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.

微生物在人类健康和疾病中发挥着重要作用。微生物和宿主之间的相互作用是一种互惠关系，在很大程度上仍未得到充分探索。当前的计算资源缺乏手动和一致策划的数据来将宏基因组数据与病原微生物、微生物核心基因和疾病表型联系起来。我们通过手动管理和持续整合微生物-疾病关联来开发 MicroPhenoDB 数据库数据。MicroPhenoDB 提供了超过 22 个人体部位的 1781 种微生物和 542 种人类疾病表型之间的 5677 个非冗余关联。MicroPhenoDB 还提供了 27,277 个独特的进化枝特异性核心基因和 685 个微生物之间的 696,934 个关系。使用实验因素本体论 (EFO) 对疾病表型进行分类和描述。开发了一种改进的评分模型，以根据证据指标对关联进行优先级排序。MicroPhenoDB 中的序列搜索选项可以快速识别样本中现有的病原微生物，而无需运行通常的宏基因组数据处理和组装。MicroPhenoDB 通过用户友好的 Web 界面和 Web 服务应用程序编程界面提供数据浏览、搜索和可视化。MicroPhenoDB 是第一个详细描述病原微生物、核心基因和疾病表型之间关系的数据库平台。它将加速宏基因组数据分析并协助研究解码与人类疾病相关的微生物。MicroPhenoDB 可通过 http://www.liwzlab.cn/microphenodb 和 http://lilab2.sysu.edu.cn/microphenodb 获得。