Microbial Community Structure and Diversity Estimates

All samples were rarefied to a depth of 7,200 sequences, which was the minimum number obtained for any given sample. We used Observed OTUs, Shannon and Faith’s PD indices as alpha diversity metrics to explore within-sample microbial heterogeneity. Beta diversity (between-sample diversity) was calculated using the weighted UniFrac metric (Lozupone et al., 2011). A principal coordinate analysis (PCoA) was used to visualize the results and the effect of the different variables under study such as the sucrose concentration, breed, individual, and sampling time. Rarefaction curves and beta diversity metrics were estimated using the “core-metrics-phylogenetic” plug-in implemented in the Qiime2 pipeline.