MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

Authored by Marta Ginovart, Anna Gras, Granda Pablo Araujo

Date Published: 2016

DOI: 10.1016/j.csbj.2016.08.001

Sponsors: Ecuador National Secretary of Higher Education

Platforms: NetLogo

Model Documentation: Other Narrative Flow charts

Model Code URLs: http://mosimbio.upc.edu/en/publications/publications-by-year/MbTtool_V5.nlogo

Abstract

Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions(MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolismbased on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3-, NO2-, N-2) to biomass synthesis and twenty-four microbialempirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience. (C) 2016 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

Tags

Individual-based model Escherichia-coli Saccharomyces-cerevisiae True yield prediction Chemotropic growth Gibbs energy-dissipation Paracoccus-denitrificans Growth yields Oxidative-phosphorylation Biomass yields