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?