Fig. 1

Species-level milk microbial biodiversity comparisons between enterotypes. A Boxplots showing the alpha diversity indices for richness (Chao1) and evenness (Shannon). Boxes represent the interquartile range (IQR; Q1 and Q3), with the line inside marking the median. Whiskers extend to the smallest and largest values within 1.5 times the interquartile range, with points beyond these considered outliers. Each point represents a sample's diversity score. A non-parametric Kruskal–Wallis test followed by post-hoc Wilcoxon rank sum test was performed for pairwise comparisons between enterotypes. Asterisks indicate statistically significance levels (*p = 0.05; ** p = 0.01; *** p = 0.001; **** p = 0.0001). B Bidimensional Principal Coordinate Analysis (PCoA) based on Jensen-Shannon Distance (JSD) dissimilarity matrix illustrating differences in the microbiome profiles among the different enterotypes. Colours represent different enterotypes, while ellipses indicate 95% confidence intervals of the multivariate t-distribution around centroids of each groupings with enterotype as factor. Differences were assessed statistically using PERMANOVA and pairwise comparisons results are provided in Additional file 2: Table S1