Perspectives in flow-based microfluidic gradient generators for characterizing bacterial chemotaxis

Chemotaxis is a phenomenon which enables cells to sense concentrations of certain chemical species in their microenvironment and move towards chemically favorable regions. Recent advances in microbiology have engineered the chemotactic properties of bacteria to perform novel functions, but traditional methods of characterizing chemotaxis do not fully capture the associated cell motion, making it difficult to infer mechanisms that link the motion to the microbiology which induces it. Microfluidics offers a potential solution in the form of gradient generators. Many of the gradient generators studied to date for this application are flow-based, where a chemical species diffuses across the laminar flow interface between two solutions moving through a microchannel. Despite significant research efforts, flow-based gradient generators have achieved mixed success at accurately capturing the highly subtle chemotactic responses exhibited by bacteria. Here we present an analysis encompassing previously published versions of flow-based gradient generators, the theories that govern their gradient-generating properties, and new, more practical considerations that result from experimental factors. We conclude that flow-based gradient generators present a challenge inherent to their design in that the residence time and gradient decay must be finely balanced, and that this significantly narrows the window for reliable observation and quantification of chemotactic motion. This challenge is compounded by the effects of shear on an ellipsoidal bacterium that causes it to preferentially align with the direction of flow and subsequently suppresses the cross-flow chemotactic response. These problems suggest that a static, non-flowing gradient generator may be a more suitable platform for chemotaxis studies in the long run, despite posing greater difficulties in design and fabrication.