A Modular Micro-Chemostat System for High-Throughput Continuous Cultivations

Journal article, 2026

Improving the fidelity of computational eukaryotic models will require an enormous amount of high quality and reproducible data from biological experiments. In this study we present and demonstrate a modular 12-channel micro-chemostat system. This micro-chemostat is designed for use by Genesis, a Robot Scientist developed to automate scientific research in yeast systems biology. We performed bioreactor characterization experiments to evaluate the performance of the micro-chemostat system. We also cultivated the Saccharomyces cerevisiae reference strain, BY4741, at three different dilution rates (0.1, 0.2, and 0.3 h⁻¹) and under two aeration conditions (microaerobic and aerobic), resulting in six different conditions. The bioreactor performance fulfilled our requirements, and enabled substrate-limited continuous cultivation of yeast. Furthermore, the empirical results from the biological experiments were consistent with the literature, suggesting that results obtained from our system are comparable to those reported for other platforms in the field. Based on the evidence presented in this study, we conclude that the 12-channel micro-chemostat system is a suitable platform for yeast systems biology research. The modular design of the micro-chemostat system enables future scaling to hundreds or thousands of concurrent chemostats and facilitates integration with autonomous agents for automated optimization and improvement of eukaryotic model systems.