Shaping bacterial population behavior through computer-interfaced control of individual cells

Remy Chait, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik and Călin C. Guet ()
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Remy Chait: Institute of Science and Technology Austria
Jakob Ruess: Institute of Science and Technology Austria
Tobias Bergmiller: Institute of Science and Technology Austria
Gašper Tkačik: Institute of Science and Technology Austria
Călin C. Guet: Institute of Science and Technology Austria

Nature Communications, 2017, vol. 8, issue 1, 1-11

Abstract: Abstract Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell–cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.

Date: 2017
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DOI: 10.1038/s41467-017-01683-1

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