A little bit late to the party on this but jut wanted to point out that there is a compositonally aware differential abundance tool that actually tests differential variance in addition to abundance. This might help you identify taxa with high variance which you could interpret as less “stable”. Check out the Corncob R package. There is also a qiime2 q2-corncob plugin but I personally haven’t used that version so I’m not sure how it would compare against the complete R package.
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