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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

View abstract on PubMed

Summary
This summary is machine-generated.

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

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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.