MiMeDB

MiMeDB integrates curated multi-omic data linking microbes, microbial genomes, microbial metabolites, biochemical reactions, mass spectrometry and NMR spectra, and exposome sources to support investigation of microbiome-associated metabolism and human health.

Key Features:

• Multi-Omic Integration: Links microbial taxa, genomic sequences, proteomic data, and metabolic profiles to enable systems-level analysis.
• Extensive Data Coverage: Contains data for 1,904 microbes (bacteria and fungi), 24,254 metabolites or exposure chemicals, and 22,054 biochemical reactions.
• Spectral Data: Includes over 648,861 mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectra.
• Genomic Content: Aggregates genomic data comprising approximately 6.4 million genes and 7.6 billion DNA bases.
• Search and Query Types: Supports text, sequence, spectral, chemical structure, and relational queries for analytical interrogation.
• Health and Bioactivity Data: Records 626 health effects or bioactivities, biosample concentrations, and associated human protein targets.
• Exposome Connections: Links metabolites to primary exposome sources including food, drugs, cosmetics, and pollutants.
• Cross-References: Provides cross-links to FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank.

Scientific Applications:

• Microbiome research: Enables mapping of microbial metabolites to taxa and genomes to study microbial contributions to human physiology and disease.
• Metabolomics and biomarker discovery: Supports identification and characterization of metabolite biomarkers using MS and NMR spectral data.
• Systems biology: Facilitates integration of genomic, proteomic, and metabolic data to model microbial metabolic pathways and interactions.
• Exposome studies: Allows investigation of links between environmental exposures (food, drugs, cosmetics, pollutants) and microbial metabolic outputs.

Methodology:

Constructed through meticulous curation and linkage of diverse datasets, with each entry supported by 3,112 literature references.