Longitudinal analysis of beta diversity

I have a little question for the community. I’m performing a study, involving microbiota composition, on a population of samples in which I have diseased subjects and “healthy” controls. The diseased subjects were sampled at two different times (T0 and T1). I calculated alpha and beta diversity (e.g Shannon index and Bray-Curtis) for diseased group and performed comparison between the alpha diversity of samples at T0 and T1 by using “qiime longitudinal pairwise-differences”. I would like to perform the same analysis for beta-diversity determining if a modification in microbiota composition between the two time-points happened. I tried to use “qiime longitudinal pairwise-distances” but it requires to specify at least two group while I have only one group (diseased) sampled at two time-points. Any suggestions???

Thanks for your help!!

Are the healthy controls only sampled at one time point?

We have an open issue to make the “group column” optional in that action. The reason it has not been implemented sooner is that pairwise-distances on a single group is not too informative — the distances are always positive and almost always > 0, so this test is really only useful for demonstrating that one group changed more than another group did over the same time periods. Contrast that with pairwise-differences, for which it is actually meaningful to show that, e.g., alpha diversity significantly increased or decreased for a single group.

There is another possibility for you: calculate the PCoA coordinates and use those as input for pairwise-differences. Would that accomplish what you are after?

Hi Nicolas
I agree with you that the distances in pairs on a single group are not too instructive. Unfortunately those who performed the experimental design did not think to sample the checks at the second time (I think it is indispensable). I will try to follow your suggestion with the PCoA coordinates.
Thanks for your help

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