Shaping bacterial population behavior through computer interfaced control of individual cells Journal Article


Author(s): Chait, Remy; Ruess, Jakob; Bergmiller, Tobias; Tkačik, Gašper; Guet, Cǎlin C
Article Title: Shaping bacterial population behavior through computer interfaced control of individual cells
Affiliation IST Austria
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.
Journal Title: Nature Communications
Volume: 8
Issue 1
ISSN: 2041-1723
Publisher: Nature Publishing Group  
Date Published: 2017-12-01
Start Page: Article number: 1535
Copyright Statement: CC BY
URL:
DOI: 10.1038/s41467-017-01683-1
Notes: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tka č ik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007 – 2013) under REA grant agreement no.[291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16- CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).
Open access: yes (OA journal)