Basic logic and use of PERMANOVA for microbiome data

Basic logic and use of PERMANOVA for microbiome data


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!


statistical test


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