So I am not sure about the advantage of performing the differential abundance analysis at the genus level. Can you explain more? Thanks in advance.
Reasons for doing the testing at the genus level would include (1) that it can be faster if you have a lot of ASVs, though that's not a great reason to restrict your analysis to less specific taxonomic levels, or (2) because you suspect that differences below the genus level are unimportant, which (in my opinion) often isn't likely.
Because of both of the caveats that I mentioned here, I typically do differential abundance testing at the ASV level, not at the level of a specific taxonomy.
Hope this helps!
Thanks for your reply.