Modeling the dynamics of microbial communities and their response to perturbations

In this project, we plan to investigate the effect of perturbations on microbial communities by developing community models, benchmarking these models on in vitro and in vivo data and finally carrying out perturbations in silico. More specifically, we will model the dynamics of microbial communities using ordinary differential equations (our domain of expertise). We plan to base our model on the generalized Lotka-Volterra equations, with modifications to take into account (possibly logistic) nutrient-dependent growth, stochasticity and immigration.
Dynamical properties of the models will be examined using numerical simulations, linear stability and bifurcation analysis, and asymptotic reduction of the set of equations where possible. Extra insight will be gained by interpreting our findings in a (reduced) phase space. We aim towards modeling microbial communities on two different scales: first small scale systems with only a few interacting microbial species, and second large-scale communities. The former has the advantage of allowing for a complete detailed (bifurcation) analysis of the system and experimental verification, while the latter will build on these results and try to generalize them to larger networks.