摘要

       抗生素抗性基因 (ARG) 已成为医学和环境领域的全球首要问题之一。宏基因组分析已在 ARG 相关研究中广泛采用，揭示了 ARG 在从医疗环境到自然栖息地的各种环境中普遍存在，甚至在饮用水和古老的永久冻土中。凭借可访问的宏基因组数据集的巨大资源，构建抗生素抗性组的全球概况作为其系统发育和生态分布的指导将是可行和有益的。并且这些信息应该通过一个开放的网页共享，以避免不必要的数据处理重复和不兼容的搜索方式造成的偏见。结果 使用 ARG 在线分析平台的标准方法下载并分析了两个数据集集合，全基因组数据库（WGD，54,718 个完整和草拟的细菌基因组）和宏基因组数据库（MGD，7 个生态类型的 854 个宏基因组数据集）。 ARGs-OAP v1.0)。评估 WGD 和 MGD 的代表性以全面覆盖细菌基因组和宏基因组中的 ARG。此外，本研究开发了一个 ARGs 在线搜索平台（ARGs-OSP，http://args-osp.herokuapp.com/），使其他研究人员可以通过搜索和下载功能访问数据。最后，通过评估 1 类整合酶和总 ARG 在不同环境中的共存情况，证明了 ARG-OAP 的灵活使用。

       The antibiotic resistant genes (ARGs) have been emerging as one of the top global issue s in both medical and environmental fields. The metagenomic analysis has been widely adopted in ARG-related studies, revealing a universal presence of ARGs in diverse environments from medical settings to natural habitats, even in drinking water and ancient permafrost. With the tremendous resources of accessible metagenomic datasets, it would be feasible and beneficial to construct a global profile of antibiotic resistome as a guidance of its phylogenetic and ecological distribution. And such information should be shared by an open webpage to avoid the unnecessary repeat of data processing and the bias caused by incompatible search method. Results Two dataset collections, the Whole Genome Database (WGD, 54,718 complete and draft bacterial genomes) and the Metagenomic Database (MGD, 854 metagenomic datasets of 7 eco-types), were downloaded and analyzed using a standard method of ARG online analysis platform (ARGs-OAP v1.0). The representativeness of WGD and MGD was evaluated to have a comprehensive coverage of ARGs in bacterial genomes and metagenomes. Besides, an ARGs online searching platform (ARGs-OSP, http://args-osp.herokuapp.com/) was developed in this study to make the data accessible to other researchers via the search and download functionality. Finally, flexible usage of the ARGs-OAP was demonstrated by evaluating the co-occurrence of class 1 integrases and total ARGs across different environments. 

https://www.researchgate.net/publication/325570899_ARGs-OSP_online_searching_platform_for_antibiotic_resistance_genes_distribution_in_metagenomic_database_and_bacterial_whole_genome_database