High-throughput optofluidic screening for improved microbial cell factories via real-time micron-scale productivity monitoring

Matthew Rienzo, Ke-Chih Lin, Kellen C Mobilia, Eric K Sackmann, Volker Kurz, Adam H Navidi, Jarett King, Robert M Onorato, Lawrence K Chao, Tony Wu, Hanxiao Jiang, Justin K Valley (+2 others)
2021 Lab on a Chip  
The industrial synthetic biology sector has made huge investments to achieve relevant miniaturized screening systems for scalable fermentation. Here we present the first example of a high-throughput (>103 genotypes per week) perfusion-based screening system to improve small-molecule secretion from microbial strains. Using the Berkeley Lights Beacon® system, the productivity of each strain could be directly monitored in real time during continuous culture, yielding phenotypes that correlated
more » ... ngly (r2 > 0.8, p < 0.0005) with behavior in industrially relevant bioreactor processes. This method allows a much closer approximation of a typical fed-batch fermentation than conventional batch-like droplet or microplate culture models, in addition to rich time-dependent data on growth and productivity. We demonstrate these advantages by application to the improvement of high-productivity strains using whole-genome random mutagenesis, yielding mutants with substantially improved (by up to 85%) peak specific productivities in bioreactors. Each screen of ∼5 × 103 mutants could be completed in under 8 days (including 5 days involving user intervention), saving ∼50-75% of the time required for conventional microplate-based screening methods.
doi:10.1039/d1lc00389e pmid:34160512 fatcat:mxoxuhe4qvdkflcln6wul3buqy