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.