Duality diagram function and between class analyses presented in the form of a 3D PCA plot and selected significant OTUs in form of boxplots.

The 3D graph (A) shows the relationship between sample groups and OTUs driving the sample differences. OTUs significantly different between groups were selected in Ade4 using the relative abundance table and confidence level of 95%; only OTUs with total abundance higher than 0.001 were retained in the analysis. The large circles represent treatment groups while small black circles represent OTUs. Only OTUs that are significantly associated with differences between groups are enlarged and coloured in the same colour as the sample they are distinguishing from others. Some of the significant OTUs are given in views B, C and D while all OTUs selected by Ade4 analysis are given in Figure S3. The boxes represent the limits of the second and third quartiles; the whiskers indicate the data within 1.5 times the interquartile range and the dots are outliers.