ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
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DOI：
10.1038/s41598-020-65659-w
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发表时间：
2020-05-26
影响因子：
4.6
通讯作者：
Motamedian, Ehsan
中科院分区：
文献类型：
--
作者：
Karimian, Emadoddin;Motamedian, Ehsan
能够更真实地模拟微生物群落的新方法的开发需要它们的结果与实验结果进行定量比较。在这项研究中，一个新的集成代理和约束为基础的建模框架简称ACBM已被提出，集成了基于代理和基于约束的建模方法。ACBM在三维空间中对细胞群体进行建模，以预测空间和时间动态以及代谢相互作用。当用于模拟C. beijerinckii和F. prausnitzii和B.青春期的，ACBM改进了以前两个模型的预测。此外，当转录组学数据与E.大肠杆菌考虑细胞内的限制代谢，ACBM准确地预测生长速率，半速率常数，和浓度的生物质，葡萄糖和酸性产品随着时间的推移。结果还表明，与对数期相比，该框架能够预测早期稳定期的代谢变化。最后，ACBM被实施来估计在非均质进料下的饥饿细胞，并且得出结论，在具有高体积的生物反应器中，一定百分比的细胞总是受到饥饿。
The development of new methods capable of more realistic modeling of microbial communities necessitates that their results be quantitatively comparable with experimental findings. In this research, a new integrated agent and constraint based modeling framework abbreviated ACBM has been proposed that integrates agent-based and constraint-based modeling approaches. ACBM models the cell population in three-dimensional space to predict spatial and temporal dynamics and metabolic interactions. When used to simulate the batch growth of C. beijerinckii and two-species communities of F. prausnitzii and B. adolescent., ACBM improved on predictions made by two previous models. Furthermore, when transcriptomic data were integrated with a metabolic model of E. coli to consider intracellular constraints in the metabolism, ACBM accurately predicted growth rate, half-rate constant, and concentration of biomass, glucose, and acidic products over time. The results also show that the framework was able to predict the metabolism changes in the early stationary compared to the log phase. Finally, ACBM was implemented to estimate starved cells under heterogeneous feeding and it was concluded that a percentage of cells are always subject to starvation in a bioreactor with high volume.