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:: 2018-09-12

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.

Copy to clipboard


                    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

Copy to clipboard


                    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.

Copy to clipboard


                    
@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         = {2018},

  month        = {9}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1186/s12866-018-1256-y

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 12 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

Metabolite profiling: from diagnostics to systems biology
journal, September 2004

Fernie, Alisdair R.; Trethewey, Richard N.; Krotzky, Arno J.
Nature Reviews Molecular Cell Biology, Vol. 5, Issue 9
DOI: 10.1038/nrm1451

Exometabolite niche partitioning among sympatric soil bacteria
journal, September 2015

Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine
Nature Communications, Vol. 6, Issue 1
DOI: 10.1038/ncomms9289

Geomicrobiology beyond Earth: microbe–mineral interactions in space exploration and settlement
journal, July 2010

Cockell, Charles S.
Trends in Microbiology, Vol. 18, Issue 7
DOI: 10.1016/j.tim.2010.03.005

Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach
journal, January 2014

Zha, Ying; Westerhuis, Johan A.; Muilwijk, Bas
BMC Biotechnology, Vol. 14, Issue 1
DOI: 10.1186/1472-6750-14-22

Metabolic Footprinting for the Study of Microbial Biodiversity
journal, May 2009

Pope, G. A.; MacKenzie, D. A.; Defernez, M.
Cold Spring Harbor Protocols, Vol. 2009, Issue 5
DOI: 10.1101/pdb.prot5222

Microbial syntrophy: interaction for the common good
journal, May 2013

Morris, Brandon E. L.; Henneberger, Ruth; Huber, Harald
FEMS Microbiology Reviews, Vol. 37, Issue 3
DOI: 10.1111/1574-6976.12019

Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms
journal, January 2012

Paczia, Nicole; Nilgen, Anke; Lehmann, Tobias
Microbial Cell Factories, Vol. 11, Issue 1
DOI: 10.1186/1475-2859-11-122

Sex-specific mating pheromones in the nematode Panagrellus redivivus
journal, December 2012

Choe, A.; Chuman, T.; von Reuss, S. H.
Proceedings of the National Academy of Sciences, Vol. 109, Issue 51
DOI: 10.1073/pnas.1218302109

Current and emerging mass-spectrometry technologies for metabolomics
journal, March 2008

Bedair, Mohamed; Sumner, Lloyd W.
TrAC Trends in Analytical Chemistry, Vol. 27, Issue 3
DOI: 10.1016/j.trac.2008.01.006

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

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism
journal, February 2016

Kosina, Suzanne M.; Danielewicz, Megan A.; Mohammed, Mujahid
ACS Synthetic Biology, Vol. 5, Issue 7
DOI: 10.1021/acssynbio.5b00236

Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology
journal, September 2008

Mapelli, Valeria; Olsson, Lisbeth; Nielsen, Jens
Trends in Biotechnology, Vol. 26, Issue 9
DOI: 10.1016/j.tibtech.2008.05.008

Dynamic substrate preferences predict metabolic properties of a simple microbial consortium
journal, January 2017

Erbilgin, Onur; Bowen, Benjamin P.; Kosina, Suzanne M.
BMC Bioinformatics, Vol. 18, Issue 1
DOI: 10.1186/s12859-017-1478-2

Web-based resources for mass-spectrometry-based metabolomics: A user’s guide
journal, March 2009

Tohge, Takayuki; Fernie, Alisdair R.
Phytochemistry, Vol. 70, Issue 4
DOI: 10.1016/j.phytochem.2009.02.004

Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype
journal, October 2012

Baran, Richard; Bowen, Benjamin P.; Price, Morgan N.
ACS Chemical Biology, Vol. 8, Issue 1
DOI: 10.1021/cb300477w

Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)
journal, September 2007

Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave
Metabolomics, Vol. 3, Issue 3
DOI: 10.1007/s11306-007-0082-2

Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002
journal, January 2011

Baran, Richard; Bowen, Benjamin P.; Northen, Trent R.
Molecular BioSystems, Vol. 7, Issue 12
DOI: 10.1039/c1mb05196b

Metabolic footprinting and systems biology: the medium is the message
journal, June 2005

Kell, Douglas B.; Brown, Marie; Davey, Hazel M.
Nature Reviews Microbiology, Vol. 3, Issue 7
DOI: 10.1038/nrmicro1177

IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
Nucleic Acids Research, Vol. 40, Issue D1
DOI: 10.1093/nar/gkr1044

Elucidating the microbial resuscitation cascade in biological soil crusts following a simulated rain event: Microbial resuscitation in biological soil crusts
journal, May 2013

Angel, Roey; Conrad, Ralf
Environmental Microbiology
DOI: 10.1111/1462-2920.12140

Capturing atmospheric carbon: biological and nonbiological methods
journal, October 2013

Nogia, Panchsheela; Sidhu, Gurpreet Kaur; Mehrotra, Rajesh
International Journal of Low-Carbon Technologies, Vol. 11, Issue 2
DOI: 10.1093/ijlct/ctt077

High-throughput classification of yeast mutants for functional genomics using metabolic footprinting
journal, May 2003

Allen, Jess; Davey, Hazel M.; Broadhurst, David
Nature Biotechnology, Vol. 21, Issue 6
DOI: 10.1038/nbt823

Metabolomics: the apogee of the omics trilogy
journal, March 2012

Patti, Gary J.; Yanes, Oscar; Siuzdak, Gary
Nature Reviews Molecular Cell Biology, Vol. 13, Issue 4
DOI: 10.1038/nrm3314

Works referencing / citing this record:

Tools and resources for metabolomics research community: A 2017-2018 update
journal, November 2018

Misra, Biswapriya B.; Mohapatra, Subhashree
ELECTROPHORESIS, Vol. 40, Issue 2
DOI: 10.1002/elps.201800428

The microbial exometabolome: ecological resource and architect of microbial communities
journal, March 2020

Douglas, Angela E.
Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 375, Issue 1798
DOI: 10.1098/rstb.2019.0250

Similar Records in DOE PAGES and OSTI.GOV collections:

Designing Metabolic Division of Labor in Microbial Communities

Journal Article Thommes, Meghan ; Wang, Taiyao ; Zhao, Qi ; ... - mSystems

ABSTRACT Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A “gedanken” (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. Wemore »« less
Cited by 57
https://doi.org/10.1128/mSystems.00263-18
Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Journal Article Swenson, Tami L. ; Karaoz, Ulas ; Swenson, Joel M. ; ... - Nature Communications

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negativelymore »« less
Cited by 82
https://doi.org/10.1038/s41467-017-02356-9

Full Text Available
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data

Journal Article Ponsero, Alise J. ; Bomhoff, Matthew ; Blumberg, Kai ; ... - Nucleic Acids Research

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each ‘omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same samplemore »« less
https://doi.org/10.1093/nar/gkaa637

Full Text Available
Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

Technical Report Orphan, Victoria Jeanne

Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions betweenmore »« less
https://doi.org/10.2172/1164471

Full Text Available
Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

Technical Report Baliga, Nitin S

Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks.more »« less
https://doi.org/10.2172/1014987

Full Text Available

Other research related to this 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
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