Basic logic and use of PERMANOVA for microbiome data

Question

[xgeneral57]

PERMANOVA is frequently used in microbiome studies when analyzing beta diversity. While I know that basics of PERMANOVA are similar to ANOVA (with some differences related to permutation), I have a hard time understanding the logic of this analysis in the context of beta diversity analysis. - In particular, we perform statistical tests for vectors of data, e.g., to compare the abundance of OTU X in cases vs. abundance of OTU X in controls. When working with beta diversity though we deal with a distance matrix (e.g. based on Bray-Curtis) for pairs of samples and not vectors. Can someone please explain to me what quantities are compared against each other using PERMANOVA?
- Should one compute different distance matrices for each category (e.g., one for cases and one for controls) or just one matrix that includes samples from all categories? Many thanks!

Answer 1

[matteolifilipe]

A bit late but might help anyone. We use PERMANOVA to compare centroids of groups of samples, usually represented through PCoA or NMDS. The matrices visualized are usually beta-diversity indexes previously obtained. Thus, there is no need to calculate multiple matrices, as one matrice will hold the beta-diversity measure for all samples, for that reason a meta-parameter is usually provided (i.e. treatment). At last, the significance of centroids can be accessed by p values.