MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes

Guocai Yao,Wenliang Zhang,Minglei Yang,Huan Yang,Jianbo Wang,Haiyue Zhang,Lai Wei,Zhi Xie,Weizhong Li

doi:10.1016/j.gpb.2020.11.001

Guocai Yao, Wenliang Zhang + Show 7 more

Open Access

https://doi.org/10.1016/j.gpb.2020.11.001

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Abstract

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.

Highlights

The human body feeds a large number of microbes, mainly composed of bacteria, followed by archaea, fungi, viruses, and protozoa
We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data
We collected and curated the microbedisease associations from the Infectious Diseases Society of America (IDSA) guideline [22], the National Cancer Institute (NCI) Thesaurus OBO Edition (NCIT) [23], and the Human Microbe-Disease Association Database (HMDAD) [18] and Disbiome [19] databases, and connected microbial core genes derived from the MetaPhlAn2 dataset [24] to pathogenic microbes and human diseases

Summary

Introduction

The human body feeds a large number of microbes, mainly composed of bacteria, followed by archaea, fungi, viruses, and protozoa. These computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We collected and curated the microbedisease associations from the IDSA guideline [22], the National Cancer Institute (NCI) Thesaurus OBO Edition (NCIT) [23], and the HMDAD [18] and Disbiome [19] databases, and connected microbial core genes derived from the MetaPhlAn2 dataset [24] to pathogenic microbes and human diseases.

Results

Conclusion