16S Microbiome Assessment in Pneumonic Calves from a farm in BC Canada

The primary goal of the study was to determine differences between the microbiomes of healthy (HLT), pneumonic (POS), and previously pneumonic (PRV) calves from a single dairy farm dealing with a high prevalence of Mycoplasmopsis bovis. 16S rRNA sequencing was completed by Norgen Biotek Corp. on the Illumina MiSeq platform. All fastq sequences generated are accessible on NCBI's Sequence Read Archive repository under the BioProject accession number PRJNA1389668. Amplicon sequence variants (ASVs) were constructed using DADA2 in QIIME2. Taxonomic classification was completed using the SILVA v138 reference database. Subsequent analyses were completed in R Statistics. This dataset includes the sample metadata (Supplementary Table 1), relative abundance distribution across genera and species (Supplementary Table 2), the differential abundance results from the ANCOM-BC2 analysis using the ANCOMBC v1.2.8 R package (Supplementary Table 3), and the taxa-taxa correlation results from the SECOM analysis which was also implemented in the ANCOMBC R package (Supplementary Table 4). Our study focused on Mycoplasmopsis bovis (M. bovis) abundance in pneumonic calves. Briefly, we found that M. bovis was more associated with the loss of commensal taxa that were enriched in healthy animals and was significantly enriched in pneumonia positive animals. Overall, these findings suggest that M. bovis is associated with dysbiosis within the respiratory microbiota and may influence BRD pathogenesis. ANCOM-BC2 data displays the log2 fold change, p-value, and BH-adjusted q-value as well as other differential abundance metrics for each comparison. For clinical group comparisons, healthy animals were the reference. SECOM data outlines the taxa-taxa abundance correlations for each taxa among the dataset. Both nonlinear (distance) and linear (Pearson) correlation was calculated and the associated BH-adjusted p-value.本研究的核心目标为明确某牛支原体（Mycoplasmopsis bovis）流行率较高的奶牛场中，健康（HLT）、患肺炎（POS）及既往患肺炎（PRV）犊牛的微生物组差异。16S rRNA测序由Norgen Biotek公司在Illumina MiSeq平台上完成。所有生成的fastq序列可在NCBI序列读取档案（Sequence Read Archive）数据库中获取，对应的BioProject收录号为PRJNA1389668。扩增子序列变异体（Amplicon sequence variants, ASVs）通过QIIME2中的DADA2工具构建得到。分类学注释采用SILVA v138参考数据库完成。后续分析均基于R统计软件开展。本数据集包含样本元数据（补充表1）、属及种水平的相对丰度分布（补充表2）、采用ANCOMBC v1.2.8 R包进行ANCOM-BC2分析得到的差异丰度结果（补充表3），以及基于ANCOMBC R包实现的SECOM分析得到的分类群间相关性结果（补充表4）。 本研究聚焦于患肺炎犊牛中的牛支原体（Mycoplasmopsis bovis, M. bovis）丰度。简言之，本研究发现牛支原体与健康动物中富集的共生分类群的丢失显著相关，且在肺炎阳性犊牛体内丰度显著升高。综上，上述结果表明牛支原体与呼吸道微生物群失调存在关联，或可影响牛呼吸道疾病（Bovine Respiratory Disease, BRD）的发病机制。 ANCOM-BC2数据包含各比较组的log2倍变化值、p值、BH校正q值及其他差异丰度统计指标。在临床分组比较中，以健康动物作为参照组。 SECOM数据概述了本数据集内各分类群间的丰度相关性。本研究计算了非线性（距离）及线性（Pearson）相关性，并给出了对应的BH校正p值。