Bacteriophage Bioinformatics

Dear Colleagues,

The continued rise of antibiotic resistance to critical heights together with an increasing number of bacterial pathogens harkens back to the pre-penicillin era when producing new antibiotics was an urgent societal need. While promising antimicrobial agents were identified nearly a century ago and long before the discovery of penicillin, their therapeutic potential was never realized and they were rarely used clinically. Indeed, the first such agents were identified as bacteriophages.  However, at that time researchers had neither the proper equipment nor a sufficient understanding of bacteriophage biology to realize the antibiotic potential of phages, possibilities to do high throughput screening (HTS) of protein/ligand interactions, quantitative methods of comparative analysis, which will provide information about these agents, their activity and specificity.  Presently, the situation has radically changed; complementary structural, biochemical, and computational efforts have provided significant insight into how bacteriophages recognize and destroy their bacterial targets.  Indeed, hybrid approaches combining structural methods, bioinformatics analysis of sequence databases, biophysical characterization of phage interactions with various  ligands/proteins and computational statistics with high throughput biochemical methods have provided a wealth of information regarding phage-pathogen interactions, the functions of phage-encoded proteins, and the dependence of phage populations on animal or human microbiomes. As a result, phage therapy is beginning to become a more broadly used treatment against clinically challenging bacterial infections. However, despite these successful efforts, improvements in the analyses and comparison of various components of bacteriophages and their interactions with pathogenic hosts are necessary to understand the principles of regulation of bacteriophage activity. In this context, hybrid approaches that include bioinformatics, biophysical, biochemical, single molecule, and microbiological approaches have the potential to accelerate the development of phage-based therapeutics and usher in a new era antibiotics.

This Special Issue of Viruses will highlight innovations in the application of hybrid methods to analyze bacteriophage activity and function and in the search for bacteriophages that can be rationally engineered to function as powerful antibiotic therapeutics. Approaches that can be used to identify phages with therapeutic potential and/or to create  synthetic phages with desired antibiotic properties have the potential to transform the emerging field of phage therapy. We encourage submissions of reviews or original research manuscripts addressing the following topics:

1)   Tools for the analysis of phage genomes and/or comparative assessments of available software packages.
2)   How prediction bacteriophage type (virulent vs. temperate) can be accomplished via computational analysis of phage genomes. Classification of phages based on their genome sequences
3)   Applications of bioinformatics in verification and classification of the phage proteins
4)   Optimization of high throughput approaches in the analysis of phages utilizing bioinformatics approaches.
5)   Methods to analyze phage-bacterium interactions analysis and links to their life state: virulent or temperate.
6)    Design, and applications of synthetic phages in pharmaceutics and food industries.

Prof. Dr. Elena Orlova
Dr. Marc C. Morais
Guest Editors

Manuscript Submission Information

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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.

• viruses
• bacteriophage
• bacteriophage classification
• genome
• bioinformatics
• computational tools
• structural organisation
• infectivity
• function
• structural methods
• electron microscopy
• X-ray
• NMR
• high throughput screening

• Bacteriophage Bioinformatics 2nd Edition in Viruses (3 articles)