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

doi:10.1186/s12866-018-1256-y

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

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 datasetsmore »

Authors:

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]

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

Publication Date:: 2018-09-12

Grant/Contract Number:: AC02-05CH11231

Type:: Accepted Manuscript

Journal Name:: BMC Microbiology

Additional Journal Information:: Journal Volume: 18; Journal Issue: 1; Journal ID: ISSN 1471-2180

Publisher:: BioMed Central

Research Org:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Country of Publication:: United States

Language:: English

OSTI Identifier:: 1477382


                    Kosina, Suzanne M., Greiner, Annette M., Lau, Rebecca K., Jenkins, Stefan, Baran, Richard, Bowen, Benjamin P., and Northen, Trent R.. Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.  United States: N. p.,  
        Web.  doi:10.1186/s12866-018-1256-y.

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                    Kosina, Suzanne M., Greiner, Annette M., Lau, Rebecca K., Jenkins, Stefan, Baran, Richard, Bowen, Benjamin P., & Northen, Trent R.. Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.  United States.  doi:10.1186/s12866-018-1256-y.

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                    Kosina, Suzanne M., Greiner, Annette M., Lau, Rebecca K., Jenkins, Stefan, Baran, Richard, Bowen, Benjamin P., and Northen, Trent R.. 2018.  
        "Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes".  United States.  
        doi:10.1186/s12866-018-1256-y.  https://www.osti.gov/servlets/purl/1477382.

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@article{osti_1477382,

  title        = {Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes},

  author       = {Kosina, Suzanne M. and Greiner, Annette M. and Lau, Rebecca K. and Jenkins, Stefan and Baran, Richard and Bowen, Benjamin P. and Northen, Trent R.},

  abstractNote = {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.},

  doi          = {10.1186/s12866-018-1256-y},

  journal      = {BMC Microbiology},

  number       = 1,

  volume       = 18,

  place        = {United States},

  year         = {2018},

  month        = {9}

}

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Free Publicly Accessible Full Text
Accepted Manuscript (DOE)
Publisher's Version of Record
10.1186/s12866-018-1256-y
https://doi.org/10.1186/s12866-018-1256-y

Works referenced in this record:

Engineering microbial consortia: a new frontier in synthetic biology
journal, September 2008

Brenner, Katie; You, Lingchong; Arnold, Frances H.
Trends in Biotechnology, Vol. 26, Issue 9, p. 483-489
DOI: 10.1016/j.tibtech.2008.05.004

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

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