Impact of confined geometries on hopping and trapping of motile bacteria in porous media

We use a random walk particle-tracking (RWPT) approach to elucidate the impact of porous media confinement and cell-cell interactions on bacterial transport. The model employs stochastic alternating motility states consisting of hopping movement and trapping reorientation. The stochastic motility patterns are defined based on direct visualization of individual trajectory data. We validate our model against experimental data, at single-cell resolution, of bacterial E. coli motion in three-dimensional confined porous media. Results show that the model is able to efficiently simulate the spreading dynamics of motile bacteria as it captures the impact of cell-cell interaction and pore confinement, which marks the transition to a late-time subdiffusive regime. Furthermore, the model is able to qualitatively reproduce the observed directional persistence. Our RWPT model constitutes a meshless simple method which is easy to implement and does not invoke ad hoc assumptions but represents the basis for a multiscale approach to the study of bacterial dispersal in porous systems.