Hi Ana
Certainly a timely query as we have been struggling with this for many months now as we try and tackle our 1st sponge genomes.... we have spent our careers working in the opposite direction (i.e. trying to eliminate host cells from the microbial fraction), which seems to be much easier than obtaining clean sponge cell preps!
From our experience it seems to be entirely host species-specific so it is difficult to give one size fits all advice. We have trialled cell separations in percoll, ficoll, various manual filtrations, restriction digests etc etc (I have cc'd Sara Bell here who has done a lot of this optimisation and may be able to provide you with some of the specific protocols), however the thing that seems to have worked best for our current Ircinia species was to leave the 'dirty' DNA in water at 4 degrees for a few months. For some reason (which we have not yet managed to understand), during this time the contaminating microbial DNA appeared to preferentially degrade, leaving us with a high quality and almost pure sponge DNA preparation. It makes no real sense, but it seemed to work so you could give this a go.
Best of Luck!
Nicole
-----Original Message-----
From: Sponge biology and chemistry list [mailto:[log in to unmask]] On Behalf Of Deborah Gochfeld
Sent: Friday, 8 September 2017 9:50 PM
To: [log in to unmask]
Subject: Re: Removal of bacterial cells
Ana and others,
Could you please share recommendations on this topic with the list?
Thanks!
Deb
Sent from my iPad
> On Sep 8, 2017, at 3:00 AM, Ana Riesgo <[log in to unmask]> wrote:
>
> Dear spongers,
> We are trying to remove bacterial cells from heavily populated sponges
> to get clean sponge DNA for NGS. We are considering Percoll, centrifugation and filtering, or commercial kits such as that from NEB. What would you recommend?
> Cheers,
> Ana
>
> Sent from my iPhone
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