Can we use Qiime2 to estimate microbial community composition from amplicon reads of multiple 16S V-regions?
QIIME 2 doesn’t care very much about which particular amplicon you are looking at, but we don’t have anything that would merge (I don’t think this is really possible) that information or use it to constrain OTUs/Taxonomic resolution (seems possible, but not aware of software that can do this either). So the best you’d be able to do right now is analyze each amplicon independently and look for a consensus in the interpretation of the data (treating each amplicon as a kind of replicate of your sample).
Thank you so much for the quick reply! I appreciate it.
Any suggestions on how to combine the abundance data (AVS or OTUs) generated from different amplicon regions to reach a consensus interpretation? Thank you!
I don’t think there is such a way to integrate the abundance data itself (as you don’t have comparable features anymore). That means for an ASV from region X, we know what sample it belonged to, but we don’t know what bacteria it came from, so we can’t tie it to a different ASV from region Y, because we don’t know what bacteria that ASV came from either. The best we can do is split the amplicon and analyze independently.
What you’ll need to do instead is consider these as replicated studies, each independent, but answering/asking/observing the same question/thing.