Microbial microdroplet culture system (MMC): An integrated platform for automated, high‐throughput microbial cultivation and adaptive evolution

TLDR

Conventional microbial cultivation is labor‑intensive and low‑throughput, whereas droplet microfluidics offers highly parallel, efficient high‑throughput culture systems. The authors developed a microbial microdroplet culture system (MMC) to enable automated, high‑throughput cultivation and adaptive evolution of microorganisms. MMC integrates droplet microfluidics and automated handling, and its performance was validated by comparing growth curves of six strains against shake flasks and well plates. MMC produced accurate, reproducible droplet manipulation, achieved the highest incipient growth rates for all six strains, and enabled an 18‑day adaptive evolution that yielded two E.

Abstract

Abstract Conventional microbial cell cultivation techniques are typically labor intensive, low throughput, and poorlyparallelized, rendering them inefficient. The development of automated, modular microbial cell micro‐cultivation systems, particularly those employing droplet microfluidics, have gained attention for their high‐throughput, highly paralellized and efficient cultivation capabilities. Here, we report the development of a microbial microdroplet culture system (MMC), which is an integrated platform for automated, high‐throughput cultivation and adaptive evolution of microorganisms. We demonstrated that the MMC yielded both accurate and reproducible results for the manipulation and detection of droplets. The superior performance of MMC for microbial cell cultivation was validated by comparing the growth curves of six microbial strains grown in MMC, conventional shake flasks or well plates. The highest incipient growth rate for all six microbial strains was achieved by using MMC. We also conducted an 18‐day process of adaptive evolution of methanol‐essential Escherichia coli strain in MMC and obtained two strains exhibiting higher growth rates compared with the parent strain. Our study demonstrates the power of MMC to provide an efficient and reliable approach for automated, high‐throughput microbial cultivation and adaptive evolution.