I cannot decide which reference I should use to map my gut microbiome 16S data. Greengenes seems to be the best choice, but last time it was updated in 2013 and metagenomics has moved far ahead since then. Won't I be missing a huge part of biodiversity, if I use it?
Also, this article keeps me worried. SILVA and Greengenes have a rather small overlap in taxonomy. It makes me want to make my own reference DB, but that'd be a serious standalone project.
What do you use to map gut 16S? Is there really nothing better than these two arguably accurate ref DBs?
Genbank also offers a 16S database these days. Dont know how good it is.
It's not very good, it only has 20,792 sequences. I guess that's improvement over what it was a few years ago (back then it was ~10k seqs)..