Modeling a microbial consortium

Our strategy was based on an input with a quorum sensing molecule production, a molecular communication between two organisms, and an output with the antimicrobial peptides effect. We needed to use a model to simulate this biological system and analyze if this communication was feasible:

Would the quorum sensing molecule (CAI-1) induce a sufficient answer to activate the sensor (Vibrio harveyi)? Would the receptor be able to produce enough molecular message (diacetyl) to communicate with the effector Pichia pastoris? Would the effector produce enough antimicrobial peptides to deliver the guessed output, which is the lysis of V. cholerae to reach a non-toxic concentration?

A model was also crucial regarding the entrepreneurship and the integrated human practices parts of our project: we needed to show to clients and investors, but also to citizens, how our system would work, how we will dimensionate our device, and how long do you have to wait before drinking a non-contaminated water.

We had four principal objectives:

• Demonstrate the feasibility
• Confirm our wet lab strategy
• Design the device
• Estimate the waiting time

Approaches

Working with a complex biological system involving three microorganisms and several molecules, the Systemic Biology Graphical Notation (SBGN) was a perfect way to ordinate the system and represent the interactions between organisms and the molecules involved. The SBGN representation was convenient to elaborate the system of Ordinary Differential Equations (ODEs). This mathematical model have been used to simulate our system, as predictive modeling. Our model had impacts on wetlab strategy and device design, and was modified with experimental data, which is summed up in Integration. Finally, to talk to non-mathematicians, a user-friendly interface was created.