HI @Hajar,
That is a confusing output, but it makes absolute sense and is not misleading when you consider what gneiss is comparing here.
You are running gneiss on a feature table of sequence variants that have had taxonomic lineages assigned to them. There is no reason to expect that each unique sequence variant would have its own unique taxonomic lineage, and in fact many are going to be assigned the same exact lineage, some even the same species. It looks like you are examining genus-level results in gneiss, so it is absolutely sensible to expect that there will be multiple sequence variants with the same genus assignment, and there is no reason to expect that all of those will display the same behavior.
Nothing misleading here. You have multiple sequence variants with the same taxonomic assignments that behave differently under your experimental conditions.
Did you see this topic? Look around — it is possible but only with some level of effort. What you are doing now is the "correct" way to do things. Collapsing by taxonomy will reduce potentially important information.
I hope that helps!