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Advances in the Study of Phage–Host Interactions
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Advances in the Study of Phage–Host Interactions

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (15 August 2023) | Viewed by 17076

Special Issue Editor

Dr. Luís Melo

E-Mail Website
Guest Editor
1. CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
2. LABBELS–Associate Laboratory, 4710-057 Braga, Portugal
Interests: bacteriophages biofilms; prophagesstap hylococci; Helicobacter pylori
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am pleased to launch a Special Issue entitled Advances in the Study of Phage–host Interactions.

This Special Issue works as a platform for publishing original research and reviews exploring the interactions between phages and their bacterial hosts on multiple levels.

We are predominantly interested in attracting studies that use different omics approaches to study  phage–host interactions from the single-cell level up to ecological communities. New approaches for studying interactions at the physical and molecular levels using cutting-edge technologies are also welcome.

We aim to recruit top phage researchers to contribute to this Special Issue and sincerely hope that the provided information will attract your interest and encourage you to provide your contributions to this call.

Dr. Luís Melo
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 therapy
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • single-cell
  • biofilms
  • communities

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Published Papers (4 papers)

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Research

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17 pages, 2548 KiB  
Article
Genetic and Phenotypic Analysis of Phage-Resistant Mutant Fitness Triggered by Phage–Host Interactions
by Yanze Mi, Yile He, Jinhui Mi, Yunfei Huang, Huahao Fan, Lihua Song, Xiaoping An, Shan Xu, Mengzhe Li and Yigang Tong
Int. J. Mol. Sci. 2023, 24(21), 15594; https://doi.org/10.3390/ijms242115594 - 26 Oct 2023
Cited by 3 | Viewed by 1998
Abstract
The emergence of phage-resistant bacterial strains is one of the biggest challenges for phage therapy. However, the emerging phage-resistant bacteria are often accompanied by adaptive trade-offs, which supports a therapeutic strategy called “phage steering”. The key to phage steering is to guide the [...] Read more.
The emergence of phage-resistant bacterial strains is one of the biggest challenges for phage therapy. However, the emerging phage-resistant bacteria are often accompanied by adaptive trade-offs, which supports a therapeutic strategy called “phage steering”. The key to phage steering is to guide the bacterial population toward an evolutionary direction that is favorable for treatment. Thus, it is important to systematically investigate the impacts of phages targeting different bacterial receptors on the fitness of the bacterial population. Herein, we employed 20 different phages to impose strong evolutionary pressure on the host Pseudomonas aeruginosa PAO1 and examined the genetic and phenotypic responses of their phage-resistant mutants. Among these strains with impaired adsorptions, four types of mutations associated with bacterial receptors were identified, namely, lipopolysaccharides (LPSs), type IV pili (T4Ps), outer membrane proteins (OMPs), and exopolysaccharides (EPSs). PAO1, responding to LPS- and EPS-dependent phage infections, mostly showed significant growth impairment and virulence attenuation. Most mutants with T4P-related mutations exhibited a significant decrease in motility and biofilm formation ability, while the mutants with OMP-related mutations required the lowest fitness cost out of the bacterial populations. Apart from fitness costs, PAO1 strains might lose their resistance to antibiotics when counteracting with phages, such as the presence of large-fragment mutants in this study, which may inspire the usage of phage–antibiotic combination strategies. This work provides methods that leverage the merits of phage resistance relative to obtaining therapeutically beneficial outcomes with respect to phage-steering strategies. Full article
(This article belongs to the Special Issue Advances in the Study of Phage–Host Interactions)
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14 pages, 2131 KiB  
Article
Isolation and Characterization of the First Zobellviridae Family Bacteriophage Infecting Klebsiella pneumoniae
by Roman B. Gorodnichev, Maria A. Kornienko, Maja V. Malakhova, Dmitry A. Bespiatykh, Valentin A. Manuvera, Oksana V. Selezneva, Vladimir A. Veselovsky, Dmitry V. Bagrov, Marina V. Zaychikova, Veronika A. Osnach, Anna V. Shabalina, Oleg V. Goloshchapov, Julia A. Bespyatykh, Anna S. Dolgova and Egor A. Shitikov
Int. J. Mol. Sci. 2023, 24(4), 4038; https://doi.org/10.3390/ijms24044038 - 17 Feb 2023
Cited by 2 | Viewed by 3412
Abstract
In order to address the upcoming crisis in the treatment of Klebsiella pneumoniae infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be developed. One approach would be to use (bacterio)phages and/or phage derivatives for therapy. In [...] Read more.
In order to address the upcoming crisis in the treatment of Klebsiella pneumoniae infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be developed. One approach would be to use (bacterio)phages and/or phage derivatives for therapy. In this study, we present a description of the first K. pneumoniae phage from the Zobellviridae family. The vB_KpnP_Klyazma podovirus, which forms translucent halos around the plaques, was isolated from river water. The phage genome is composed of 82 open reading frames, which are divided into two clusters located on opposite strands. Phylogenetic analysis revealed that the phage belongs to the Zobellviridae family, although its identity with the closest member of this family was not higher than 5%. The bacteriophage demonstrated lytic activity against all (n = 11) K. pneumoniae strains with the KL20 capsule type, but only the host strain was lysed effectively. The receptor-binding protein of the phage was identified as a polysaccharide depolymerase with a pectate lyase domain. The recombinant depolymerase protein showed concentration-dependent activity against all strains with the KL20 capsule type. The ability of a recombinant depolymerase to cleave bacterial capsular polysaccharides regardless of a phage’s ability to successfully infect a particular strain holds promise for the possibility of using depolymerases in antimicrobial therapy, even though they only make bacteria sensitive to environmental factors, rather than killing them directly. Full article
(This article belongs to the Special Issue Advances in the Study of Phage–Host Interactions)
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16 pages, 2225 KiB  
Article
Biological Features and In Planta Transcriptomic Analyses of a Microviridae Phage (CLasMV1) in “Candidatus Liberibacter asiaticus”
by Cheng Wang, Fang Fang, Yun Li, Ling Zhang, Jinghua Wu, Tao Li, Yongqin Zheng, Qian Xu, Shuting Fan, Jianchi Chen, Xiaoling Deng and Zheng Zheng
Int. J. Mol. Sci. 2022, 23(17), 10024; https://doi.org/10.3390/ijms231710024 - 2 Sep 2022
Cited by 2 | Viewed by 1766
Abstract
“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy [...] Read more.
“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy for CLas/HLB control. However, little is known about the CLasMV1 biology. In this study, we analyzed the population dynamics of CLasMV1 between the insect vector of CLas, the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) and the holoparasitic dodder plant (Cuscuta campestris Yunck.); both acquired CLasMV1-infected CLas from an HLB citrus. All CLas-positive dodder samples were CLasMV1-positive, whereas only 32% of CLas-positive ACP samples were identified as CLasMV1-positive. Quantitative analyses showed a similar distribution pattern of CLasMV1 phage and CLas among eight citrus cultivars by presenting at highest abundance in the fruit pith and/or the center axis of the fruit. Transcriptome analyses revealed the possible lytic activity of CLasMV1 on CLas in fruit pith as evidenced by high-level expressions of CLasMV1 genes, and CLas genes related to cell wall biogenesis and remodeling to maintain the CLas cell envelope integrity. The up-regulation of CLas genes were involved in restriction–modification system that could involve possible phage resistance for CLas during CLasMV1 infection. In addition, the regulation of CLas genes involved in cell surface components and Sec pathway by CLasMV1 phage could be beneficial for phage infection. This study expanded our knowledge of CLasMV1 phage that will benefit further CLas phage research and HLB control. Full article
(This article belongs to the Special Issue Advances in the Study of Phage–Host Interactions)
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Review

