Why does Greengenes assign more features at the class and order ranks than Silva?

[Nicholas_Bokulich]

It is important to note that (unless if classifying samples with known composition, e.g., mock communities), more features classified as species does not necessarily mean better, because you don't know if those classifications are correct.

I agree with @Mehrbod_Estaki regarding the relative strengths and weaknesses of working with larger/more diverse/more recently updated databases. This ties into my point about species-level classifications being correct. To work off of @Mehrbod_Estaki's example, imagine the true species is A. glycaniphila — GG would classify this to species (A. muciniphila) because there is no ambiguity in the genus, but SILVA would probably classify to genus level if it cannot distinguish A. muciniphila from A. glycaniphila (e.g., because they have identical seqs for the marker gene fragment that you sequenced). Which would you prefer, a correct genus-level classification or an incorrect species-level classification?

@Negin

One thing about the greengenes though is that for me, I had some that were actually unassigned but were not empty or NAs in the taxonomy data because they were showns by g__, p__, etc. for different levels. Make sure you remove those as well, cause they are not assigned. Not sure why greengenes shows them like this instead of empty though.

You should not remove those. Those are GG's method of handling taxonomically ambiguous clades, see the original publication for a full description and see this topic for more details:

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!