Fig. 3

Alpha and beta diversity of theC. gallinadigestive gland-associated microbiome and the surrounding environmental microbiomes. (A) Principal coordinate analysis (PCoA) based on unweighted UniFrac distances between the microbial profiles of C. gallina digestive glands and environmental samples (seawater and sediments) shows a significant separation between groups (permutation test with pseudo-F ratio, p-value ≤ 0.001). Color gradients indicate sampling sites (Marina di Ravenna, Lido di Savio, Cesenatico, and Rimini) according to the legend in the plot. The first and second principal components (PCo1 and PCo2) are plotted, and the percentage of variance in the data set explained by each axis is reported. Ellipses include a 95% confidence area based on the standard error of the weighted average of the sample coordinates. (B) Box-and-whiskers distribution of alpha diversity calculated using Faith’s phylogenetic diversity (PD), the number of observed ASVs, and the Shannon index. Significant p-values (Wilcoxon rank-sum test controlled for multiple testing using FDR) are indicated in the figure by the following symbols: * p-value ≤ 0.05; ** p-value ≤ 0.01; *** p-value ≤ 0.001