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.

附加文件1：表S1。本研究纳入的全部样本的元数据文件。
表S2：分配至各分类学层级的扩增子序列变体（Amplicon Sequence Variants，ASVs）。
表S3：按样本ID分组的已注释物种的读段计数与平均丰度。
表S4：按垫料类型与垫料状态划分的门水平计数占比。
表S5：针对4个非异常值低产垫料样本的门水平计数占比。
表S6：垫料状态、类型与α多样性指标之间关联的建模结果（线性混合模型（Linear Mixed Model，LMM）输出）。
表S7：按垫料类型划分的使用组与未使用组样本的门水平差异丰度检验结果。
表S8：按垫料类型划分的使用组与未使用组样本的纲水平差异丰度检验结果。
表S9：按垫料类型划分的使用组与未使用组样本的属水平差异丰度检验结果。
表S10：本研究16S rRNA序列数据分析中纳入的潜在乳腺炎致病菌列表。
表S11：按垫料类型与垫料状态划分的携带潜在乳腺炎致病菌的属的计数占比。
表S12：按垫料类型划分的携带潜在乳腺炎致病菌的类群的属水平差异丰度检验结果（比较使用组与未使用组样本）。
表S13：模拟群落与阴性对照样本的读段计数及属水平计数占比。