A New Method of Genome-Scale Metabolic Model Validation for Biogeochemical Application
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Date
2017-09-06
Authors
Shapiro, Benjamin
Journal Title
Journal ISSN
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Publisher
University of Oregon
Abstract
We propose a new method to integrate genome-scale metabolic models into biogeochemical reaction modeling. This method predicts rates of microbial metabolisms by combining flux balance analysis (FBA) with microbial rate laws. We applied this new hybrid method to methanogenesis by Methanosarcina barkeri.
Our results show that the new method predicts well the progress of acetoclastic, methanol, and diauxic metabolism by M. barkeri. The hybrid method represents an improvement over dynamic FBA. We validated genome-scale metabolic models of Methanosarcina barkeri, Methanosarcina acetivorans, Geobacter metallireducens, Shewanella oneidensis, Shewanella putrefaciens and Shewanella sp. MR4 for application to biogeochemical modeling. FBA was used to predict the response of cell metabolism, and ATP and biomass yield. Our analysis provides improvements to these models for the purpose of applications to natural environments.
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Keywords
Biogeochemical reaction modeling, Flux balance analysis, Genome-scale, Geobacter, Methanosarcina, Shewanella