meaning of ambiguous taxonomic labels in Greengenes

[Nicholas_Bokulich]

Hi @Ishanmanandhar,
Please see this topic for more details about what those different labels mean:

ASV collaps question

@shinseung, Those two labels are distinct: The first indicates that the sequence could not be classified beyond kingdom level (which probably indicates that it is really non-bacterial, e.g., host DNA). The second consists entirely of labels from the reference database you used. So QIIME is able to classify that sequence to the genus (or species?) level, but unfortunately the top match is to reference sequence(s) that are totally unannotated in the database. I hope that clarifies!

@Ishanmanandhar

How important it to filter out and is there any way to perform this in Qiime2?

I would filter this one but not the others (there is some discussion elsewhere on this forum regarding motivations for this):

@Ishanmanandhar

k__Bacteria; ; ; ; ;

@Ishanmanandhar

Some of them are also assigned with unusual names like DS-18, iii1-8 ,does those numbers denote anything(k__Bacteria;p__Acidobacteria;c__iii1-8;o__DS-18) ?

Probably uncultivated/unknown clades of bacteria, but that nomenclature is specific to the reference database and is not coming from QIIME 2, so you should contact the authors of those databases for more details on their nomenclature.

Good luck!