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Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight

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Listed:
  • François Bertaux

    (28 rue du Docteur Roux
    2 rue Simone Iff
    Lesaffre International)

  • Sebastián Sosa-Carrillo

    (28 rue du Docteur Roux
    2 rue Simone Iff
    Université Paris Cité)

  • Viktoriia Gross

    (28 rue du Docteur Roux
    2 rue Simone Iff
    Université Paris Cité and INSERM)

  • Achille Fraisse

    (28 rue du Docteur Roux
    2 rue Simone Iff)

  • Chetan Aditya

    (28 rue du Docteur Roux
    2 rue Simone Iff
    Université Paris Cité)

  • Mariela Furstenheim

    (28 rue du Docteur Roux)

  • Gregory Batt

    (28 rue du Docteur Roux
    2 rue Simone Iff)

Abstract

Small-scale, low-cost bioreactors provide exquisite control of environmental parameters of microbial cultures over long durations. Their use is gaining popularity in quantitative systems and synthetic biology. However, existing setups are limited in their measurement capabilities. Here, we present ReacSight, a strategy to enhance bioreactor arrays for automated measurements and reactive experiment control. ReacSight leverages low-cost pipetting robots for sample collection, handling and loading, and provides a flexible instrument control architecture. We showcase ReacSight capabilities on three applications in yeast. First, we demonstrate real-time optogenetic control of gene expression. Second, we explore the impact of nutrient scarcity on fitness and cellular stress using competition assays. Third, we perform dynamic control of the composition of a two-strain consortium. We combine custom or chi.bio reactors with automated cytometry. To further illustrate ReacSight’s genericity, we use it to enhance plate-readers with pipetting capabilities and perform repeated antibiotic treatments on a bacterial clinical isolate.

Suggested Citation

  • François Bertaux & Sebastián Sosa-Carrillo & Viktoriia Gross & Achille Fraisse & Chetan Aditya & Mariela Furstenheim & Gregory Batt, 2022. "Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31033-9
    DOI: 10.1038/s41467-022-31033-9
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    References listed on IDEAS

    as
    1. Remy Chait & Jakob Ruess & Tobias Bergmiller & Gašper Tkačik & Călin C. Guet, 2017. "Shaping bacterial population behavior through computer-interfaced control of individual cells," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    2. Chetan Aditya & François Bertaux & Gregory Batt & Jakob Ruess, 2021. "A light tunable differentiation system for the creation and control of consortia in yeast," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    3. Dirk Benzinger & Mustafa Khammash, 2018. "Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    4. Andreas Milias-Argeitis & Marc Rullan & Stephanie K. Aoki & Peter Buchmann & Mustafa Khammash, 2016. "Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    5. Peter Rugbjerg & Nils Myling-Petersen & Andreas Porse & Kira Sarup-Lytzen & Morten O. A. Sommer, 2018. "Diverse genetic error modes constrain large-scale bio-based production," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
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    Cited by:

    1. Joaquín Gutiérrez Mena & Sant Kumar & Mustafa Khammash, 2022. "Dynamic cybergenetic control of bacterial co-culture composition via optogenetic feedback," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Sebastián Sosa-Carrillo & Henri Galez & Sara Napolitano & François Bertaux & Gregory Batt, 2023. "Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Gita Naseri, 2023. "A roadmap to establish a comprehensive platform for sustainable manufacturing of natural products in yeast," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Lucas Henrion & Juan Andres Martinez & Vincent Vandenbroucke & Mathéo Delvenne & Samuel Telek & Andrew Zicler & Alexander Grünberger & Frank Delvigne, 2023. "Fitness cost associated with cell phenotypic switching drives population diversification dynamics and controllability," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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