Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
9.0
4.9
Journals
IJMS
Special Issues
Bacteriophages as Tools in Applied Sciences
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Bacteriophages as Tools in Applied Sciences

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 (30 January 2023) | Viewed by 20235

Special Issue Editors

Dr. Aleš Podgornik

E-Mail Website
Guest Editor
Faculty for Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
Interests: bacteria–phage interaction analysis; continuous phage cultivation; phage purification
Dr. Piotr Golec

E-Mail Website
Guest Editor
Department of Molecular Virology, University of Warsaw, Warsaw, Poland
Interests: phage molecular biology; phage display; phage therapy; bacteria–phage interaction analysis; new strategies in the treatment of MDR bacteria; phage-based nanoparticle synthesis

Special Issue Information

Dear Colleagues,

Bacteriophages, in short phages, are viruses that infect bacteria. Though they are relatively simple, composed of genetic material surrounded by a protective protein capsid, they are the most abundant biological entities in the biosphere, with the highest numbers observed in seawater and marine sediments. In addition to their profound impact on the Earth microbiome, phages have been employed in a number of areas of human life and in diverse industries. They have been used in phage therapy since their initial discovery, and as natural enemies of bacteria, phages are an effective alternative to antibiotic-based treatments of bacterial infections (particularly the drug-resistant ones). Historically, bacteriophages played a pivotal role in the development of many fundamental biological concepts, such as identification of nucleic acids as genetic material, definition of a gene, establishment of the triplet nature of the genetic code as well as discovery of messenger RNA, light-dependent and light-independent DNA repair mechanisms and the restriction–modification phenomenon. Nowadays, phages are used in food preservation and in decontamination processes. They also serve as gene carriers in transduction and as biological systems for the identification and surface presentation of peptides displaying desired properties such as those that bind or synthesize nanoparticles.

For this Special Issue “Bacteriophages as Tools in Applied Sciences”, we warmly invite you to submit an original work or a review in translational phage research.

Dr. Aleš Podgornik
Dr. Piotr Golec
Guest Editors

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
  • phage display
  • phage molecular biology
  • phage proteomics
  • phage transcriptomics
  • phage recombination
  • phage structure analysis
  • phage-based nanoparticle synthesis

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.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

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

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

21 pages, 3944 KiB  
Article
Isolation, Characterization, and Comparative Genomic Analysis of Bacteriophage Ec_MI-02 from Pigeon Feces Infecting Escherichia coli O157:H7
by Mohamad Ismail Sultan-Alolama, Amr Amin, Ranjit Vijayan and Khaled A. El-Tarabily
Int. J. Mol. Sci. 2023, 24(11), 9506; https://doi.org/10.3390/ijms24119506 - 30 May 2023
Cited by 3 | Viewed by 3134
Abstract
The most significant serotype of Shiga-toxigenic Escherichia coli that causes foodborne illnesses is Escherichia coli O157:H7. Elimination of E. coli O157:H7 during food processing and storage is a possible solution. Bacteriophages have a significant impact on bacterial populations in nature due to their [...] Read more.
The most significant serotype of Shiga-toxigenic Escherichia coli that causes foodborne illnesses is Escherichia coli O157:H7. Elimination of E. coli O157:H7 during food processing and storage is a possible solution. Bacteriophages have a significant impact on bacterial populations in nature due to their ability to lyse their bacterial host. In the current study, a virulent bacteriophage, Ec_MI-02, was isolated from the feces of a wild pigeon in the United Arab Emirates (UAE) for potential future use as a bio-preservative or in phage therapy. Using a spot test and an efficiency of plating analysis, Ec_MI-02 was found to infect in addition to the propagation host, E. coli O157:H7 NCTC 12900, five different serotypes of E. coli O157:H7 (three clinical samples from infected patients, one from contaminated green salad, and one from contaminated ground beef). Based on morphology and genome analysis, Ec_MI-02 belongs to the genus Tequatrovirus under the order Caudovirales. The adsorption rate constant (K) of Ec_MI-02 was found to be 1.55 × 10−8 mL/min. The latent period was 50 min with a burst size of almost 10 plaque forming units (pfu)/host cell in the one-step growth curve when the phage Ec_MI-02 was cultivated using the propagation host E. coli O157:H7 NCTC 12900. Ec_MI-02 was found to be stable at a wide range of pH, temperature, and commonly used laboratory disinfectants. Its genome is 165,454 bp long with a GC content of 35.5% and encodes 266 protein coding genes. Ec_MI-02 has genes encoding for rI, rII, and rIII lysis inhibition proteins, which supports the observation of delayed lysis in the one-step growth curve. The current study provides additional evidence that wild birds could also be a good natural reservoir for bacteriophages that do not carry antibiotic resistance genes and could be good candidates for phage therapy. In addition, studying the genetic makeup of bacteriophages that infect human pathogens is crucial for ensuring their safe usage in the food industry. Full article
(This article belongs to the Special Issue Bacteriophages as Tools in Applied Sciences)
►▼ Show Figures

