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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

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Persistent virulent phages exist across bacterial isolates

Peter Erdmann Dougherty1,2, Charles Bernard3, Alexander Byth Carstens1

  • 1Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark.

Nature Microbiology
|December 30, 2025
PubMed

Insights

Contrary to expectations, virulent phage genomes were discovered in bacterial assemblies. This suggests persistent infections occur without significant host death, challenging traditional phage classifications.

Area of Science:

  • Microbiology
  • Virology
  • Genomics

Background:

  • Virulent phages, defined by their lytic cycle and host death, are not expected in bacterial genome assemblies.
  • The traditional dichotomy classifies phages as either virulent (lytic) or temperate (lysogenic).

Purpose of the Study:

  • To investigate the presence of virulent phage genomes in bacterial assemblies.
  • To challenge the assumption that virulent phages cannot persist within bacterial populations.

Main Methods:

  • Analysis of over 267,000 publicly available Escherichia coli genome assemblies.
  • Bioinformatic analyses and culture experiments.

Main Results:

  • Identification of 373 virulent phage genomes within Escherichia coli assemblies.
  • Association of these genomes with specific phage taxa, particularly jumbo phages like Chimalliviridae.
  • Evidence suggesting persistent infections without substantial host mortality.
  • Discovery of 285 related phage genomes in other bacterial taxa.

Conclusions:

  • Virulent phage genomes can be found in bacterial assemblies, indicating non-canonical lifestyles.
  • The virulent-temperate dichotomy may be an oversimplification.
  • Persistent infections by previously uncharacterized phages are likely common.

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