Which is better, V1-V3 or V3-V4 regions for 16S amplicons using 2x300 bp illumina sequencing? Are both good to target bacteria and archaea?
you can choose any of them but i my opinion V3-V4 primers are most commonly used. And this region is best suited for 2*300bp MiSeq platform.
Additionally, universal primers targeting both bacteria and archaea are not that efficient. They cover most of the bacteria and archaea are underrepresented. I would suggest you to use universal bacterial primers for bacteria and universal archaeal primers for archaea. In this way you can get better magnification on both communities.
Thank you! For us is not possible to sequence bot communities sepparately, due to lack of enough money to do that. But I guess we'll use V3-V4 then.
A nice alternative is using Nanopore sequencing and sequence the complete 16 S rDNA ORF, so no bias by V region analysis to tax id . You can easily multiplex 24 samples or more
Yes, I know, or Pacbio, but the prices are too expensive for us, we barely will be able to aford Illumina, that is why I would like to decide on the best primers to take advantage of the results we could get.
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