---
_id: '613'
abstract:
- lang: eng
  text: '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.'
acknowledgement: 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
  Tkačik 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).
article_number: '1535'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Remy P
  full_name: Chait, Remy P
  id: 3464AE84-F248-11E8-B48F-1D18A9856A87
  last_name: Chait
  orcid: 0000-0003-0876-3187
- first_name: Jakob
  full_name: Ruess, Jakob
  id: 4A245D00-F248-11E8-B48F-1D18A9856A87
  last_name: Ruess
  orcid: 0000-0003-1615-3282
- first_name: Tobias
  full_name: Bergmiller, Tobias
  id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
  last_name: Bergmiller
  orcid: 0000-0001-5396-4346
- first_name: Gasper
  full_name: Tkacik, Gasper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkacik
  orcid: 0000-0002-6699-1455
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
citation:
  ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population
    behavior through computer interfaced control of individual cells. <i>Nature Communications</i>.
    2017;8(1). doi:<a href="https://doi.org/10.1038/s41467-017-01683-1">10.1038/s41467-017-01683-1</a>
  apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., &#38; Guet, C. C. (2017).
    Shaping bacterial population behavior through computer interfaced control of individual
    cells. <i>Nature Communications</i>. Nature Publishing Group. <a href="https://doi.org/10.1038/s41467-017-01683-1">https://doi.org/10.1038/s41467-017-01683-1</a>
  chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin
    C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control
    of Individual Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2017.
    <a href="https://doi.org/10.1038/s41467-017-01683-1">https://doi.org/10.1038/s41467-017-01683-1</a>.
  ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping
    bacterial population behavior through computer interfaced control of individual
    cells,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group,
    2017.
  ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial
    population behavior through computer interfaced control of individual cells. Nature
    Communications. 8(1), 1535.
  mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer
    Interfaced Control of Individual Cells.” <i>Nature Communications</i>, vol. 8,
    no. 1, 1535, Nature Publishing Group, 2017, doi:<a href="https://doi.org/10.1038/s41467-017-01683-1">10.1038/s41467-017-01683-1</a>.
  short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications
    8 (2017).
corr_author: '1'
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2025-09-11T07:34:12Z
day: '01'
ddc:
- '576'
- '579'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1038/s41467-017-01683-1
ec_funded: 1
external_id:
  isi:
  - '000415323000008'
file:
- access_level: open_access
  checksum: 44bb5d0229926c23a9955d9fe0f9723f
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:16:05Z
  date_updated: 2020-07-14T12:47:20Z
  file_id: '5190'
  file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf
  file_size: 1951699
  relation: main_file
file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: '         8'
isi: 1
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '291734'
  name: International IST Postdoc Fellowship Programme
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
  issn:
  - 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '7191'
pubrep_id: '911'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shaping bacterial population behavior through computer interfaced control of
  individual cells
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2017'
...