I found several databases but none of them matched the search I want to perform. I have a couple of metabolites which I would like to look up and see if they are associated with certain bacteria that may be part of the microbiota.
Dr. David Wishart presented MiMeDB - Microbiome Metabolome Database (at November 2021 Nature Conference "Reshaping Microbiome through Nutrition). The release of the database was planned for January 2022: if you'll stay tuned with the Metabolomics Innovation Centre (LinkedIn), you'll know when it is launched. It is anticipated to have an integrated microbiome, metabolome and diet data.
In the meantime, HMDB database includes many subdatabases of metabolites (including microbial in origin). ECMDB, PAMDB, YMDB and FooDB may be helpful. Check https://www.metabolomicscentre.ca/software for all databases.
Hello Lorenzo, I think that this is very challenging thing for many of us. For me was very helpful this Review: Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K., & Dorrestein, P. C. (2021). Mass spectrometry-based metabolomics in microbiome investigations. Nature Reviews Microbiology, 1-18.
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