Comparative Analysis of Milk Microbiota

To compare the microbiota structure among the milk groups, alpha diversity indices (Shannon, Simpson reciprocal diversity, and Chao1 index) were established to compare the microbial richness among the milk groups. Moreover, beta diversity indices, such as principal component analysis (PCA) and principal coordinate analysis (PCoA; weighted and unweighted UniFrac distances for PCoA), were used to explore the clustering of subjects [33 (link),34 (link),35 (link)]. The Wilcoxon rank-sum (Mann–Whitney 2-sample) test was performed to evaluate the alpha diversity indices among the milk groups using the SPSS 20 statistical software (SPSS Inc., Chicago, IL, USA). Furthermore, the Linear Discriminant Analysis Effect Size (LEfSe) algorithm, including the bar and Cladogram graphs, was also applied to identify and evaluate the more abundant taxa in one group compared to the other groups [36 (link)]. Venn diagrams (Venny 2.1) were used to depict the unique and shared sets of taxa lists between the milk groups.