Hi @Lauren_O_Connell and @colinbrislawn,
exact mode looks for taxonomy annotations that match the full string — e.g., You want to
include only Enterobacteriales, Campylobacterales, and Vibrionales, so this command is looking for taxonomy annotations that exactly match those strings, NOT taxonomies that contain those terms as substrings (e.g., k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales…)
So it makes sense that all taxa are being filtered out (since you are telling QIIME2 to only include taxa that perfectly match those terms), and I do not believe this is a bug.
You should either:
contains mode instead of
exact, and include some of the level information that is contained in Greengenes taxonomy annotations (it looks like you are using Greengenes). So instead of
o__Vibrionales, and it should not be filtering out other groups (unless if there are other orders that contain one of these terms as a prefix, which seems unlikely)
- write the complete taxonomy strings for taxa that you explicitly wish to include — but this is probably not what you want in this case, since it looks like you want ALL taxa that fall into those orders. This approach would make sense only if you want a very narrow group (e.g., all sequence variants that match a particular species)
I hope that helps!