Hi, is there any general concensus on which would be the best 16S rRNA primers to use to cover both bacterial and archaela community? What about fungal ITS?
In the literature I've came across Takahashi et al. 2015 (Pro341F and Pro805R). Earth microbiome on the other hand recommends 515F (Parada et al., 2016) and 806R (Apprill et al., 2015) or 926R (Quince et al., 2011).
For fungal community I've seen everything from 18S region, ITS2, ITS1. We're planning to use commercial company for the service which already has some selected primers in their offer for mentioned communities so I'm also wondering whether would be better to go with their selection since any primer modifications would mean additional optimisation of the PCR protocol for which I have my doubts that they will/could handle.
What would be your advice on the topic?
Thanks in advance!