Araujo Pablo Granda, Gras Anna, Ginovart Marta
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.
Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona, Spain.
Comput Struct Biotechnol J. 2016 Aug 26;14:325-32. doi: 10.1016/j.csbj.2016.08.001. eCollection 2016.
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.
对细胞代谢进行建模是研究微生物行为和相互作用的一个战略因素，特别是对于生物技术过程而言。对微生物活动进行建模的一个关键因素是计算微生物代谢产生的营养物质数量和产物。通过平衡反应来表示代谢途径，对于生物学家、生态学家、建模人员和工程师来说是一项复杂且耗时的任务。一种新的计算工具已被设计出来，并在开放获取框架NetLogo中实现，该工具使用热力学电子当量模型的方法，通过微生物代谢反应（MMR）来表示微生物途径。这个名为MbT-Tool（基于热力学的代谢）的计算工具可以为不同的微生物功能群编写MMR，如好氧异养菌、硝化菌、反硝化菌、产甲烷菌、硫酸盐还原菌、硫化物氧化菌和发酵菌。MbT-Tool代码包含18个有机和20个无机还原半反应、4种用于生物量合成的氮源（NH4(+)、NO3(-)、NO2(-)、N2）以及24个微生物经验公式，其中一个可由用户确定（CnHaObNc）。MbT-Tool是一个开源程序，能够基于热力学概念编写MMR，适用于广泛的学术研究，这些研究旨在设计、优化和模拟微生物活动，而无需任何丰富的化学、微生物学和编程经验。
