I'm wondering if anyone has any reference about the % coverage for Bacteria and Archaea using universal primers 341F and 806R. So far I know using these universal primers the percentage of coverage for Arqueas is lower, however, I'm not finding a reference about it. Could anybody help me??
I appreciate any help.
Thanks a lot
One thing you can try in lieu of references, it to extract the V3V4 (341F and 806R) amplicon region from either GreenGenes, SILVA, GenBank, or some other reference database (which you'd have to import into ). From this output, you can determine how much coverage each reference database has for your taxa / amplicon region of interest. You can use some of the tools within RESCRIPt to help compare between the different reference databases.
Here are recent papers by Wasimuddin et al. 2019 and Abellan-Schneyder et al. 2020, that may be of help.
In Silva, I found Archaea primers (50%) (52.7%)
Bacteria(79%) (79.2%). https://www.arb-silva.de/browser/ssu-138.1/silva-ref-nr/testprime/1158271/
I'll look in the other reference database too.
I just wanted to clarify that you can also download / import sequence files into QIIME 2 and use qiime feature-classifier extract-reads command, and then visualize output.
I have the problem that although using those universal primers on environmental samples that should have archaea i get no archaea at all although the reference database has some archaeal seqs.
Is this the case with you? Please update here what you have finalized
Glad for your contact
Unfortunately, not exactly my case. I've always got archea even using universal primers. What happened in my case was a question from a reviewer questioning whether universal primers were efficient in identifying both bacteria and archaea. My answer was: according to Quast et al., 2013 ~80 % coverage for Bacteria and ~50 % for Archaea.
Sorry if I couldn`t help you. Please, if you want we can talk more about it. Let me know. Good luck.