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

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

doi:10.1186/s12866-018-1256-y

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

Abstract

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 »« less

Authors:: Kosina, Suzanne M.; Greiner, Annette M.; Lau, Rebecca K.; Jenkins, Stefan; Baran, Richard; Bowen, Benjamin P.; Northen, Trent R.

Publication Date:: Wed Sep 12 00:00:00 EDT 2018

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

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

OSTI Identifier:: 1618595

Alternate Identifier(s):: OSTI ID: 1477382

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: BMC Microbiology

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

Publisher:: Springer Science + Business Media

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    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 Kingdom: N. p., 2018. 
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 Kingdom.  https://doi.org/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. Wed .  
"Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes".  United Kingdom.  https://doi.org/10.1186/s12866-018-1256-y.

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@article{osti_1618595,

  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 Kingdom},

  year         = {Wed Sep 12 00:00:00 EDT 2018},

  month        = {Wed Sep 12 00:00:00 EDT 2018}

}

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Additional file 1: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
figure, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 PDF file (1.56 MB)
DOI: 10.6084/m9.figshare.7081916
This figure is a supplement to the current record

Additional file 1: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
figure, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 PDF file (1.56 MB)
DOI: 10.6084/m9.figshare.7081916.v1
This figure is a supplement to the current record

Additional file 2: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
preprint, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 PDF file (414.81 kB)
DOI: 10.6084/m9.figshare.7081928
This preprint is a supplement to the current record

Additional file 2: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
preprint, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 PDF file (414.81 kB)
DOI: 10.6084/m9.figshare.7081928.v1
This preprint is a supplement to the current record

Additional file 3: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
dataset, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 XLSX file (659.08 kB)
DOI: 10.6084/m9.figshare.7081940
This dataset is a supplement to the current record

Additional file 3: of Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes
dataset, September 2018

Kosina, Suzanne; Greiner, Annette; Lau, Rebecca
figshare-Supplementary information for journal article at DOI: 10.1186/s12866-018-1256-y, 1 XLSX file (659.08 kB)
DOI: 10.6084/m9.figshare.7081940.v1
This dataset is a supplement to the current record