PCA plot generated using the Ade4 R phylogenetic package [24].

Principal Component Analysis combined with duality diagram functions (dudi) [32] was used to perform Between-Class Analysis (bca) with respect to sample assignment to treatment groups. Monte Carlo test based on 999 permutations demonstrates that groups are significantly (Monte Carlo P-value = 0.003) different. The graph shows sample and group relationship with respect to microbiota structure. The OTU table used for the analysis was 100 times rarefied (normalised) and OTUs with abundance lower than 0.001 were removed.