Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

doi:10.1186/s12859-017-1478-2

Title: Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

Authors:: Erbilgin, Onur; Bowen, Benjamin P.; Kosina, Suzanne M.; Jenkins, Stefan; Lau, Rebecca K.; Northen, Trent R.

Publication Date:: 2017-01-23

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

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

OSTI Identifier:: 1618529

Alternate Identifier(s):: OSTI ID: 1379688

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: BMC Bioinformatics

Additional Journal Information:: Journal Name: BMC Bioinformatics Journal Volume: 18 Journal Issue: 1; Journal ID: ISSN 1471-2105

Publisher:: Springer Science + Business Media

Country of Publication:: United Kingdom

Language:: English

Subject:: 60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Microbiology; Quantitative metabolomics; Substrate preferences; Predicting community function

Citation Formats


                    Erbilgin, Onur, Bowen, Benjamin P., Kosina, Suzanne M., Jenkins, Stefan, Lau, Rebecca K., and Northen, Trent R. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium.  United Kingdom: N. p., 2017. 
        Web.  doi:10.1186/s12859-017-1478-2.

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                    Erbilgin, Onur, Bowen, Benjamin P., Kosina, Suzanne M., Jenkins, Stefan, Lau, Rebecca K., & Northen, Trent R. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium.  United Kingdom.  doi:10.1186/s12859-017-1478-2.

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                    Erbilgin, Onur, Bowen, Benjamin P., Kosina, Suzanne M., Jenkins, Stefan, Lau, Rebecca K., and Northen, Trent R. Mon .  
        "Dynamic substrate preferences predict metabolic properties of a simple microbial consortium".  United Kingdom.  doi:10.1186/s12859-017-1478-2.

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@article{osti_1618529,

  title        = {Dynamic substrate preferences predict metabolic properties of a simple microbial consortium},

  author       = {Erbilgin, Onur and Bowen, Benjamin P. and Kosina, Suzanne M. and Jenkins, Stefan and Lau, Rebecca K. and Northen, Trent R.},

  abstractNote = {},

  doi          = {10.1186/s12859-017-1478-2},

  journal      = {BMC Bioinformatics},

  number       = 1,

  volume       = 18,

  place        = {United Kingdom},

  year         = {2017},

  month        = {1}

}

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DOI: 10.1186/s12859-017-1478-2

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Fig. 1: Modeling usage parameters. Example curve fitting to Behrends model (cyan). Blue square indicates the modeled T₅₀ parameter of the Behrends model, or inflection point of the curve, and the width parameter of the model is depicted by the green bar centered at T₅₀. The orange square represents themore »

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Works referenced in this record:

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

Bacillus subtilis Metabolism and Energetics in Carbon-Limited and Excess-Carbon Chemostat Culture
journal, December 2001

Dauner, M.; Storni, T.; Sauer, U.
Journal of Bacteriology, Vol. 183, Issue 24
DOI: 10.1128/JB.183.24.7308-7317.2001

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment
journal, August 2015

Silva, Leslie P.; Northen, Trent R.
Current Opinion in Biotechnology, Vol. 34
DOI: 10.1016/j.copbio.2015.03.015

Time-Resolved Metabolic Footprinting for Nonlinear Modeling of Bacterial Substrate Utilization
journal, February 2009

Behrends, V.; Ebbels, T. M. D.; Williams, H. D.
Applied and Environmental Microbiology, Vol. 75, Issue 8
DOI: 10.1128/AEM.01742-08

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

On r- and K-Selection
journal, November 1970

Pianka, Eric R.
The American Naturalist, Vol. 104, Issue 940
DOI: 10.1086/282697

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
journal, March 2010

Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent
Systematic Biology, Vol. 59, Issue 3
DOI: 10.1093/sysbio/syq010

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
journal, April 2000

Castresana, J.
Molecular Biology and Evolution, Vol. 17, Issue 4
DOI: 10.1093/oxfordjournals.molbev.a026334

Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment
journal, September 2010

Rojo, Fernando
FEMS Microbiology Reviews, Vol. 34, Issue 5
DOI: 10.1111/j.1574-6976.2010.00218.x

Update on the cometabolism of organic pollutants by bacteria
journal, July 2013

Nzila, Alexis
Environmental Pollution, Vol. 178
DOI: 10.1016/j.envpol.2013.03.042

Rapid and sensitive quantification of amino acids in soil extracts by capillary electrophoresis with laser-induced fluorescence
journal, April 2008

Warren, C.
Soil Biology and Biochemistry, Vol. 40, Issue 4
DOI: 10.1016/j.soilbio.2007.11.011

Understanding carbon catabolite repression in Escherichia coli using quantitative models
journal, February 2015

Kremling, A.; Geiselmann, J.; Ropers, D.
Trends in Microbiology, Vol. 23, Issue 2
DOI: 10.1016/j.tim.2014.11.002

Metabolome-Proteome Differentiation Coupled to Microbial Divergence
journal, October 2010

Wilmes, Paul; Bowen, Benjamin P.; Thomas, Brian C.
mBio, Vol. 1, Issue 5
DOI: 10.1128/mBio.00246-10

