Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes

Journal Article · 11 September 2018 · BMC Microbiology

DOI: https://doi.org/10.1186/s12866-018-1256-y · OSTI ID:1477382

Kosina, Suzanne M. ^[1]; Greiner, Annette M. ^[1]; Lau, Rebecca K. ^[2]; Jenkins, Stefan ^[1]; Baran, Richard ^[1]; Bowen, Benjamin P. ^[2]; Northen, Trent R. ^[2]

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1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Background: As microbiome research becomes increasingly prevalent in the fields of human health, agriculture and biotechnology, there exists a need for a resource to better link organisms and environmental chemistries. Exometabolomics experiments now provide assertions of the metabolites present within specific environments and how the production and depletion of metabolites is linked to specific microbes. This information could be broadly useful, from comparing metabolites across environments, to predicting competition and exchange of metabolites between microbes, and to designing stable microbial consortia. Here, we introduce Web of Microbes (WoM; freely available at: http://webofmicrobes.org), the first exometabolomics data repository and visualization tool. Description: WoM provides manually curated, direct biochemical observations on the changes to metabolites in an environment after exposure to microorganisms. The web interface displays a number of key features: (1) the metabolites present in a control environment prior to inoculation or microbial activation, (2) heatmap-like displays showing metabolite increases or decreases resulting from microbial activities, (3) a metabolic web displaying the actions of multiple organisms on a specified metabolite pool, (4) metabolite interaction scores indicating an organism's interaction level with its environment, potential for metabolite exchange with other organisms and potential for competition with other organisms, and (5) downloadable datasets for integration with other types of -omics datasets. Conclusion: We anticipate that Web of Microbes will be a useful tool for the greater research community by making available manually curated exometabolomics results that can be used to improve genome annotations and aid in the interpretation and construction of microbial communities.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1477382
• Alternate ID(s): OSTI ID: 1618595
• Journal Information: BMC Microbiology, Journal Name: BMC Microbiology Journal Issue: 1 Vol. 18; ISSN 1471-2180
• Publisher: BioMed CentralCopyright Statement
• Country of Publication: United States
• Language: English