Persistent virulent phages exist across bacterial isolates

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.