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dc.contributor.authorTaffs, Reed L.
dc.contributor.authorAston, John E.
dc.contributor.authorBrileya, Kristen A.
dc.contributor.authorJay, Zackary J.
dc.contributor.authorKlatt, Christian G.
dc.contributor.authorMcGlynn, Shawn E.
dc.contributor.authorInskeep, William P.
dc.contributor.authorWard, David M.
dc.contributor.authorCarlson, Ross P.
dc.date.accessioned2017-07-12T19:23:36Z
dc.date.available2017-07-12T19:23:36Z
dc.date.issued2009
dc.identifier.citationTaffs R, Aston JE, Brileya K , Jay Z, Klatt CG, McGlynn S, Mallette N, Montross S, Gerlach R, Inskeep WP, Ward DM, Carlson RP, "In silico approaches to study mass and energy flows in microbial consortia: A syntrophic case study," BMC Systems Biology 2009 3(1):114en_US
dc.identifier.issn1752-0509
dc.identifier.urihttps://scholarworks.montana.edu/xmlui/handle/1/13231
dc.description.abstractBackground: Three methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode analysis to the study of mass and energy flows in microbial communities. Each has distinct advantages and disadvantages suitable for analyzing systems with different degrees of complexity and a priori knowledge. These approaches were tested and compared using data from the thermophilic, phototrophic mat communities from Octopus and Mushroom Springs in Yellowstone National Park (USA). The models were based on three distinct microbial guilds: oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria. Two phases, day and night, were modeled to account for differences in the sources of mass and energy and the routes available for their exchange.ResultsThe in silico models were used to explore fundamental questions in ecology including the prediction of and explanation for measured relative abundances of primary producers in the mat, theoretical tradeoffs between overall productivity and the generation of toxic by-products, and the relative robustness of various guild interactions.Conclusion: The three modeling approaches represent a flexible toolbox for creating cellular metabolic networks to study microbial communities on scales ranging from cells to ecosystems. A comparison of the three methods highlights considerations for selecting the one most appropriate for a given microbial system. For instance, communities represented only by metagenomic data can be modeled using the pooled method which analyzes a community's total metabolic potential without attempting to partition enzymes to different organisms. Systems with extensive a priori information on microbial guilds can be represented using the compartmentalized technique, employing distinct control volumes to separate guild-appropriate enzymes and metabolites. If the complexity of a compartmentalized network creates an unacceptable computational burden, the nested analysis approach permits greater scalability at the cost of more user intervention through multiple rounds of pathway analysis. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1752-0509/3/114en_US
dc.titleIn silico approaches to study mass and energy flows in microbial consortia: A syntrophic case studyen_US
dc.typeArticleen_US
mus.citation.extentfirstpage114en_US
mus.citation.issue1en_US
mus.citation.journaltitleBMC Systems Biologyen_US
mus.citation.volume3en_US
mus.identifier.categoryEngineering & Computer Scienceen_US
mus.identifier.doi10.1186/1752-0509-3-114en_US
mus.relation.collegeCollege of Engineeringen_US
mus.relation.departmentCenter for Biofilm Engineering.en_US
mus.relation.departmentChemical & Biological Engineering.en_US
mus.relation.departmentChemical Engineering.en_US
mus.relation.departmentMicrobiology & Immunology.en_US
mus.relation.universityMontana State University - Bozemanen_US
mus.relation.researchgroupCenter for Biofilm Engineering.en_US
mus.data.thumbpage11en_US


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