Metagenomic data sets from diverse environments have been growing rapidly. To ensure accessibility and reusability, tools that quickly and informatively correlate new microbiomes with existing ones are in demand. Here, we introduce Microbiome Search Engine 2 (MSE 2), a microbiome database platform for searching query microbiomes in the global metagenome data space based on the taxonomic or functional similarity of a whole microbiome to those in the database. MSE 2 consists of (i) a well-organized and regularly updated microbiome database that currently contains over 250,000 metagenomic shotgun and 16S rRNA gene amplicon samples associated with unified metadata collected from 798 studies, (ii) an enhanced search engine that enables real-time and fast (<0.5 s per query) searches against the entire database for best-matched microbiomes using overall taxonomic or functional profiles, and (iii) a Web-based graphical user interface for user-friendly searching, data browsing, and tutoring. MSE 2 is freely accessible via http://mse.ac.cn. For standalone searches of customized microbiome databases, the kernel of the MSE 2 search engine is provided at GitHub (https://github.com/qibebt-bioinfo/meta-storms).

中文翻译：

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微生物组搜索引擎2：用于在整个微生物组一级对全球微生物组进行分类和功能搜索的平台

来自不同环境的元基因组数据集正在迅速增长。为了确保可访问性和可重用性，需要将新微生物群落与现有微生物群落快速，信息丰富地关联的工具。在这里，我们介绍微生物组搜索引擎2（MSE 2），这是一个微生物组数据库平台，用于基于整个微生物组与数据库中微生物组的分类或功能相似性，在全球元基因组数据空间中搜索查询微生物组。MSE 2由（i）一个组织良好且定期更新的微生物组数据库组成，该数据库目前包含250,000多个宏基因组shot弹枪和16S rRNA基因扩增子样本，这些样本与从798个研究中收集的统一元数据相关；（ii）增强的搜索引擎，可实时进行且速度快（<0。每个查询5 s）使用整体分类或功能配置文件在整个数据库中搜索最匹配的微生物组，以及（iii）基于Web的图形用户界面，用于用户友好的搜索，数据浏览和辅导。可通过http://mse.ac.cn免费访问MSE 2。要独立搜索定制的微生物组数据库，请在GitHub（https://github.com/qibebt-bioinfo/meta-storms）中提供MSE 2搜索引擎的内核。