Parameters used to describe bacteria in weak, intermediate, and strong confinement, as defined in the text.

All parameters are defined in the text and their values are obtained from experiments as detailed in §2.4 and S2 Text, with the exception of , which is determined directly from the simulation. We note that the values of α0 are taken directly from the experiments in [28], which indicate that this parameter surprisingly decreases with increasing confinement. Thus, while we expect that both transport parameters χ0 and Db0 are tuned by confinement in a similar way, with both proportional to , it appears from the experiments that the ratio of the proportionality constants for each is also confinement-dependent. That is, experiments suggest that confinement more strongly hinders directed (quantified by χ0) versus undirected (quantified by Db0) spreading. While more work needs to be done to fully unravel why this is the case, in absence of a theoretical model for the confinement-dependence of α0, we directly use the experimental values in our work. Furthermore, in the absence of any experimental data assessing the influence of cell density on α, we make the simplest possible assumption that cell-cell collisions hinder both χ0 and Db0 through the same crowding correction factor μcrowd(b), which quantifies the reduction in free space available to the cells. Thus, we take α = α0. Future experiments could further probe this density dependence and motivate the introduction of additional extensions to our model.