Hi!
I did the same thing you are describing by obtaining core features with Qiime2.
After it, you can manually copy and paste core features at chosen percentage to make a Venn diagrams using online tools Venny or interactivenn to get unique and shared features (from both sources lists of unique and shared features may be obtained by directly copying from the website or by downloading a diagram as a .txt file). I did is like this at the first time, but since I wanted to get reproducible scripts, later I used list intersections in Python to obtain the lists of unique and shared features.
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