Additional file 7 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

Additional file 7: Table S7. Count software analysis of the 15 taxonomic classes (A) and list of the most influential KOs (B) identified by the principal coordinate analysis presented in Fig. 2B. A: From left to right: the KO id, the number of gains and expansions for the given ortholog (overall) and their the sum, the gains and expansions in RefSeq genomes, the gains and expansions in fecal MAGs and the taxonomic class the analysis was conducted for. In the last two columns, the overall gene losses and contractions are presented as well but are grayed out on account of not examining them because we used MAGs. On the smaller subtable to the right, we present the KOs that were identified multiple times in the independent Count analyses (we performed 15 analyses one for each class that we built a phylogeny). B: From left to right: the KO id, the coordinates and the contribution of each feature based on which we selected the top twenty (as most influential) to present in Fig. 2. For the top hundred most influential vectors (a.k.a. features) we present the KO description as well. Bold font indicates features that were identified both in the Count analysis for the Bacteroidia, Clostridia or Spirochaetia classes and among the top 100 most influential features in the PCoA analysis.

补充文件7：表S7。涵盖两项内容：(A) 15个分类类群的Count软件分析结果，(B) 图2B所示主坐标分析（Principal Coordinate Analysis, PCoA）鉴定得到的最具影响力KOs（KEGG同源基因簇，KEGG Orthologs）列表。
A部分：从左至右依次为：KO编号、给定同源基因的总获得与扩增数量及其总和、RefSeq参考序列数据库（Reference Sequence Database）基因组中的获得与扩增数量、粪便宏基因组组装基因组（Metagenome-Assembled Genomes, MAGs）中的获得与扩增数量，以及本次分析对应的分类类群。最后两列同时列出了总基因丢失与收缩情况，但因本研究仅采用MAGs开展分析，未对该类指标进行分析，故以灰色标注。右侧的小型子表展示了在独立Count分析中重复鉴定到的KOs：我们针对每个构建了系统发育树的类群各开展一次分析，共计完成15次独立分析。
B部分：从左至右依次为：KO编号、各特征的坐标及贡献值，基于上述指标我们选取了排名前20的特征（即最具影响力的特征）用于图2的展示。对于排名前100的最具影响力向量（亦称特征），我们同时补充了KO的功能描述。加粗字体表示同时满足以下两类条件的特征：一是在拟杆菌纲（Bacteroidia）、梭菌纲（Clostridia）或螺旋体纲（Spirochaetia）的Count分析中鉴定得到的特征，二是PCoA分析中排名前100的最具影响力特征。