MicroPhenoDB

MicroPhenoDB links metagenomic data, pathogenic microbes, microbial core genes, and human disease phenotypes through manually curated, integrated microbe–disease associations for studying microbial contributions to human disease.

Key Features:

• Extensive Data Integration: Contains 5,677 non-redundant associations between 1,781 microbes and 542 human disease phenotypes across over 22 human body sites.
• Core Gene Associations: Includes 696,934 connections between 27,277 unique clade-specific core genes and 685 microbes.
• Disease Phenotype Classification: Annotates disease phenotypes using the Experimental Factor Ontology (EFO).
• Prioritization Score Model: Ranks microbe–disease associations based on evidential metrics.
• Rapid Sequence Search: Provides a sequence search to identify pathogenic microbes in samples without requiring metagenomic assembly.

Scientific Applications:

• Metagenomic Data Analysis: Decoding microbial community composition and associations with disease phenotypes using curated association and core gene data.
• Pathogen Discovery: Rapid identification of potential pathogens in metagenomic samples via sequence search and association evidence.
• Genetic Research: Linking clade-specific core genes to microbes and disease phenotypes to investigate microbial pathogenic mechanisms.
• Clinical Studies: Supporting exploration of microbial contributions to human disease for diagnostic and therapeutic research.

Methodology:

Manual curation of microbe–disease association data, Experimental Factor Ontology (EFO) classification of phenotypes, and a prioritization score model based on evidential metrics.