Additional file 1 of The microbiome of common bedding materials before and after use on commercial dairy farms

Additional file 1: Table S1. Metadata file for all samples included in this study. Table S2. ASVs assigned to each taxonomic level. Table S3. Read counts and mean abundance of assigned species stratified by sample ID. Table S4. Proportion of phylum-level counts, by bedding type and status. Table S5. Proportion of phylum-level counts, for the four non-outlier low-yielding bedding samples. Table S6. Modeling results for associations between bedding status and type, and alpha diversity metrics (LMM output). Table S7. Results from phylum-level differential abundance testing of used versus unused samples, by bedding type. Table S8. Results from class-level differential abundance testing of used versus unused samples, by bedding type. Table S9. Results from genus-level differential abundance testing of used versus unused samples, by bedding type. Table S10. List of potential mastitis pathogens considered in the analysis of 16S rRNA sequence data. Table S11. Proportion of genus-level counts for genera that contain potential mastitis pathogens, by bedding type and status. Table S12. Results from genus-level differential abundance testing of taxa that contain potential mastitis pathogens, comparing used versus unused samples, by bedding type. Table S13. Read counts and proportion of genus-level counts for the mock community and negative control samples.