Yang Chen, Xue Boyuan, Yuan Qianqian, Wang Shaojie, Su Haijia
State Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory of Bioprocess, and Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.
Comput Struct Biotechnol J. 2024 Jun 27;23:2861-2871. doi: 10.1016/j.csbj.2024.06.033. eCollection 2024 Dec.
Interaction simulation for co-culture systems is important for optimizing culture conditions and improving yields. For industrial production, the environment significantly affects the spatial-temporal microbial interactions. However, the current research on polymicrobial interactions mainly focuses on interaction patterns among strains, and neglects the environment influence. Based on the resource competition relationship between two strains, this research set up the modules of cellular physicochemical properties, nutrient uptake and metabolite release, cellular survival, cell swimming and substrate diffusion, and investigated the spatial-temporal strain-environment interactions through module coupling and data mining. Furthermore, in an - consortium, the total net reproduction rate decreased as glucose was consumed. gradually dominated favorable positions due to its higher glucose utilization capacity, reaching 100 % abundance with a competitive strength of 0.86 for glucose. Conversely, decreased to 0 % abundance with a competitive strength of 0.14. The simulation results of environment influence on strain competitiveness showed that inoculation ratio and dissolved oxygen strongly influenced strain competitiveness. Specifically, strain competitiveness increased with higher inoculation ratio, whereas competitiveness increased as dissolved oxygen increased, in contrast to . On the other hand, substrate diffusion condition, micronutrients and toxins had minimal influence on strain competitiveness. This method offers a straightforward procedure without featured downscaling and provides novel insights into polymicrobial interaction simulation.
共培养系统的相互作用模拟对于优化培养条件和提高产量非常重要。对于工业生产而言，环境会显著影响微生物的时空相互作用。然而，目前关于多微生物相互作用的研究主要集中在菌株之间的相互作用模式，而忽略了环境的影响。基于两种菌株之间的资源竞争关系，本研究建立了细胞物理化学性质、养分吸收和代谢产物释放、细胞存活、细胞游动和底物扩散等模块，并通过模块耦合和数据挖掘研究了菌株与环境的时空相互作用。此外，在一个菌群中，随着葡萄糖的消耗，总净繁殖率下降。由于其较高的葡萄糖利用能力，逐渐占据有利位置，葡萄糖竞争强度为0.86时丰度达到100%。相反，竞争强度为0.14时丰度降至0%。环境对菌株竞争力影响的模拟结果表明，接种比例和溶解氧强烈影响菌株竞争力。具体而言，菌株竞争力随着接种比例的提高而增加，而与相反，的竞争力随着溶解氧的增加而增加。另一方面，底物扩散条件、微量营养素和毒素对菌株竞争力的影响最小。该方法提供了一个简单的程序，无需进行特定的降尺度处理，并为多微生物相互作用模拟提供了新的见解。
