FoodGenVir database

The foodGenVir database contains those MAGs obtained from food and food-related environments samples that were collected in the MASTER project and that harbored antimicrobial resistance (AMR) genes. In total, 1828 samples from food and food-producing environments that were successfully sequenced in MASTER and included in the analyses, which lead to 14,815 high-quality MAGs. The high-quality MAGs were recovered from the metagenomic samples by following the assembly-based pipeline described in Pasolli et al. (2019). The taxonomic assignment of these MAGs was performed by using phylophlan_metagenomics against the MetaRefSGB. The resulting MAGs were screened for AMR genes using the TORMES pipeline (Quijada et al., 2019) against the ResFinder database (Zankari et al., 2012; downloaded at version from 24/10/2022). In total, 928 MAGs harbored AMR genes. The current release contains the assembled-genome FASTA files from the AMR-carrying MAGs and a MASTER_MAGs_FGV.tsv table, that contains the taxonomic information of each MAG as well as the different AMR genes found in its genome and the antimicrobial compounds that those genes confer resistance to according to the ResFinder database.foodGenVir数据库收录了MASTER项目采集自食品及食品相关环境样本的宏基因组组装基因组（Metagenome-Assembled Genomes，MAGs），此类MAGs均携带抗菌药物耐药（Antimicrobial Resistance，AMR）基因。MASTER项目中共完成1828份食品及食品生产环境样本的测序并纳入分析，最终得到14815条高质量MAGs。 上述高质量MAGs通过Pasolli等（2019）报道的基于组装的分析流程，从宏基因组样本中组装获得。采用phylophlan_metagenomics工具对照MetaRefSGB数据库完成MAGs的分类学注释。随后借助TORMES分析流程（Quijada等，2019），对照ResFinder数据库（Zankari等，2012；2022年10月24日下载的版本）对所得MAGs开展抗菌耐药基因筛查。 最终共有928条MAGs携带抗菌耐药基因。 本版数据库包含携带AMR基因的MAGs的组装基因组FASTA格式文件，以及MASTER_MAGs_FGV.tsv表格；该表格记录了每条MAG的分类学信息、其基因组中检出的各类AMR基因，以及依据ResFinder数据库，这些基因所对应的耐药抗菌化合物类型。