Microfluidic confinement reveals how bacteria cross one-micrometer-wide passages by flagellar wrapping

Microfluidic devices are widely used to replicate the physical constraints bacteria experience in natural and host-associated environments. However, even with advanced microfluidic confinement, it has remained unclear how motile bacteria generate propulsion when channel dimensions approach the size of the cell itself. This question is especially relevant for biological systems where micron-scale bottlenecks act as selective gates. As the authors state, “Confined spaces are omnipresent in the micro-environments, including soil aggregates and intestinal crypts, yet little is known about how bacteria behave under such conditions where movement is challenging due to spatial confinement.

To address this problem, the authors use a microfluidic approach inspired by an insect gut sorting organ that contains passages only about one micrometer wide. They hypothesize that a noncanonical motility mode, flagellar wrapping around the bacterial cell body, allows bacteria to move efficiently under extreme microfluidic confinement. By combining in vivo observations with a microfluidic chip, they directly test how bacterial swimming mechanics change when motion is restricted to quasi one-dimensional channels.

“Here, we developed a microfluidic device mimicking the host’s sorting organ, wherein bacterial cells are confined in a quasi-one-dimensional fashion, and revealed that this bacterium wraps flagellar filaments around its cell body like a screw thread to control fluid flow and generate propulsion for smooth and directional movement in narrow passages.”, the authors explained. 

The study integrates biological imaging with a purpose-built microfluidic device microfabricated from PDMS using soft lithography. The device consists of straight, open channels with both width and depth constrained to approximately one micrometer, effectively forcing bacteria into single-file motion. To mimic the viscoelastic properties of host environments, the channels were filled with methylcellulose, strongly suppressing diffusion and bulk flow. High-speed fluorescence microscopy enabled direct visualization of flagellar configurations inside the microfluidic channels. The authors complemented these experiments with hydrodynamic simulations to quantify how wrapped and unwrapped flagella generate flow under confinement. Genetic manipulation of the flagellar hook was then used to tune mechanical flexibility and assess its impact on microfluidic motility.

Within the microfluidic channels, Caballeronia insecticola exhibited smooth and directional movement at speeds comparable to those measured inside the host gut. The bacteria repeatedly transitioned into a wrapped flagellar state, where the filament coils tightly around the cell body and acts like a screw to drive motion along the channel walls. In contrast, closely related species that failed to wrap their flagella showed little or no displacement in the same microfluidic geometry. Hydrodynamic modeling demonstrated that wrapping maintains propulsion even as the gap between the cell and the channel wall approaches zero. Importantly, the ability to move effectively in the microfluidic device strongly correlated with successful colonization of the host, linking microfluidic performance to biological function.

This work demonstrates how microfluidic confinement can expose motility strategies that are not apparent in bulk fluid environments. By recreating one-micrometer-scale passages in a microfluidic device, the authors show that flagellar wrapping provides a clear mechanical advantage for bacterial swimming under extreme spatial restriction. As the authors conclude, “Flagellar wrapping likely represents an evolutionary innovation, enabling bacteria to break through confined environments using their motility machinery.” More broadly, this study highlights how microfluidic models can bridge physical constraints, cellular mechanics, and ecological outcomes in bacterial systems.

Figures are reproduced from Yoshioka, A., Shimada, Y.Y., Omori, T. et al. Bacteria break through one-micrometer-square passages by flagellar wrapping. Nat Commun 17, 713 (2026). https://doi.org/10.1038/s41467-025-67507-9 under a Creative Commons Attribution 4.0 International License.

Read the original article: Bacteria break through one-micrometer-square passages by flagellar wrapping

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