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Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback

View ORCID ProfileJoaquín Gutiérrez, View ORCID ProfileSant Kumar, View ORCID ProfileMustafa Khammash
doi: https://doi.org/10.1101/2022.06.13.495893
Joaquín Gutiérrez
1Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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  • ORCID record for Joaquín Gutiérrez
Sant Kumar
1Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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Mustafa Khammash
1Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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  • For correspondence: mustafa.khammash@bsse.ethz.ch
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Abstract

Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. However, the difficulty of controlling the composition of microbial consortia over time hinders their optimal use in many applications. Here, we present a fully automated, high-throughput platform that combines real-time measurements and computer-controlled optogenetic modulation of bacterial growth to implement precise and robust compositional control of a two-strain E. coli community. Additionally, we develop a general framework for dynamic modeling of synthetic genetic circuits in the physiological context of E. coli and use a host-aware model to determine the optimal control parameters of our closed-loop compositional control system. Our platform succeeds in stabilizing the strain ratio of multiple parallel co-cultures at arbitrary levels and in changing these targets over time, opening the door for the implementation of dynamic compositional programs in synthetic bacterial communities.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/santkumar/evotron.git

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted June 14, 2022.
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Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback
Joaquín Gutiérrez, Sant Kumar, Mustafa Khammash
bioRxiv 2022.06.13.495893; doi: https://doi.org/10.1101/2022.06.13.495893
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Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback
Joaquín Gutiérrez, Sant Kumar, Mustafa Khammash
bioRxiv 2022.06.13.495893; doi: https://doi.org/10.1101/2022.06.13.495893

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