title: MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.
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 (Metabolism based 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 (-), N2) to biomass synthesis and twenty-four microbial empirical 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.
authors.affiliation: Chemical Engineering Faculty, Central University of Ecuador, Ciudad Universitaria - Ritter s/n y Bolivia, P.O. Box. 17-01-3972, Quito, Ecuador; Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona, Spain.
authors.forename: Pablo Granda
authors.initials: PG
authors.lastname: Araujo
authors.affiliation: Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Gras
authors.affiliation: Department of Mathematics, Universitat Politència de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Ginovart
keywords: Energy-transfer-efficiency; MbT-Tool; Microbial metabolic reaction; Microbial metabolism; Microbial yield prediction; Thermodynamics