Fig. 2

Clustering analysis of mammary gland microbiota based on the distribution of core OTUs. Rows correspond to individual core OTUs (core OTUs defined as those present in at least 75% of samples in each niche and with a relative abundance of > 0.01% of the community). Columns correspond to individual samples. The “Normalized Abundance” key relates colors to the normalized proportions of OTUs (relative abundance of each OTU divided by the Euclidean length of the column vector). The top dendogram shows how samples are clustered based on their Bray–Curtis dissimilarities (using unweighted pair group method with arithmetic averaging (UPGMA)). The significance of clustering patterns has been calculated based on 9999 permutations and p-values calculated based on PERMANOVA. The left dendogram shows how OTUs correlate (co-occur) with each other based on their Spearman’s correlation coefficient. The “Phylum” key relates the left annotations to the corresponding phylum of each genus. The “Niche“ and “Parity“ keys relate samples to their originating niche (teat canal vs. milk) and parity group (primiparous vs. multiparous). The VENN diagram shows the distribution of core OTUs within each niche of the mammary gland; “green“ shows the proportion of OTUs that were exclusively core in teat canal microbiota, “blue“ shows the proportion of OTUs that were exclusively core in milk microbiota, and “orange” shows the proportion of OTUs that were identified as core microbiota in both niches