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High-throughput 3D tracking of bacteria on a standard phase contrast microscope

Author

Listed:
  • K.M. Taute

    (FOM Institute AMOLF)

  • S. Gude

    (FOM Institute AMOLF)

  • S.J. Tans

    (FOM Institute AMOLF)

  • T.S. Shimizu

    (FOM Institute AMOLF)

Abstract

Bacteria employ diverse motility patterns in traversing complex three-dimensional (3D) natural habitats. 2D microscopy misses crucial features of 3D behaviour, but the applicability of existing 3D tracking techniques is constrained by their performance or ease of use. Here we present a simple, broadly applicable, high-throughput 3D bacterial tracking method for use in standard phase contrast microscopy. Bacteria are localized at micron-scale resolution over a range of 350 × 300 × 200 μm by maximizing image cross-correlations between their observed diffraction patterns and a reference library. We demonstrate the applicability of our technique to a range of bacterial species and exploit its high throughput to expose hidden contributions of bacterial individuality to population-level variability in motile behaviour. The simplicity of this powerful new tool for bacterial motility research renders 3D tracking accessible to a wider community and paves the way for investigations of bacterial motility in complex 3D environments.

Suggested Citation

  • K.M. Taute & S. Gude & S.J. Tans & T.S. Shimizu, 2015. "High-throughput 3D tracking of bacteria on a standard phase contrast microscope," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9776
    DOI: 10.1038/ncomms9776
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    Cited by:

    1. Yann S Dufour & Sébastien Gillet & Nicholas W Frankel & Douglas B Weibel & Thierry Emonet, 2016. "Direct Correlation between Motile Behavior and Protein Abundance in Single Cells," PLOS Computational Biology, Public Library of Science, vol. 12(9), pages 1-25, September.
    2. Oliver Pohl & Marius Hintsche & Zahra Alirezaeizanjani & Maximilian Seyrich & Carsten Beta & Holger Stark, 2017. "Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-24, January.
    3. Christina Kurzthaler & Suvendu Mandal & Tapomoy Bhattacharjee & Hartmut Löwen & Sujit S. Datta & Howard A. Stone, 2021. "A geometric criterion for the optimal spreading of active polymers in porous media," Nature Communications, Nature, vol. 12(1), pages 1-10, December.

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