Phage–Host Interactions: From Communities to Single Particles

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 20509

Special Issue Editors


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Guest Editor
Helmholtz Centre Munich, Technical University of Munich, 80333 München, Germany
Interests: phageome; virome; phage-host interactions; phage therapy

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Co-Guest Editor
Helmholtz Centre Munich, Technical University of Munich, 80333 München, Germany
Interests: phageome; virome; phage-host interactions; phage therapy

E-Mail Website
Co-Guest Editor
Helmholtz Centre Munich, Technical University of Munich, 80333 München, Germany
Interests: phageome; virome; phage-host interactions; phage therapy

Special Issue Information

Dear Colleagues,

I am delighted to launch a Special Issue entitled Phage–Host Interactions: From Communities to Single Particles together with an expert editorial team.

This Special Issue acts as a platform for publishing original research and reviews exploring the interactions between phages and their bacterial hosts on multiple levels—from communities to single cells or single-phage-single-host—using model systems. We also welcome studies that investigate the role of phages in shaping bacterial diversity and physiology and shed some light on the underlying mechanisms behind phage-mediated changes in bacteria. We are particularly interested in attracting studies that use cutting-edge technologies in molecular biology, system biology, biochemistry, ecology, and computer science to explore interactions between phages and bacteria in different ecosystems.

We aim to recruit top phage researchers to contribute to this Special Issue of viruses and sincerely hope that the provided information will attract your interest and encourage you to provide your contribution(s) to this call.

Prof. Dr. Li Deng
Dr. Mohammadali Khan Mirzaei
Dr. Jinling Xue
Guest Editors

Manuscript Submission Information

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Keywords

  • phageome
  • virome
  • phage-host interactions
  • phage therapy

Published Papers (6 papers)

