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

• Represent microbial metabolism based on thermodynamics.
• Write microbial metabolic reactions to represent environmental processes.
• An open-source computational tool to study microbial activity
• The basis of metabolic behaviour-rules embedded in an individual-based model.

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.

Image highlights: MbT-Tool is a computational tool to represent the microbial metabolism through a microbial metabolic reactions using a thermodynamic approach based on the energy-transfer-efficiency between catabolic and anabolic processes. The MbT-Tool has been implemented in the open-source platform NetLogo, which makes this tool accessible to chemists, biologists, ecologists, engineers and modellers, among others.Figure optionsDownload as PowerPoint slide