Dataset 2: Read count tables

The read count table was first processed by dividing all counts with two, since mapping was performed as proper pairs (mapping of a forward and reverse read), this is referred to as the raw count table (see item A). The raw count table was normalized according to genome size for each microorganism, followed by total sum scaling. The resulting table is referred to as the count table (see item B and C). The microorganisms listed in the tables were aggregated to genus level. For the antimicrobial resistome analysis, raw read counts are provided for all genes divided by two (see item D) and normalized according to the total bacterial reads per sample (mapping to the databases: bacteria, bacteria_draft and HumanMicrobiome) as fragments per kilo base reference per million bacterial fragments (FPKM) (see item E). The FPKM table was also aggregated to resistance against antimicrobial classes (see item F), and the class-level information for each AMR-genes are available as see item G.本数据集的读长计数表（read count table）首先经过如下处理：由于比对阶段采用成对比对策略（即正反向读段的配对比对），需将所有计数结果除以2，处理后的数据即为原始计数表（详见条目A）。随后，针对每种微生物，基于其基因组大小对原始计数表进行归一化处理，再执行总求和缩放，最终得到的计数表详见条目B与条目C。表格中收录的微生物已被聚合至属水平。针对抗菌耐药组（antimicrobial resistome）分析，本研究提供了所有基因的原始读长计数数据，且已将其除以2（详见条目D）；随后以每个样本中总细菌读段（比对至细菌、细菌草图及人类微生物组数据库的读段）为基准，将其归一化为每千碱基参考序列每百万细菌片段数（FPKM, Fragments Per Kilobase of reference per Million bacterial fragments），详见条目E。该FPKM计数表还被聚合至抗菌药物类别抗性层面，且各抗微生物耐药（AMR, Antimicrobial Resistance）基因的类别级信息详见条目G。