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MiMeDB 2.0: the Human Microbial Metabolome Database for 2026.
Ray Kruger1, Eponine Oler1, Sukanta Saha1,2
1Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.
Nucleic Acids Research
|November 22, 2025
Summary
The updated Microbial Metabolome Database (MiMeDB 2.0) now links millions of microbial genes and metabolites to human health and disease. This enhanced resource aids microbiome research with improved data and visualization tools.
Area of Science:
- Microbiome Research
- Metabolomics
- Bioinformatics
Background:
- The human microbiome plays a crucial role in health, disease, and diet.
- Understanding microbial metabolites is key to deciphering host-microbe interactions.
- Previous versions of the Microbial Metabolome Database (MiMeDB) provided foundational data.
Purpose of the Study:
- To present the substantial expansion and redesign of the Microbial Metabolome Database (MiMeDB 2.0).
- To enhance the resource's comprehensiveness, usability, and visualization capabilities for microbiome research.
- To facilitate the investigation of microbial metabolites and their impact on human health, diet, and disease.
Main Methods:
- Systematic addition of millions of annotated microbial genes and pathways.
- Incorporation of thousands of new metabolites and expanded pathway/reaction coverage.
- Broader representation of eukaryotic gut microbes and inclusion of extensive metabolite spectral data.
Main Results:
- MiMeDB 2.0 contains over 12.9 million microbial genes, 23.1 million pathways, 29,295 metabolites, and 21,829 reactions.
- The database now includes 3,725 microbial species/strains and over 514,000 metabolite spectra.
- New features include enhanced search filters, species-specific queries, and redesigned visualization tools.
Conclusions:
- MiMeDB 2.0 is a significantly expanded and user-friendly platform for molecular-level microbiome investigation.
- The database strengthens metabolite identification and discovery through improved spectral data and search functionalities.
- This resource supports comprehensive exploration of microbial roles in human health, diet, and disease.
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