State-of-the-Art Bacteriophage Research in the Nordic Countries

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

Deadline for manuscript submissions: closed (30 December 2022) | Viewed by 8266

Special Issue Editor

Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014 Helsinki, Finland
Interests: bacteriophage; phage therapy; phage genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacteriophage research began more than a century ago and has contributed to our understanding of several aspects of biology. In the Nordic countries, phage research has a strong position, with the research topics varying from basic research such as phage genomics and structure analysis to applications such as phage display and phage therapy. This Special Issue will focus on different aspects of phage research carried out in the Nordic countries. We wish to present the Nordic phage research in its full scope, and welcome submissions from researchers working in the Nordic countries focusing on, but not limited to, phage genetics and evolution, phage structures, phage–host interactions, phage ecology, phage therapy and biocontrol, and phage display.

Dr. Saija Johanna Kiljunen
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

  • phage
  • bacteriophage
  • phage–host interactions
  • phage structure
  • phage genomics and evolution
  • phage therapy
  • phage display

Published Papers (5 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

12 pages, 2626 KiB  
Article
A Novel Prophage-like Insertion Element within yabG Triggers Early Entry into Sporulation in Clostridium botulinum
by François P. Douillard, Inês Martins Portinha, Yağmur Derman, Cédric Woudstra, Tommi Mäklin, Martin B. Dorner, Hannu Korkeala, Adriano O. Henriques and Miia Lindström
Viruses 2023, 15(12), 2431; https://0-doi-org.brum.beds.ac.uk/10.3390/v15122431 - 14 Dec 2023
Viewed by 769
Abstract
Sporulation is a finely regulated morphogenetic program important in the ecology and epidemiology of Clostridium botulinum. Exogenous elements disrupting sporulation-associated genes contribute to sporulation regulation and introduce diversity in the generally conserved sporulation programs of endospore formers. We identified a novel prophage-like [...] Read more.
Sporulation is a finely regulated morphogenetic program important in the ecology and epidemiology of Clostridium botulinum. Exogenous elements disrupting sporulation-associated genes contribute to sporulation regulation and introduce diversity in the generally conserved sporulation programs of endospore formers. We identified a novel prophage-like DNA segment, termed the yin element, inserted within yabG, encoding a sporulation-specific cysteine protease, in an environmental isolate of C. botulinum. Bioinformatic analysis revealed that the genetic structure of the yin element resembles previously reported mobile intervening elements associated with sporulation genes. Within a pure C. botulinum culture, we observed two subpopulations of cells with the yin element either integrated into the yabG locus or excised as a circular DNA molecule. The dynamics between the two observed conformations of the yin element was growth-phase dependent and likely mediated by recombination events. The yin element was not required for sporulation by C. botulinum but triggered an earlier entry into sporulation than in a related isolate lacking this element. So far, the yin element has not been found in any other C. botulinum strains or other endospore-forming species. It remains to be demonstrated what kind of competitive edge it provides for C. botulinum survival and persistence. Full article
(This article belongs to the Special Issue State-of-the-Art Bacteriophage Research in the Nordic Countries)
Show Figures

Figure 1

11 pages, 3963 KiB  
Article
Three Phages from a Boreal Lake during Ice Cover Infecting Xylophilus, Caulobacter, and Polaromonas Species
by Elina Laanto and Hanna M. Oksanen
Viruses 2023, 15(2), 307; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020307 - 22 Jan 2023
Cited by 1 | Viewed by 1462
Abstract
Although the important role of microbes in freshwater is well understood, studies on phage–host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. [...] Read more.
Although the important role of microbes in freshwater is well understood, studies on phage–host systems in such environments during ice cover are completely lacking. Here, we describe the isolation and characterization of three new bacteriophages infecting Xylophilus sp., Caudobacter sp., and Polaromonas sp. from freshwater samples taken under the ice cover of Lake Konnevesi, Finland. Lumi, Kuura, and Tiera bacteriophages have tailed icosahedral virions and double-stranded DNA. Lumi is a siphophage with a genome of 80,496 bp, and Kuura and Tiera are podophages, and their genomes are 43,205 and 45,327 bp in length, resembling viruses in the class Caudoviricetes. Their host ranges were very limited among the winter-isolated bacterial strains from Konnevesi, each infecting only their own hosts. They can infect efficiently at 4 °C, showing that they are adapted to living in lake water under ice cover. Analysis of the viral genome sequences showed that a significant number of the gene products of each virus are unique, indicating that there is unexplored viral diversity in freshwaters. To our knowledge, Lumi and Tiera are the first phages isolated on the Xylophilus sp. and Polaromonas sp. strains, allowing their exploitation in further studies of freshwater bacterial–phage interactions. Full article
(This article belongs to the Special Issue State-of-the-Art Bacteriophage Research in the Nordic Countries)
Show Figures

Figure 1

10 pages, 18450 KiB  
Communication
Biophysical Properties of Bifunctional Phage-Biosensor
by Vilhelmiina Juusti, Janne Kulpakko, Elizabeth Cudjoe, Ville N. Pimenoff and Pekka Hänninen
Viruses 2023, 15(2), 299; https://0-doi-org.brum.beds.ac.uk/10.3390/v15020299 - 20 Jan 2023
Viewed by 1669
Abstract
Biosensor research is a swiftly growing field for developing rapid and precise analytical devices for biomedical, pharmaceutical, and industrial use and beyond. Herein, we propose a phage-based biosensor method to develop a sensitive and specific system for biomedical detection. Our method is based [...] Read more.
Biosensor research is a swiftly growing field for developing rapid and precise analytical devices for biomedical, pharmaceutical, and industrial use and beyond. Herein, we propose a phage-based biosensor method to develop a sensitive and specific system for biomedical detection. Our method is based on in vitro selected phages and their interaction with the targeted analytes as well as on optical properties that change according to the concentration of the model analyte. The green fluorescent protein (GFP) was chosen as our model analyte as it has its own well-known optical properties. Brilliant green was used as a reporter component for the sensor. Its presence enables a color intensity (absorbance) change when the analyte is present in the solution. Furthermore, the reporter dye functioned as a quencher for an additional lanthanide label in our assay. It mediated the specific phage-derived interference in the signal measured with the time-resolved luminescence. Most importantly, our results confirmed that the presented bifunctional phage with its liquid crystal properties enabled the measurement of GFP in a concentration-dependent, quantitative manner with a limit of detection of 0.24 µg/mL. In the future, our novel method to develop phage-based biosensors may provide highly sensitive and specific biosensors for biomedical or otherwise-relevant targets. Full article
(This article belongs to the Special Issue State-of-the-Art Bacteriophage Research in the Nordic Countries)
Show Figures

Figure 1

14 pages, 2960 KiB  
Article
Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics
by Anders S. Nilsson
Viruses 2022, 14(11), 2483; https://0-doi-org.brum.beds.ac.uk/10.3390/v14112483 - 09 Nov 2022
Cited by 3 | Viewed by 1390
Abstract
Cocktail is an easy-to-use computer program for mathematical modelling of bacteriophage (phage) infection kinetics in a chemostat. The infection of bacteria by phages results in complicated dynamic processes as both have the ability to multiply and change during the course of an infection. [...] Read more.
Cocktail is an easy-to-use computer program for mathematical modelling of bacteriophage (phage) infection kinetics in a chemostat. The infection of bacteria by phages results in complicated dynamic processes as both have the ability to multiply and change during the course of an infection. There is a need for a simple way to visualise these processes, not least due to the increased interest in phage therapy. Cocktail is completely self-contained and runs on a Windows 64-bit operating system. By changing the publicly available source code, the program can be developed in the directions that users see fit. Cocktail’s models consist of coupled differential equations that describe the infection of a bacterium in a vessel by one or two (interfering) phages. In the models, the bacterial population can be controlled by sixteen parameters, for example, through different growth rates, phage resistance, metabolically inactive cells or biofilm formation. The phages can be controlled by eight parameters each, such as different adsorption rates or latency periods. As the models in Cocktail describe the infection kinetics of phages in vitro, the program is primarily intended to generate hypotheses, but the results can however be indicative in the application of phage therapy. Full article
(This article belongs to the Special Issue State-of-the-Art Bacteriophage Research in the Nordic Countries)
Show Figures

Figure 1

16 pages, 2156 KiB  
Article
Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing
by Ane Beth Sloth, Babak Bakhshinejad, Malte Jensen, Camilla Stavnsbjerg, Mikkel Baldtzer Liisberg, Maria Rossing and Andreas Kjaer
Viruses 2022, 14(11), 2402; https://0-doi-org.brum.beds.ac.uk/10.3390/v14112402 - 29 Oct 2022
Cited by 3 | Viewed by 2339
Abstract
The principal presumption of phage display biopanning is that the naïve library contains an unbiased repertoire of peptides, and thus, the enriched variants derive from the affinity selection of an entirely random peptide pool. In the current study, we utilized deep sequencing to [...] Read more.
The principal presumption of phage display biopanning is that the naïve library contains an unbiased repertoire of peptides, and thus, the enriched variants derive from the affinity selection of an entirely random peptide pool. In the current study, we utilized deep sequencing to characterize the widely used Ph.DTM-12 phage display peptide library (New England Biolabs). The next-generation sequencing (NGS) data indicated the presence of stop codons and a high abundance of wild-type clones in the naïve library, which collectively result in a reduced effective size of the library. The analysis of the DNA sequence logo and global and position-specific frequency of amino acids demonstrated significant bias in the nucleotide and amino acid composition of the library inserts. Principal component analysis (PCA) uncovered the existence of four distinct clusters in the naïve library and the investigation of peptide frequency distribution revealed a broad range of unequal abundances for peptides. Taken together, our data provide strong evidence for the notion that the naïve library represents substantial departures from randomness at the nucleotide, amino acid, and peptide levels, though not undergoing any selective pressure for target binding. This non-uniform sequence representation arises from both the M13 phage biology and technical errors of the library construction. Our findings highlight the paramount importance of the qualitative assessment of the naïve phage display libraries prior to biopanning. Full article
(This article belongs to the Special Issue State-of-the-Art Bacteriophage Research in the Nordic Countries)
Show Figures

Figure 1

Back to TopTop