Data for: Integrating genome-scale metabolic models into the prediction of microbial kinetics in natural environments

Published: 31 March 2020| Version 2 | DOI: 10.17632/nm8fp8mcbn.2
Qusheng Jin


The goal of the MATLAB code is to simulateg the metabolism of Methanosarcina barkeri by linking COBRA toolbox with PHREEQC. COBRA toolbox specializes in the analysis of genome-scale metabolic models, and PHREEQC is a software package for simulating geochemical reactions. The two software tools are linked using Microsoft COM. The simulation is for a laboratory experiment that grew M. barkeri with acetate in laboratory reactors. At each time step, PHREEQC is applied to simulate chemical speciation in growth media, and the partition of gases between the liquid media and headspace of the reactors. The output includes the variations with time in the concentrations of chemical compounds and biomass. The MATLAB code is applied to simulate the laboratory experiments of Fukuzaki et al. (1990). They grew Methanosarcina barkeri at 37 oC in batch reactors of 50 mL of complex growth media and 75 mL headspace. The media had pH 7.1 and contained 19.7 mM acetate and 9.3 mM ammonium. We compare the simulation results to the acetate concentrations reported by Fukuzaki et al. (1990). A total of 5 files are required to simulate the laboratory experiments of Fukuzaki et al. (1990). Table 1 lists the four files coded by us. The simulation also requires a genome-scale metabolic model for M. barkeri, which we use the model developed by Gonnerman et al. (2013). This model with the name of M_barkeri_model can be downloaded from Gonnerman et al. (2013). MATLAB CODE File “iMG746_ac_CX_fukuzaki” have the following outline: Initial model parameters Load MATLAB resources Set model boundary conditions (including “RxnID”) Load iPHREEQC resources (including “RxnID” and “writePhreeqc_ac”) Setup data structures Save initial conditions Run simulation ‘for’ loop IPHREEQC speciation (including “writePhreeqc_ac”) Calculate FT value Run FBA on respiration network to predict respiration rate (including “RxnID”) Run FBA on biosynthesis network to predict growth rate (including “RxnID”) Integrate extracellular concentrations (including “RxnID”) Save new concentrations to data structure Start next loop Export data structure to file (including “RxnID”) Plot select model and experimental data (including “RxnID”, “Fukuzaki”) The execution of the files requires the installation of MATLAB (v. 2016b), COBRA Toolbox for MATLAB (v. 3.0), IPHREEQC and IPHREEQC COM (v. 3.4.0), and Gruobi Optimization Solver (v. 6.5.2).