Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.
研究问题：宏基因组数据与病原微生物、微生物核心基因和疾病表型关联与量化，以及构建关联关系的数据库平台。研究方法：研究人员通过人工编审和计算方法系统整理集成病原微生物、微生物核心基因和人类疾病表型的关联数据，以及毒力因子基因和抗生素耐药性基因的相关信息；通过赋予不同研究证据的不同权重优化评分模型，以量化微生物与人类疾病的相关性。主要成果1：对微生物-疾病表型关联性的数据集进行整合和标准化注释，获得人类疾病表型与微生物关联性的高质量数据集。主要成果2：通过改进评分模型对微生物-疾病关联进行定量描述，以科学的量化分值评估微生物与疾病表型关联性强弱。主要成果3：数据库平台提供用户友好界面和API网络应用，以完成在线数据浏览、搜索和可视化分析服务，其序列检索能够快速识别宏基因组样品中存在的病原微生物，避免了宏基因组数据常规处理的繁杂步骤。主要成果4：利用MicroPhenoDB提供的数据和分析工具，作者完成了多个微生物与疾病表型相关的数据分析案例。数据库链接 http://www.liwzlab.cn/microphenodb 和http://lilab2.sysu.edu.cn/microphenodb





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