Shear and Confinement Control Bacterial Accumulation in Narrow Ducts

Advancements in medicine and environmental remediation depend on understanding bacterial transport and accumulation under flow and in complex confinement. Here, we study the transport of Escherichia coli in microfluidic channels of different cross-section, and demonstrate that bacterial concentration increases with confinement and decreases with flow velocity. Bacterial accumulation can reach several-fold above inlet concentrations, with the highest levels occurring in narrower channels under slower flow conditions. The system has a transient dynamic before reaching equilibrium, with concentration fronts propagating downstream at velocities slower than the average fluid flow. Our analysis of bacterial flux densities reveals that upstream swimming along channel edges increases with confinement, while upstream velocities increase with flow rate due to selective pressure favoring stronger swimmers at higher shear rates. These findings demonstrate that confined channels act as physical filters that selectively transport bacteria based on their swimming capabilities, providing insight into macroscopic transport processes in biological networks, soil systems, and microfluidic applications.