In a recent study, we profiled the response of fish gut microbiota to a dietary intervention. Besides sampling the luminal contents and mucosal tissue from the proximal and distal intestine, we also collected feed and water samples. To avoid rarefying the ASV table, I used the DECODE plugin for the visualization of beta-diversity. However, the resulting PCoA biplot clustered specific sets of samples (mucosal tissue + water + feed) into one straight line, which is very different from PCoA results produced by the QIIME2 core metrics.
rpca-biplot.qzv (1.2 MB)
Command lines I used to generate the RPCA results.
qiime deicode rpca
qiime emperor biplot