ECMDB: the E-coli Metabolome Database
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The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ∼1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry.
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The gut microbiota contributes metabolites to the human metabolome.
“The importance of the gut microbiota in contributing metabolites to the human metabolome has also recently emerged (50,66).”
From The food metabolome: a window over dietary exposure (2014) · cites this paper as [66]
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- Authors
- Guo, A. C., Jewison, T., Wilson, M., Liu, Y., Knox, C., Djoumbou, Y., Lo, P., Mandal, R., Krishnamurthy, R., & Wishart, D. S.
- Affiliations
- University of Alberta (CA)
- Corresponding author
- Wishart, David S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-10-29
- Volume
- 41
- Issue
- D1
- Pages
- D625-D630
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3531117
- OpenAlex
- W2139138803
- Cited by
- 164
- References
- 34
- Citations by year
- 2026: 6 · 2025: 11 · 2024: 6 · 2023: 14 · 2022: 10 · 2021: 15 · 2020: 10 · 2019: 12 · 2018: 19 · 2017: 15 · 2016: 14 · 2015: 10 · 2014: 11 · 2013: 8 · 2012: 2
- FWCI
- 3.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- NPARC (submittedVersion)
- Funders
- Genome Canada
- Genome Alberta
- Canadian Institutes of Health Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- Escherichia coli, metabolomics, metabolite annotation, intracellular metabolite concentrations, metabolic pathways, metabolic reactions
- MeSH terms
- Internet, Escherichia coli Proteins, Databases, Genetic, Escherichia coli K12, Metabolome
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