Fig. 2.

Beta-diversity of the bacterial communities of intramammary secretions during the first week of lactation. Principal coordinate analysis (PCoA) was used for visualization of Bray-Curtis dissimilarities of the bacterial communities of intramammary secretions. Color codes and symbols were used to differentiate samples based on a days in milk (DIM), b BstYI variants within day 0, c BstYI variants within day 1, and d BstYI variants within day 6. Prior to calculation of Bray-Curtis dissimilarities, the OTU table was normalized using cumulative sum scaling (CSS) transformation. PERMANOVA (9999 permutations) was performed on a repeated measurement model that included DIM, BstYI variants, and the interaction between DIM and BstYI variants as fixed factors and the effect of individual cows as a random factor nested within the BstYI variants. For all tests, p values < 0.05 were considered significant