Figure 1

13 pages, 1964 KiB  
Article
Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS
by Ane Beth Sloth, Babak Bakhshinejad, Camilla Stavnsbjerg, Maria Rossing and Andreas Kjaer
Int. J. Mol. Sci. 2023, 24(6), 5396; https://doi.org/10.3390/ijms24065396 - 11 Mar 2023
Cited by 4 | Viewed by 3399
Abstract
Next-generation sequencing (NGS) has raised a growing interest in phage display research. Sequencing depth is a pivotal parameter for using NGS. In the current study, we made a side-by-side comparison of two NGS platforms with different sequencing depths, denoted as lower-throughput (LTP) and [...] Read more.
Next-generation sequencing (NGS) has raised a growing interest in phage display research. Sequencing depth is a pivotal parameter for using NGS. In the current study, we made a side-by-side comparison of two NGS platforms with different sequencing depths, denoted as lower-throughput (LTP) and higher-throughput (HTP). The capacity of these platforms for characterization of the composition, quality, and diversity of the unselected Ph.D.TM-12 Phage Display Peptide Library was investigated. Our results indicated that HTP sequencing detects a considerably higher number of unique sequences compared to the LTP platform, thus covering a broader diversity of the library. We found a larger percentage of singletons, a smaller percentage of repeated sequences, and a greater percentage of distinct sequences in the LTP datasets. These parameters suggest a higher library quality, resulting in potentially misleading information when using LTP sequencing for such assessment. Our observations showed that HTP reveals a broader distribution of peptide frequencies, thus revealing increased heterogeneity of the library by the HTP approach and offering a comparatively higher capacity for distinguishing peptides from each other. Our analyses suggested that LTP and HTP datasets show discrepancies in their peptide composition and position-specific distribution of amino acids within the library. Taken together, these findings lead us to the conclusion that a higher sequencing depth can yield more in-depth insights into the composition of the library and provide a more complete picture of the quality and diversity of phage display peptide libraries. Full article
(This article belongs to the Special Issue Bacteriophages as Tools in Applied Sciences)
►▼ Show Figures

Figure 1

16 pages, 2603 KiB  
Article
Characterization and Genomic Analysis of Escherichia coli O157:H7 Phage UAE_MI-01 Isolated from Birds
by Mohamad Ismail Sultan-Alolama, Amr Amin, Khaled A. El-Tarabily and Ranjit Vijayan
Int. J. Mol. Sci. 2022, 23(23), 14846; https://doi.org/10.3390/ijms232314846 - 27 Nov 2022
Cited by 7 | Viewed by 2996
Abstract
Verotoxin-producing Escherichia coli O157:H7 is responsible for the majority of foodborne outbreaks worldwide and may lead to death. Bacteriophages are natural killers of bacteria. All previously reported E. coli O157:H7 phages were isolated from ruminants or swine. Here, we report for the first [...] Read more.
Verotoxin-producing Escherichia coli O157:H7 is responsible for the majority of foodborne outbreaks worldwide and may lead to death. Bacteriophages are natural killers of bacteria. All previously reported E. coli O157:H7 phages were isolated from ruminants or swine. Here, we report for the first time a phage isolated from bird feces in the United Arab Emirates (UAE), designated as UAE_MI-01, indicating birds as a good source of phages. Thus, phages could be a tool for predicting the presence of the host bacteria in an animal or the environment. UAE_MI-01 was found to be a lytic phage that was stable at wide ranges of pH, temperature, and chemical disinfectants, and with a burst size of almost 100 plaque-forming units per host cell after a latent period of 20 min and an adsorption rate constant (K) of 1.25 × 10−7 mL min−1. The phage genome was found to be 44,281 bp long with an average GC content of 54.7%. The presence of the phage indicates the presence of the host cell E. coli O157:H7 in wild birds. Therefore, other birds, mainly poultry, could be also investigated for the presence of this pathogenic bacterium. To the best of our knowledge, this is the first report of an E. coli O157:H7 bacteriophage isolated from a bird. Full article
(This article belongs to the Special Issue Bacteriophages as Tools in Applied Sciences)
►▼ Show Figures

