What is MiMeDB?

The Microbial Metabolites Database (MiMeDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human microbiome. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain and link metabolite data, microbe data, host data, health and bioactivity data, and exposure data. Many data fields in the database are hyperlinked to other databases (FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, and GenBank). The Microbial Metabolites Database supports extensive text, sequence, spectral, chemical structure and relational query searches.

MiMeDB (The Human Microbial Metabolome Database) is a freely available, web-enabled database containing detailed information about the small molecules produced by the human microbiome. Many microbially produced chemicals play important roles in human health and disease with some (such as butyric acid) offering protection against inflammation and cancer and others (such as indoxyl sulfate) causing damage to the kidneys, heart and brain. While all microbes synthesize primary metabolites required for their own survival, they also produce a variety of exotic compounds arising from their ability to grow on many unusual substrates or host-derived food sources. For instance, many of the metabolites produced by human microbes arise from the transformation of xenobiotics arising from human consumption such as food constituents, food additives, phytochemicals, drugs, cosmetics and other exogenous or man-made chemicals. Microbes also chemically transform many host-produced (human) metabolites as well as previously host-transformed (phase I and phase II) xenobiotics. As a result, the human microbiome is believed to produce or process >55,000 different compounds – many of which affect human health, behavior and disease.

MiMeDB not only houses metabolite data (structure, names, descriptions, chemical taxonomy, chemical ontology, physico-chemical data, spectra, etc.), it also contains detailed information about the microbes that produce these chemicals, the enzymatic reactions responsible for their production (substrates and products), the bioactivity of the chemicals and even the anatomical location of these chemicals (and microbes).

MiMeDB classifies metabolites as co-host, host or microbial metabolites. This determination is made by an analysis of the chemical reactions (including the mediating enzymes and spontaneous reactions) that lead to that chemical. A microbial-only metabolite is a metabolite that can only be produced by microbial enzymes or microbially-mediated reactions. To qualify as such there must be no evidence that the metabolite has an origin other than via a microbe. A microbial-host co-metabolite is a chemical that arises from a combination of human and microbial metabolism as determined by its reaction sequence, the enzymes involved or reaction origins. In other words, the chemical must arise from at least one microbial-specific reaction with a microbial enzyme and at least one human-specific reaction with a human enzyme. A host metabolite includes items coming from what the host consumes or absorbs (if it is a food, drug, cosmetic or other synthetic compound). A host metabolite could also include a chemical that arises from human-only enzymes or human enzyme reactions.

MiMeDB also contains the food, physiological or environmental sources of many of the identified substrate chemicals, the microbial proteins and genes that catalyze the reactions, detailed genetic maps of the responsible microbes, extensive microbial taxonomy data, as well as the health effects and human protein targets that these microbial metabolites act upon. In this regard MiMeDB is a unique, multi-omic database that brings extensive information together about the human microbiome, the metabolome (human and microbial), the proteome (human and microbial) and the genome (microbial). MiMeDB offers a variety of wide variety of browsing, searching, relational querying and viewing options as well as interactive network visualization tools that allow users to explore this complex multi-omic, multi-organism universe. MiMeDB is extensively linked to other databases including FooDB, HMDB, KEGG, PubChem, MetaCyc, ChEBI, UniProt, NCBI Taxonomy, BacMap, VMH, GenBank and ChemFOnt.

MiMeDB Content and Structure

Metabolite-Specific Data Fields

Data Field NameNumber of SubfieldsSubfield Types
Record Information5Version, status, creation date, update, MiMeDB ID
Metabolite Information 12Common name, structure, synonyms, chemical formula, average and monoisotopic molecular weight, IUPAC name, Traditional name, CAS registry number, SMILES, InChi Identifier, InChi key
Chemical Taxonomy 10Description, Kingdom, Superclass, Class, Subclass, Direct Parent, Alternative parents, Substituents, Molecular Framework, External descriptors
Ontology4Physiological effects, Disposition, Process, Role
Physical Properties2State, Predicted Properties
Spectra4Spectrum type, Description, Splash Key, Deposition Date and view
Biological Properties 4Cellular Locations, Tissue Locations, Biospecimen Locations, Associated Online Mendelian Inheritance in Man (OMIM) IDs
Human Proteins and Enzymes 2 Name, UniProt ID
Human Pathways 3Name, SMPDB/PathBank, KEGG
Metabolic Reactions 7Reaction ID, Precursor, Product, Enzyme, Reaction Type, Data Source, Reference
Health Effect and Bioactivity 8Health Outcome/Bioactivity, Metabolite Response/Effect, Related Health Condition, Evidence Type, Meaured in Matrix, Data Source, Reference, Details
Microbial Sources 5Kingdom, Phylum, Total Species, Hosts and Body Sites, Microbial Links
Exposure Sources 6Source Type, Source Sub-type, Species, Data Source, Reference, Details
External Links 15IDs from HMDB, DrugBank, Phenol Explorer, FooDB, KNapSAck, ChemSpider, KEGG, BioCyc, BiGG, Wikipedia, METLIN, PubChem, PDB, ChEBI, Food Biomarker Ontology
References 3Synthesis References, Material Data Safety Sheet, General References

Microb-Specific Data Fields

Data Field NameNumber of SubfieldsSubfield Types
Microbe Identification2Microbe Name, National Center for Biotechnology Information (NCBI) Taxonomy ID
Microbe Taxonomy9Superkingdom, Kingdom, Phylum, Class, Order, Family, Genus, Species, Strain
Microbe Properties14Gram Staining Properties, Shape, Mobility, Flagellar presence, Number of Membranes, Oxygen Requirements, Optimal Temperature, Temperature Range, Habitat, Biotic Relationship, Cell Arrangement, Sporulation, Metabolism, Energy Source
Host and Biospecimens 6Host, Body Site, Biospecimen, Details, Data Source, References
Health Effects 6Host, Related Health Condition, Biospecimen, Microbial Response/Effect, Data Source, References
Related Metabolites 6Structure, Metabolite, Class, Microbial Link, Data Source, Reference
Metabolic Reactions 8Reaction Identifier, Precursor Molecule, Product Molecule, Enzyme, Enzyme’s Source Organism, Reaction Type, Data source, References
Genome Data 1Link to Genome Page
Source Links 3NCBI Taxonomy, NCBI Genome, BacMap

The Microbiome Metabolome Database is freely available to all via the web, it does not require any login or registration and is not password-protected. All protein sequence data and chemical structures contained in the database are already available in the respective public databases.

Citing the Microbiome Metabolome Database

  1. Wishart DS, Oler E, Peters H, Guo A, Girod S, Han S, Saha S, Lui VW, LeVatte M, Gautam V, Kaddurah-Daouk R, Karu N. MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res. 2023 Jan 6;51(D1):D611-D620. PMID: 36215042

MiMeDB Tutorial