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18 pages, 1144 KiB  
Review
Bacteriophage-Mediated Cancer Gene Therapy
by Gleb Petrov, Maya Dymova and Vladimir Richter
Int. J. Mol. Sci. 2022, 23(22), 14245; https://doi.org/10.3390/ijms232214245 - 17 Nov 2022
Cited by 16 | Viewed by 9167
Abstract
Bacteriophages have long been considered only as infectious agents that affect bacterial hosts. However, recent studies provide compelling evidence that these viruses are able to successfully interact with eukaryotic cells at the levels of the binding, entry and expression of their own genes. [...] Read more.
Bacteriophages have long been considered only as infectious agents that affect bacterial hosts. However, recent studies provide compelling evidence that these viruses are able to successfully interact with eukaryotic cells at the levels of the binding, entry and expression of their own genes. Currently, bacteriophages are widely used in various areas of biotechnology and medicine, but the most intriguing of them is cancer therapy. There are increasing studies confirming the efficacy and safety of using phage-based vectors as a systemic delivery vehicle of therapeutic genes and drugs in cancer therapy. Engineered bacteriophages, as well as eukaryotic viruses, demonstrate a much greater efficiency of transgene delivery and expression in cancer cells compared to non-viral gene transfer methods. At the same time, phage-based vectors, in contrast to eukaryotic viruses-based vectors, have no natural tropism to mammalian cells and, as a result, provide more selective delivery of therapeutic cargos to target cells. Moreover, numerous data indicate the presence of more complex molecular mechanisms of interaction between bacteriophages and eukaryotic cells, the further study of which is necessary both for the development of gene therapy methods and for understanding the cancer nature. In this review, we summarize the key results of research into aspects of phage–eukaryotic cell interaction and, in particular, the use of phage-based vectors for highly selective and effective systemic cancer gene therapy. Full article
(This article belongs to the Special Issue Advances in the Study of Phage–Host Interactions)
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