Figure 1

15 pages, 13294 KiB  
Article
Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum
by Uylae Kim, Elizabeth S. Paul and Arturo Diaz
Int. J. Mol. Sci. 2022, 23(12), 6609; https://doi.org/10.3390/ijms23126609 - 14 Jun 2022
Cited by 2 | Viewed by 5288
Abstract
Microbacterium foliorum is a Gram-positive bacteria found in organic matter. Three lytic bacteriophages, KaiHaiDragon, OneinaGillian, and YuuY, were isolated from M. foliorum strain NRRL B-24224. Phage YuuY in particular expresses a broad host range as it possesses the ability to infect closely related [...] Read more.
Microbacterium foliorum is a Gram-positive bacteria found in organic matter. Three lytic bacteriophages, KaiHaiDragon, OneinaGillian, and YuuY, were isolated from M. foliorum strain NRRL B-24224. Phage YuuY in particular expresses a broad host range as it possesses the ability to infect closely related bacterial species Microbacterium aerolatum at a high plating efficiency. Characterization tests were performed on all three Microbacterium phage to assess morphology, genomic characteristics, pH and thermal stabilities, life cycle, and the type of receptor used for infection. All three phages showed similar pH stability, ranging from pH 5–11, except for KaiHaiDragon, which had a reduced infection effectiveness at a pH of 11. YuuY possessed a significantly higher temperature tolerance compared to the other Microbacterium phages as some phage particles remained viable after incubation temperatures of up to 80 °C. Based on the one-step growth curve assay, all three Microbacterium phages possessed a relatively short latent period of 90 min and an approximately two-fold burst size factor. Moreover, all three phages utilize a carbohydrate receptor to initiate infection. Based on bioinformatics analysis, YuuY, KaiHaiDragon and OneinaGillian were assigned to clusters EA10, EC, and EG, respectively. Full article
(This article belongs to the Special Issue Bacteriophages as Tools in Applied Sciences)
►▼ Show Figures

Figure 1

16 pages, 2307 KiB  
Article
A White Plaque, Associated with Genomic Deletion, Derived from M13KE-Based Peptide Library Is Enriched in a Target-Unrelated Manner during Phage Display Biopanning Due to Propagation Advantage
by Danna Kamstrup Sell, Ane Beth Sloth, Babak Bakhshinejad and Andreas Kjaer
Int. J. Mol. Sci. 2022, 23(6), 3308; https://doi.org/10.3390/ijms23063308 - 18 Mar 2022
Cited by 8 | Viewed by 4244
Abstract
The nonspecific enrichment of target-unrelated peptides during biopanning remains a major drawback for phage display technology. The commercial Ph.D.TM-7 phage display library is used extensively for peptide discovery. This library is based on the M13KE vector, which carries the lacZα sequence, [...] Read more.
The nonspecific enrichment of target-unrelated peptides during biopanning remains a major drawback for phage display technology. The commercial Ph.D.TM-7 phage display library is used extensively for peptide discovery. This library is based on the M13KE vector, which carries the lacZα sequence, leading to the formation of blue plaques on IPTG-X-gal agar plates. In the current study, we report the isolation of a fast-propagating white clone (displaying WSLGYTG peptide) identified through screening against a recombinant protein. Sanger sequencing demonstrated that white plaques are not contamination from environmental M13-like phages, but derive from the library itself. Whole genome sequencing revealed that the white color of the plaques results from a large 827-nucleotide genomic deletion. The phenotypic characterization of propagation capacity through plaque count- and NGS-based competitive propagation assay supported the higher propagation rate of Ph-WSLGYTG clone compared with the library. According to our data, white plaques are likely to arise endogenously in Ph.D. libraries due to mutations in the M13KE genome and should not always be viewed as exogenous contamination. Our findings also led to the conclusion that the deletion observed here might be an ancestral mutation already present in the naïve library, which causes target-unrelated nonspecific enrichment of white clone during biopanning due to propagation advantage. Full article
(This article belongs to the Special Issue Bacteriophages as Tools in Applied Sciences)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop