range can be divided into multiple host ranges, each defined by how far the phage can progress in the infection cycle. For example, the ability to effect genome entry (penetrative host range) is different than the ability to produce progeny (productive host range). These different host ranges reflect bacterial defense mechanisms that block phage growth and development at various stages in the infection cycle. Here, I present a comparison of the various methods used to identify bacteriophage-host relationships with a focus on what type of host range is being measured or predicted. Full article

(This article belongs to the Special Issue Bacteriophage Diversity)

► Show Figures

Journal Menu

Journal Browser

Bacteriophage Diversity

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Related Special Issue

Published Papers (10 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI