How to test for dissimilarity for my samples

I am working on a project where I want to look at differences in the microbiome following drug treatment based on several clincial variables.

For example, I have stool samples for pre and post drug treatment for a series of patients and I want to compare the diversity between pre and post treatment based on whether or not the patient responded to the drug. What is the best way to do this? I have generated a bray curtis distance matrix and was now planning on performing an anosim or adonis test, but how would I do that knowing that I want to find out are there differences in diversity between patients who did respond and those that did respond after drug treatment?

Hi @mradz ,

You should check that the experimental design etc fits, but as you have a pre/post sampling design, you could use q2-longitudinal, specifically this method for looking at changes in beta diversity pre/post:

Good luck!