Cellulosic ethanol production by natural bacterial consortia is enhanced by Pseudoxanthomonas taiwanensis
journal, January 2015

Du, Ran; Yan, Jianbin; Li, Shizhong
Biotechnology for Biofuels, Vol. 8, Issue 1
DOI: 10.1186/s13068-014-0186-7

Influence of the Crc regulator on the hierarchical use of carbon sources from a complete medium in P seudomonas : Crc and the hierarchy of substrate consumption
journal, January 2016

La Rosa, Ruggero; Behrends, Volker; Williams, Huw D.
Environmental Microbiology, Vol. 18, Issue 3
DOI: 10.1111/1462-2920.13126

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

Metabolic Footprinting: A New Approach to Identify Physiological Changes in Complex Microbial Communities upon Exposure to Toxic Chemicals
journal, June 2007

Henriques, Inês D. S.; Aga, Diana S.; Mendes, Pedro
Environmental Science & Technology, Vol. 41, Issue 11
DOI: 10.1021/es062796t

Direct Assessment of Metabolite Utilization by Pseudomonas aeruginosa during Growth on Artificial Sputum Medium
journal, January 2013

Behrends, Volker; Geier, Benedikt; Williams, Huw D.
Applied and Environmental Microbiology, Vol. 79, Issue 7
DOI: 10.1128/AEM.03609-12

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis
journal, January 2012

Halter, David; Goulhen-Chollet, Florence; Gallien, Sébastien
The ISME Journal, Vol. 6, Issue 7
DOI: 10.1038/ismej.2011.198

Growth Kinetics of Suspended Microbial Cells: From Single-Substrate-Controlled Growth to Mixed-Substrate Kinetics
journal, September 1998

Kovárová-Kovar, Karin; Egli, Thomas
Microbiology and Molecular Biology Reviews, Vol. 62, Issue 3
DOI: 10.1128/MMBR.62.3.646-666.1998

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
journal, August 2008

Görke, Boris; Stülke, Jörg
Nature Reviews Microbiology, Vol. 6, Issue 8, p. 613-624
DOI: 10.1038/nrmicro1932

BLAST-EXPLORER helps you building datasets for phylogenetic analysis
journal, January 2010

Dereeper, Alexis; Audic, Stephane; Claverie, Jean-Michel
BMC Evolutionary Biology, Vol. 10, Issue 1
DOI: 10.1186/1471-2148-10-8

TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates
journal, April 2004

Blank, L. M.
Microbiology, Vol. 150, Issue 4
DOI: 10.1099/mic.0.26845-0

Experimental Identification and Quantification of Glucose Metabolism in Seven Bacterial Species
journal, February 2005

Fuhrer, T.; Fischer, E.; Sauer, U.
Journal of Bacteriology, Vol. 187, Issue 5
DOI: 10.1128/JB.187.5.1581-1590.2005

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

Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors
journal, January 2011

Garbeva, Paolina; Silby, Mark W.; Raaijmakers, Jos M.
The ISME Journal, Vol. 5, Issue 6
DOI: 10.1038/ismej.2010.196

Matplotlib: A 2D Graphics Environment
journal, January 2007

Hunter, John D.
Computing in Science & Engineering, Vol. 9, Issue 3
DOI: 10.1109/MCSE.2007.55

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
Nucleic Acids Research, Vol. 42, Issue D1
DOI: 10.1093/nar/gkt963

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

Edgar, R. C.
Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
DOI: 10.1093/nar/gkh340

Towards synthetic microbial consortia for bioprocessing
journal, October 2012

Shong, Jasmine; Jimenez Diaz, Manuel Rafael; Collins, Cynthia H.
Current Opinion in Biotechnology, Vol. 23, Issue 5
DOI: 10.1016/j.copbio.2012.02.001

Phylogeny.fr: robust phylogenetic analysis for the non-specialist
journal, May 2008

Dereeper, A.; Guignon, V.; Blanc, G.
Nucleic Acids Research, Vol. 36, Issue Web Server
DOI: 10.1093/nar/gkn180

The NumPy Array: A Structure for Efficient Numerical Computation
journal, March 2011

van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël
Computing in Science & Engineering, Vol. 13, Issue 2
DOI: 10.1109/MCSE.2011.37

Effect of salts on the Co-fermentation of glucose and xylose by a genetically engineered strain of Saccharomyces cerevisiae
journal, January 2013

Casey, Elizabeth; Mosier, Nathan S.; Adamec, Jiri
Biotechnology for Biofuels, Vol. 6, Issue 1
DOI: 10.1186/1754-6834-6-83

Toward an Ecological Classification of soil Bacteria
journal, June 2007

Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
Ecology, Vol. 88, Issue 6
DOI: 10.1890/05-1839

Works referencing / citing this record:

Biochar Effects on Bacterial Community and Metabolic Pathways in Continuously Cotton-Cropped Soil
journal, February 2019

Han, Guangming; Chen, Quanqiu; Zhang, Shengxi
Journal of Soil Science and Plant Nutrition, Vol. 19, Issue 2
DOI: 10.1007/s42729-019-0014-z

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics
journal, January 2018

Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-017-02356-9

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