Hello!
Having only one group without control group and two time-points (pre and post) is one of the most inconvenient designs for beta diversity (IMHO).
It is pretty easy for alpha diversity, since one may use dependent t-test or dependent Wilcoxon test (depending on data distribution) to test if there is a difference between two time-points. As I understood you already did it.
It is more difficult for beta diversity since beta diversity is expressed in distances, and in your case distances between time points and between groups you want to compare are the same, so you have only one group and nothing to compare with. And performing Permanova test on paired samples will violate assumptions.
There are some workarounds you can try:
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Use Mantel test as duscussed here:
Analysing Paired Data Taken at One Timepoint - #14 by macrobiome -
Run Adonis test outside of Qiime2 with SubjectID as strata
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Use Adonis in Qiime2 with formula: "SubjectID + TimePoint".
Im not a statistician and not 100% sure about options 2 and 3. Please (all who is reading) correct me if they are not appropriate in that case.
Best,