Hello there fellow users and devs!,
Yesterday I noticed that a portion of features (Sanger amplicons in this case) remained unclassified after classifying with primer-specific databases, GTDB r220 and SILVA 138, using either vsearch or NB. After a while, I added the classification coming from NCBI Refseq database (exact same methodology as the others) and noticed that Refseq classified the majority of unclassified features as Streptomyces sp, I then checked with Nucleotide database and BLAST and got mixed result, I checked SILVA (nothing to see there) and then I checked GTDB and many Streptomyces were undefined (or didn't reach certain quality I guess), see image below,
All this just let me wondering what's happening with the classification of Streptomyces and related taxa... I found this article (https://doi.org/10.3389/fmicb.2019.02170) and got even more flustered about this. So, questions are: Is there any suggestion in the community to classify features from this group accurately? or is it 16s non valid for now/anymore to classify individuals from this genus? anything in the middle?
Let me know what you think,