Validity of using NCBI species level annotation of the reference sequences in the silva138.1 database

[pschloss]

Please see this post and let me know if you have any questions…

Classify.otu results not to a species level when database is

I’m using SILVA NR99 138.1 which as far as I can tell holds species level data on sequences. Although I understand the limitations of species-level classification of the 16S gene I’m just curious as to why: A. A lot of papers state that SILVA and RDP only go down to genus level when their fastas in fact contain species IDs (is this a newer thing from the recent years?) ? B. I was able to use Illumina’s 16S Metagenomics app to classify to a species level with the RDP database C. classify.otus …