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  • Open Access

Bacterial Motility Patterns Vary Smoothly with Spatial Confinement and Disorder

Haibei Zhang1,2,*, Miles T. Wetherington3,4,*, Hungtang Ko5, Cody E. FitzGerald2,6, Leone V. Luzzatto2,7, István A. Kovács2,6,7,8, Edwin M. Munro2,9, and Jasmine A. Nirody10,2,†

  • *These authors contributed equally to this work.
  • †Contact author: jnirody@uchicago.edu
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PRX Life 4, 013002 – Published 6 January, 2026

DOI: https://doi.org/10.1103/7hgr-pssv

Abstract

In unconfined environments, bacterial motility patterns directly reflect the internal states of the cell. Bacteria operating a run-and-tumble behavioral program swim forward when in a “run” state, and they are stalled in place when in a reorienting “tumble” state. However, in natural environments, motility dynamics are a convolution of bacterial behavior and physical constraints. Recent investigations showed that Escherichia coli swimming through highly confined porous media exhibit extended periods of “trapping” punctuated by forward “hops,” suggesting a potential shift in motility strategy. We introduce a microfluidic device to systematically explore bacterial movement in a range of spatially structured environments, bridging the extremes of unconfined and highly confined conditions. We show that run-and-tumble and hop-and-trap are not distinct locomotive modes, but end points of a continuous spectrum of motility. We present the first unifying framework, “swim-and-stall”, to characterize this continuum of observed motility patterns. We demonstrate that a single control program underlies motility across all environments tested—that is, physical structure alone shapes changes in observed output. Our results establish a quantitative link between behavioral rules and environmental context, and show that E. coli can navigate dynamic, complex habitats without reprogramming their motility strategy. This robustness may explain the evolutionary persistence of run-and-tumble behavior in a diverse range of peritrichously flagellated bacteria and inform broader models of active transport in structured media.

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PRX Life Collection on adaptation and learning

PRX Life presents a special collection on ‘Biological systems that learn’, curated by the organizers of the National Institute for Theory and Mathematics in Biology (NITMB) workshop together with early-career researchers. The papers in this collection illustrate how living systems acquire functions, showing it is useful to describe them as tunable matter with many individually adjustable degrees of freedom characterizing microscopic properties. Drawing inspiration from AI and non-biological systems that can acquire desired functions, the featured research highlights the timeliness of the topic and its potential to drive unifying frameworks for emergent collective function in living tunable matter.

Every article in this collection is subject to a rigorous peer review process, upholding the high standards applied to all papers in the journal. The PRX Life editorial team manages peer review and makes all editorial decisions.

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PRX Life 4, 013002– Published 6 January, 2026
  • Received 18 July 2025
  • Accepted 1 December 2025
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Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

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