On the formation of channels in Escherichia coli colonies and the implications of bacteriophage infection

Bacteria in the natural environment frequently grow as structured communities embedded in an extracellular matrix, where the spatial heterogeneity and complex extracellular matrices provide resistance against adverse environmental conditions such as bacteriophage infections. Recently, a macrocolony of Escherichia coli imaged using a Mesolens, was found to support a system of channels, 10 microns in width, permeating through the colony. The channels are an emergent structure, driven by the bacterial growth, and may have a role in the enchanced uptake of nutrients. In this work, we use discrete element simulations of nonmotile, rod shaped bacteria growing on a hard agar substrate to try to uncover requisite physical interactions capable of driving channel formation. We incorporate bacteriophage as point particles and address the effect the presence of these channels have on the resistance to an infection by bacteriophage. The simulations may be massively parallelised on work station graphical processing units, allowing for a rapid and versatile approach to uncovering the effect of these different physical models.