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Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis.

Ramy Karam Aziz1, Hans-Wolfgang Ackermann2, Nicola K Petty3

  • 1Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy, 11562, Cairo, Egypt. ramy.aziz@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|November 15, 2017
PubMed
Summary

Antimicrobial resistance drives interest in phage therapy. This guide helps researchers accurately describe newly isolated bacteriophages (phages) and their genomes, improving data quality for therapeutic and genomic applications.

Keywords:
AnnotationCDSElectron microscopyGenomesLocus tagORFPhagePromoterSoftwareTaxonomyTerminator

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Area of Science:

  • Microbiology and Virology
  • Genomics and Bioinformatics
  • Antimicrobial Resistance Research

Background:

  • Increasing antimicrobial resistance necessitates novel therapeutic strategies.
  • Bacteriophages (phages) are viruses that infect bacteria and show therapeutic potential.
  • Decreased genome sequencing costs enable widespread phage research and genomics education.

Purpose of the Study:

  • To address the substandard quality of phage descriptions and genome annotations.
  • To provide guidance for accurately describing newly isolated bacteriophages.
  • To support researchers, especially newcomers, in the field of phage biology.

Main Methods:

  • This chapter serves as a descriptive guide, not based on experimental data.
  • It outlines best practices for characterizing and annotating phage genomes.
  • Focuses on essential descriptive elements for newly isolated viruses.

Main Results:

  • Identified a critical need for standardized and high-quality phage descriptions.
  • Highlights common deficiencies in current phage annotation practices.
  • Establishes a framework for improved phage data reporting.

Conclusions:

  • Accurate phage description and annotation are crucial for advancing phage therapy.
  • Standardized methods will enhance the utility of phage genomes in research and education.
  • This guide aims to improve the reliability and comparability of phage data.