Gogulancea Valentina, González-Cabaleiro Rebeca, Li Bowen, Taniguchi Denis, Jayathilake Pahala Gedara, Chen Jinju, Wilkinson Darren, Swailes David, McGough Andrew Stephen, Zuliani Paolo, Ofiteru Irina Dana, Curtis Thomas P
School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.
Chemical and Biochemical Department, School of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Bucharest, Romania.
Front Microbiol. 2019 Aug 13;10:1871. doi: 10.3389/fmicb.2019.01871. eCollection 2019.
Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·10 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.
基于个体的模型（IbM）必须从研究工具转变为工程工具。为了实现这一转变，我们必须致力于开发大型的、三维的、物理和生物学上可信的模型。通过尽可能地将生物学建立在热力学基础上，可以提高生物学可信度。热力学原理在微生物生态学中具有预测能力。然而，这反过来需要一个包含pH值和化学形态的模型。物理可信度意味着合理的力学原理以及与更广泛环境的联系。在这里，我们通过提出一个基于个体的模型，将热力学、pH值、化学形态和环境条件与5·10个个体的微生物生长联系起来，朝着这个理想迈出了一步。我们在两种情况下展示了该模型：一个双功能组硝化模型和一个三功能组厌氧群落模型。在前一种情况下，pH值和与环境的联系对模拟结果有重要影响。而在后一种情况下，pH值的重要性较低，但空间排列和群落生产力（即甲烷产量）高度依赖于热力学和反应器耦合。我们得出结论，如果IbM要发挥其作为评估工程生物系统涌现特性工具的潜力，就有必要按照我们提出的思路将化学、物理、力学和生物学结合起来。我们仍然没有达到理想状态，因为我们还不能（目前）计算特定摄取率，并且必须在更大的模型中开发更长运行时间的能力。然而，我们相信这样的进展是可以实现的。理想情况下是在一个通用、快速且模块化的平台上。因为只有当未来IbM的创新能够与之前的所有进展相结合时，它们才会有用。
