Could PropagAtE be applied to SAG data?

[TsumaR]

Hello @KrisKieft,

Thank you for developing such a great tool.
I want to apply PropagAtE to bacterial SAG data.
Could it be possible?
If there is anything I should be aware of, I would appreciate it if you could let me know.

Thanks,
Ryota

[KrisKieft]

Hi,

SAG data should work if you had an active prophage infection within the cell. This may depend on the stage of infection (i.e., if enough prophage genome replication has occurred within the cell to detect).

What you should be aware of is how the sample preparation may effect PropagAtE's ability to identify active prophages. PropagAtE works best if an entire sample is extracted together, both the intracellular and extracellular DNA. This is because any released virions from lysed cells within a population will add to the prophage:host genome ratio. With a SAG you won't have this, so you'll be relying on the prophage having replicated its genome without proceeding to lysis in order for it to be identified as active. With the high number of bacteria (and other microbes) constantly infected with viruses in nature this may not be too difficult to find. This is slightly different than identifying lytic viruses within a SAG because the presence of a lytic virus would suggest an active infection (at least entry). There are certainly a few limitations to the sensitivity of PropagAtE on SAGs, but these will not effect the validity or accuracy of the results.

I hope that helps.

Kris