Single‐cell microliter‐droplet screening system (MISS Cell): An integrated platform for automated high‐throughput microbial monoclonal cultivation and picking

Abstract

Solid plates have been used for microbial monoclonal isolation, cultivation, and colony picking since 1881. However, the process is labor‐ and resource‐intensive for high‐throughput requirements. Currently, several instruments have been integrated for automated and high‐throughput picking, but complicated and expensive. To address these issues, we report a novel integrated platform, the single‐cell microliter‐droplet screening system (MISS Cell), for automated, high‐throughput microbial monoclonal colony cultivation and picking. We verified the monoclonality of droplet cultures in the MISS Cell and characterized culture performance. Compared with solid plates, the MISS Cell generated a larger number of monoclonal colonies with higher initial growth rates using fewer resources. Finally, we established a workflow for automated high‐throughput screening of Corynebacterium glutamicum using the MISS Cell and identified high glutamate‐producing strains. The MISS Cell can serve as a universal platform to efficiently produce monoclonal colonies in high‐throughput applications, overcoming the limitations of solid plates to promote rapid development in biotechnology.

Advances in the isolation, cultivation, and identification of gut microbes

“…Some of these droplets require re-separated after enrichment or manual sliding or picking [ 34 , 38 ]. Jian et al [ 39 ] introduced the single-cell microlitre-droplet screening system (MISS Cell), which is capable of generating 2.0 to 2.5 µl droplets with a throughput of 10 4 cells. MISS Cell consists of 4 interconnected modules: the sampling module, microfluidic chip module, droplet storage and culture module, and droplet detection and collection module.…”

Automated in vivo enzyme engineering accelerates biocatalyst optimization

“…Emerging biofoundries around the globe are providing automation capabilities for setting up such workflows 19,20,150 by transferring and combining available methods for modular DNA assembly, highly parallel transformation and incubation, imagebased colony identification and multi-pin picking, as well as plasmid library preparation using canonical hosts such as E. coli 151,152 or S. cerevisiae 153 as a basis. Recently, robotics-assisted modular cloning [154][155][156][157][158] , high-throughput transformation 159 and monoclonal colony cultivation and picking 160 have been introduced for other industrially relevant organisms such as P. putida or Corynebacterium glutamicum. The correctness of assembled and cloned plasmids can be verified easily with high-throughput using colony PCR or Oxford Nanopore sequencing 161 .…”