Closing the Loop: Autonomous High-Throughput Strain Characterisation from Frozen Cell Bank to Product Assay

Research Square

Abstract

Abstract Background: Modern genome editing enables rapid construction of genetic variants, which are further developed in Design-Build-Test-Learn cycles. To operate such cycles in high throughput, fully automated screening, including cultivation and analytics, is crucial. Here, we present the required steps to meet these demands, resulting in an automated microbioreactor platform that is able to close the experiment-model loop for phenotyping. Results: First, an automated deep freezer was integrated into the robotic platform to provide working cell banks at all times. A mobile cart allows flexible docking of the freezer to multiple platforms. Next, precultures were integrated within the microtiter plate for cultivation, resulting in highly reproducible maincultures as demonstrated for Corynebacterium glutamicum. To avoid manual exchange of microtiter plates after cultivation, two clean-in-place strategies were established and validated, resulting in restored sterile conditions within two hours. Combined with the previous steps, these changes enable a flexible start of experiments and greatly increase the walk-away time. Conclusions: Overall, this works demonstrates the capability of our microbioreactor platform to perform autonomous, consecutive cultivation and phenotyping experiments. As demonstrated in a case study of cutinase-secreting strains of C. glutamicum, the new procedure allows for flexible experimentation without human interaction while maintaining high reproducibility in early stage screening processes.

Authors 7

1. Laura M. Helleckes Aachen Institute of Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich

   Institute of Biotechnology, RWTH Aachen University, Aachen, Germany

2. Debora Puchta

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

3. Hannah Czech

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

4. Holger Morschett

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

5. Bertram Geinitz

   Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich

6. Wolfgang Wiechert Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich

   Computational Systems Biotechnology, RWTH Aachen University, Aachen, Germany

7. Marco Oldiges corresponding Aachen Institute of Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Forschungszentrum Jülich

   Institute of Biotechnology, RWTH Aachen University, Aachen, Germany