Peter Dougherty

Finally, this has been a proper collaborative effort, and I’m very proud to have worked with (and learned from) all co-authors. Thank you all!

What’s the difference between a persistent virulent phage and a temperate phage? Phenotypically, maybe not so much. We argue that phages exist on a spectrum, with rapid, lytically replicating virulent phages on one side, and stable, non-inducing prophages on the other.

If these phages are non-temperate, how do they persist in bacterial cultures? Given their diversity, we argue there is not a single explanation. Here we suggest three possible mechanisms for persistence: phase variation, asymmetric phage inheritance, and lysis inhibition.

In a targeted follow-up search for the three jumbo-phage clusters in bacterial assemblies beyond Escherichia, we found an additional 285 persistent jumbo-phages. The Seoul- and Goslar-like phages encoded chimallin, a protein some phages use to produce a protective phage nucleus.

We also clustered the persistent phages with all virulent Escherichia phage isolates. Most (27/37) clusters contained persistent phages, demonstrating this is broad phenomenon. However, the three clusters with a highest proportion of persistent phages were all jumbo phages.

After extensive QC, we found 373 non-temperate phage genomes. These phages were not integrated in the bacterial genome, and do not resemble phage-plasmids.

We therefore hypothesized that virulent phage genomes in bacterial assemblies represent non-temperate infections, persistent infections. To test this, we first searched 267,092 Escherichia genome assemblies for contigs resembling virulent phage genomes.

Recently, we sequenced two large jumbo phages. When we ran a BLAST search, we found similar sequences in bacterial genome assemblies. This surprised us, as there are no known temperate phages this big. These phages were also a pain to work with, forming only tiny, faint plaques.

Usually, phage lifestyles are described as either strictly virulent (lytic cycle) or temperate (lytic or lysogenic cycles). However, some phages don’t fit either label, persisting with their bacterial hosts without crashing the host population or entering classical lysogeny.

Persistent virulent phages exist in bacterial isolates Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial ce...

Are there virulent phages hiding in your bacterial culture? Here we find hundreds of virulent phage genomes in bacterial genome assemblies. Bioinformatic and experimental evidence indicate these are not contaminations, but represent persistent infections.

www.biorxiv.org/content/10.1...