Here is one of my classification result, and one of the taxa is "D_4__Nitrosopumilaceae;__ ". I already know that it cannot be confidently classified beyond family level, and it can be any taxon in Nitrosopumilaceae.
Does this mean that multiple potential genus/species can be included in this taxon? e.g., it contains many OTUs which may belong to different genus/species, but qiime2 still counts them together because there is no way to distinguish whether they belong to different species. If so, I can not say something like 'an unknown taxon in Nitrosopumilaceae was increased in the past month' based on this result, because it may contains many taxa.
Or, 'D_4__Nitrosopumilaceae;__' represents only one genus?
No, otherwise it would be classified as that genus.
Rather, this is QIIME 2's way of saying that that sequence (or sequences) resemble more than one genus in that family.
So it does not mean that it is necessarily an unknown (e.g., novel) genus, only that the genus cannot be identified because you lack the sequence resolution to differentiate multiple genera in this family.
You could try classifying sequences from that family with a different reference database, or with NCBI BLAST, to manually inspect the results — it is possible that these sequences match only a few genera or species, so you might be able to narrow down a possible ID (but be careful to inspect the results for other close hits, don't just take the top hit from BLAST).
