Primarily it looks that the archaea present in samples are too low, I don't think there is too much archaeal or bacterial biomass in plaque.

Thank you for your opinion

I also believe that there are very few archaea, however there are already many published reports where they can be isolated from dental plaque and even from within root canals where I would assume that they still exist in smaller quantities.

Thanks again.

It might be an obvious question, but have you tried to contact with some of the autors of those papers you have already read? I know sometimes they don't ansewr us, but you can try. Another thing I sometimes do is call or send an e-mail to the technical support. The extraction kit you are using may have some detail in collecting or storing the sample, wich would make it possible to extract a larger amount of DNA. It's just a suggestion, I hope it helps and works for you.

Thank you very much Catarina Martins Tahim, I wrote some e-mails trying to contact some of the researchers that assure to obtain Archaea DNA from dental plaque, one of them answered, but she did not answer my specific questions.

I am starting to think that it is not possible.

Whit respect to your suggestion about calling to the technical support, I could not find an extraction kit that considers the extraction of Archaea DNA. We use in the lab several kits, and we tried every one — neither our protocols with phenol-chloroform and some enzymes works.

I hope I can find someone who has previous experience in this extraction and can help me.

THANK YOU VERY MUCH FOR YOUR INTEREST.

Rubén Abraham Domínguez-Pérez

Although you are exchanging the post with Catarina, but I just wanted to mention that there is nothing special with DNA which can be isolated with any special method. I think in your case the first problem is the amount of sample. Further, sometimes the silica matrix based kits does not function good enough and we loose a lot of DNA. Phenol-chloroform method can be good, but make sure you remove all traces of phenol from the extracted DNA.

try MagMax microbiome for higher throughput (magnetic bead based) or PureLink Microbiome for lower throughput prep (spin column based). We did qPCR and NGS on many samples, including saliva and dental plaque- works well for all types of microorganisms