文章基本信息

标题：MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process
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作者：Pablo Araujo Granda ; Anna Gras ; Marta Ginovart 等
期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2016
卷号：14
页码：325-332
DOI：10.1016/j.csbj.2016.08.001
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出版社：Computational and Structural Biotechnology Journal
摘要：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 (C_nH_aO_bN_c). 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.
关键词：MbT-Tool ; Microbial yield prediction ; Thermodynamics ; Microbial metabolism ; Microbial metabolic reaction ; Energy-transfer-efficiency