Modeling Microbial Dynamics: Revealing the Components' Function of the coculture system consists of E. coli and Synechococcus.
In conclusion, we developed three models. First, we constructed the formaldehyde degradation and formaldehyde indication pathway with ordinary differential equations to simulate the behavior of this part. Second, we turned to flux balance analysis (FBA) for a more convincing result. We achieved this with multiple steps: choosing and verifying GEMs, modification according to the pathway, and validation of the simulation result. The simulation result of formaldehyde is consistent with data from the wet lab, which verified the model. After that, we developed an optimized model to obtain an optimized cell number ratio between Synechococcus and E. coli, which can serve as a starting point when setting up the co-culture system in reality. Third, we developed a physical model of alginate beads considering cell embedding based on diffusion and metabolite models. The finite element analysis results of different types of beads showed that the installation of a pump will increase the system’s efficiency, the increasing size of beads will decrease the photosynthesis efficiency due to light decay and the degradation efficiency will be limited due to the equilibrium between diffusion and metabolite. To sum up, our model verified the component’s function, served insights into the system’s function, and provided useful suggestions for future development on the system.
Component modularization
Component modularization offer several advantages. First, they reduce the cost and risk of system iterations. The modularity of components decreases the coupling between them, allowing modular iterations without affecting the normal operation of other parts. This reduces the complexity and failure risk of iterations. Second, they better cater to customized user needs. Users can customize a co-cultivation system to meet their specific requirements for gas elimination or detection. It also enables users to update their systems modularly. Third, they minimize the risk of leakage. Embedding all used strains restricts their growth space, reducing the risk of strains spreading to the environment due to common liquid leaks.