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Research

Jump to: Review

16 pages, 3302 KiB  
Article
Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts
by Vicente Arnau, Wladimiro Díaz-Villanueva, Jorge Mifsut Benet, Paula Villasante, Beatriz Beamud, Paula Mompó, Rafael Sanjuan, Fernando González-Candelas, Pilar Domingo-Calap and Mária Džunková
Viruses 2023, 15(5), 1196; https://doi.org/10.3390/v15051196 - 19 May 2023
Cited by 2 | Viewed by 2255
Abstract
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to [...] Read more.
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage–host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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18 pages, 4422 KiB  
Article
Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation
by Johan S. Sáenz, Bibiana Rios-Galicia, Bianca Rehkugler and Jana Seifert
Viruses 2023, 15(4), 951; https://doi.org/10.3390/v15040951 - 12 Apr 2023
Cited by 2 | Viewed by 1773
Abstract
Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. [...] Read more.
Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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20 pages, 6896 KiB  
Article
Phage K gp102 Drives Temperature-Sensitive Antibacterial Activity on USA300 MRSA
by Susan M. Lehman, Rohit Kongari, Adam M. Glass, Matthew Koert, Melissa D. Ray, Roger D. Plaut and Scott Stibitz
Viruses 2023, 15(1), 17; https://doi.org/10.3390/v15010017 - 21 Dec 2022
Cited by 2 | Viewed by 1851
Abstract
There is widespread interest in using obligately lytic bacteriophages (“phages”) to treat human bacterial infections. Among Staphylococcus aureus infections, the USA300 lineage is a frequent cause of invasive disease. We observed that phage K, a model S. aureus myophage, exhibits temperature-sensitive growth on [...] Read more.
There is widespread interest in using obligately lytic bacteriophages (“phages”) to treat human bacterial infections. Among Staphylococcus aureus infections, the USA300 lineage is a frequent cause of invasive disease. We observed that phage K, a model S. aureus myophage, exhibits temperature-sensitive growth on USA300 strains, with the wild-type phage providing poorer growth suppression in broth and forming smaller and fainter plaques at 37 °C vs. 30 °C. We isolated 65 mutants of phage K that had improved plaquing characteristics at 37 °C when compared to the parental phage. In all 65 mutants, this phenotype was attributable to loss-of-function (LoF) mutations in gp102, which encodes a protein of unknown function that has homologs only among the Herelleviridae (SPO1-like myophages infecting gram-positive bacteria). Additional experiments with representative mutants consistently showed that the temperature-sensitive plaque phenotype was specific to USA300 MRSA strains and that Gp102 disruption was correlated with improved suppression of bacterial growth in broth and improved antibacterial activity in a mouse model of upper respiratory tract infection. The same genotype and in vitro phenotypes could be replicated in close relatives of phage K. Gp102 disruption did not have a detectable effect on adsorption but did delay cell culture lysis relative to wild-type under permissive infection conditions, suggesting that gp102 conservation might be maintained by selective pressure for more rapid replication. Expression of gp102 on a plasmid was toxic to both an MSSA and a USA300 MRSA strain. Molecular modeling predicts a protein with two helix-turn-helix domains that displays some similarity to DNA-binding proteins such as transcription factors. While its function remains unclear, gp102 is a conserved gene that is important to the infection process of Kayvirus phages, and it appears that the manner in which USA300 strains defend against them at 37 °C can be overcome by gp102 LoF mutations. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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20 pages, 5596 KiB  
Article
Dual-RNAseq Analysis Unravels Virus-Host Interactions of MetSV and Methanosarcina mazei
by Finn O. Gehlert, Till Sauerwein, Katrin Weidenbach, Urska Repnik, Daniela Hallack, Konrad U. Förstner and Ruth A. Schmitz
Viruses 2022, 14(11), 2585; https://doi.org/10.3390/v14112585 - 21 Nov 2022
Cited by 4 | Viewed by 1861
Abstract
Methanosarcina spherical virus (MetSV), infecting Methanosarcina species, encodes 22 genes, but their role in the infection process in combination with host genes has remained unknown. To study the infection process in detail, infected and uninfected M. mazei cultures were compared using dual-RNAseq, qRT-PCRs, [...] Read more.
Methanosarcina spherical virus (MetSV), infecting Methanosarcina species, encodes 22 genes, but their role in the infection process in combination with host genes has remained unknown. To study the infection process in detail, infected and uninfected M. mazei cultures were compared using dual-RNAseq, qRT-PCRs, and transmission electron microscopy (TEM). The transcriptome analysis strongly indicates a combined role of virus and host genes in replication, virus assembly, and lysis. Thereby, 285 host and virus genes were significantly regulated. Within these 285 regulated genes, a network of the viral polymerase, MetSVORF6, MetSVORF5, MetSVORF2, and the host genes encoding NrdD, NrdG, a CDC48 family protein, and a SSB protein with a role in viral replication was postulated. Ultrastructural analysis at 180 min p.i. revealed many infected cells with virus particles randomly scattered throughout the cytoplasm or attached at the cell surface, and membrane fragments indicating cell lysis. Dual-RNAseq and qRT-PCR analyses suggested a multifactorial lysis reaction in potential connection to the regulation of a cysteine proteinase, a pirin-like protein and a HicB-solo protein. Our study’s results led to the first preliminary infection model of MetSV infecting M. mazei, summarizing the key infection steps as follows: replication, assembly, and host cell lysis. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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17 pages, 2781 KiB  
Article
Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches
by Carina Rohmer, Ronja Dobritz, Dilek Tuncbilek-Dere, Esther Lehmann, David Gerlach, Shilpa Elizabeth George, Taeok Bae, Kay Nieselt and Christiane Wolz
Viruses 2022, 14(11), 2471; https://doi.org/10.3390/v14112471 - 8 Nov 2022
Cited by 4 | Viewed by 3813
Abstract
Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the [...] Read more.
Staphylococcus aureus asymptomatically colonizes the nasal cavity of mammals, but it is also a leading cause of life-threatening infections. Most human nasal isolates carry Sa3 phages, which integrate into the bacterial hlb gene encoding a sphingomyelinase. The virulence factor-encoding genes carried by the Sa3-phages are highly human-specific, and most animal strains are Sa3 negative. Thus, both insertion and excision of the prophage could potentially confer a fitness advantage to S. aureus. Here, we analyzed the phage life cycle of two Sa3 phages, Φ13 and ΦN315, in different phage-cured S. aureus strains. Based on phage transfer experiments, strains could be classified into low (8325-4, SH1000, and USA300c) and high (MW2c and Newman-c) transfer strains. High-transfer strains promoted the replication of phages, whereas phage adsorption, integration, excision, or recA transcription was not significantly different between strains. RNASeq analyses of replication-deficient lysogens revealed no strain-specific differences in the CI/Mor regulatory switch. However, lytic genes were significantly upregulated in the high transfer strain MW2c Φ13 compared to strain 8325-4 Φ13. By transcriptional start site prediction, new promoter regions within the lytic modules were identified, which are likely targeted by specific host factors. Such host-phage interaction probably accounts for the strain-specific differences in phage replication and transfer frequency. Thus, the genetic makeup of the host strains may determine the rate of phage mobilization, a feature that might impact the speed at which certain strains can achieve host adaptation. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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Review

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20 pages, 1080 KiB  
Review
The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications
by Menghui Zhang, Tianyou Zhang, Meishun Yu, Yu-Lei Chen and Min Jin
Viruses 2022, 14(9), 1904; https://doi.org/10.3390/v14091904 - 28 Aug 2022
Cited by 22 | Viewed by 7350
Abstract
Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently [...] Read more.
Phages are viruses that infect bacteria. They affect various microbe-mediated processes that drive biogeochemical cycling on a global scale. Their influence depends on whether the infection is lysogenic or lytic. Temperate phages have the potential to execute both infection types and thus frequently switch their infection modes in nature, potentially causing substantial impacts on the host-phage community and relevant biogeochemical cycling. Understanding the regulating factors and outcomes of temperate phage life cycle transition is thus fundamental for evaluating their ecological impacts. This review thus systematically summarizes the effects of various factors affecting temperate phage life cycle decisions in both culturable phage-host systems and natural environments. The review further elucidates the ecological implications of the life cycle transition of temperate phages with an emphasis on phage/host fitness, host-phage dynamics, microbe diversity and evolution, and biogeochemical cycles. Full article
(This article belongs to the Special Issue Phage–Host Interactions: From Communities to Single Particles)
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