Effect of flow and active mixing on bacterial growth in a colon-like geometry

The large intestine harbors bacteria from hundreds of species, with bacterial densities reaching up to $10^{12}$ cells per gram. Many different factors influence bacterial growth dynamics and thus bacterial density and microbiota composition. One dominant force is flow which can in principle lead to a washout of bacteria from the proximal colon. Active mixing by contractions of the colonic wall together with bacterial growth might counteract such flow-forces and allow high bacterial densities to occur. As a step towards understanding bacterial growth in the presence of mixing and flow, we constructed an in-vitro setup where controlled wall-deformations of a channel emulate contractions. We investigate growth along the channel under a steady nutrient inflow. In the limits of no or very frequent contractions, the device behaves like a plug-flow reactor and a chemostat respectively. Depending on mixing and flow, we observe varying spatial gradients in bacterial density along the channel. Active mixing by deformations of the channel wall is shown to be crucial in maintaining a steady-state bacterial population in the presence of flow. The growth-dynamics is quantitatively captured by a simple mathematical model, with the effect of mixing described by an effective diffusion term.