Spatiotemporal modeling of microbial metabolism
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Author(s)
Chen, Jin
Phalak, Poonam
Gomez, Jose A.
Barton, Paul I.
Henson, Michael A.
Hoeffner, Kai
Date Issued
March 2016
Journal
BMC Systems Biology
Publisher
BioMed Central
Citation
Chen, Jin, Jose A. Gomez, Kai Hoffner, Poonam Phalak, Paul I. Barton, and Michael A. Henson. “Spatiotemporal Modeling of Microbial Metabolism.” BMC Syst Biol 10, no. 1 (March 1, 2016).
Version
Final published version
Abstract
Background
Microbial systems in which the extracellular environment varies both spatially and temporally are very common in nature and in engineering applications. While the use of genome-scale metabolic reconstructions for steady-state flux balance analysis (FBA) and extensions for dynamic FBA are common, the development of spatiotemporal metabolic models has received little attention.
Results
We present a general methodology for spatiotemporal metabolic modeling based on combining genome-scale reconstructions with fundamental transport equations that govern the relevant convective and/or diffusional processes in time and spatially varying environments. Our solution procedure involves spatial discretization of the partial differential equation model followed by numerical integration of the resulting system of ordinary differential equations with embedded linear programs using DFBAlab, a MATLAB code that performs reliable and efficient dynamic FBA simulations. We demonstrate our methodology by solving spatiotemporal metabolic models for two systems of considerable practical interest: (1) a bubble column reactor with the syngas fermenting bacterium Clostridium ljungdahlii; and (2) a chronic wound biofilm with the human pathogen Pseudomonas aeruginosa. Despite the complexity of the discretized models which consist of 900 ODEs/600 LPs and 250 ODEs/250 LPs, respectively, we show that the proposed computational framework allows efficient and robust model solution.
Conclusions
Our study establishes a new paradigm for formulating and solving genome-scale metabolic models with both time and spatial variations and has wide applicability to natural and engineered microbial systems.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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DOI of Published Version
https://doi.org/10.1186/s12918-016-0259-2
