Synthetic Biology Journal


Advances and applications of droplet-based microfluidics in evolution and screening of engineered microbial strains

Ran TU1(), Shixin LI2, Haoni LI2, Meng WANG1   

  1. 1.Key Laboratory of Systems Microbial Biotechnology,Tianjin Institute of Industrial Biotechnology,Chinese Academy of Sciences,Tianjin 300308,China
    2.College of Biotechnology,Tianjin University of Science & Technology,Tianjin 300457,China
  • Received:2021-12-03
  • Contact: Meng WANG


Engineered microbial strains are the important foundation of biofabrication. However, most strains usually need to be engineered to improve their performances to be used in industry. Therefore how to efficiently screen and isolate the improved target strains is a critical step of strain engineering. As an advanced high-throughput screening technology using micro-chip, droplet-based microfluidics technology can generate highly independent and uniformed micro- or nano- liter droplets, in which single cells can be encapsulated, inoculated, detected, and isolated for strain engineering. It is especially useful in the evolution of strains for producing extracellular products. In this review, we first introduced the basic components of the droplet-based microfluidic system and the main steps involved in strain screening. We then summarized the application of the droplet-based microfluidic technology in strain engineering according to the key factors of the technology such as the signal sources of droplet detection, the difficulties of handling droplet screening, and the application scopes of droplet sorting instruments. According to the instruments required for the droplet sorting, we concluded the application cases into two types either via fluorescence-activated droplet sorting (FADS) using microfluidic equipment or via fluorescence-activated cell sorting (FACS) using flow cytometry instrument. The FADS type using single-layer water-in-oil droplet can be further classified into cellular signature, fluorescent reporter protein, and substrate-based reaction according to the signal sources, while the FACS type can be divided into double-layers water-in-oil-in-water (W/O/W) droplet or microgel droplet according to the droplet property. At last, we outlined the challenges and prospects of the droplet microfluidic technology and provided some guidelines for its applications in synthetic biology. Compared with traditional screening methods such as shaking flask or microplate with a throughput of hundreds to thousands of samples per day in milli- or micro- liter volume, the droplet-based microfluidic technology can achieve millions of samples per day in pico- or nano- liter volume, resulting in thousand-folds increased screening speed and million-folds decreased consumption cost. By integrating with an automated station, the droplet-based microfluidic technology can be further promoted for its screening efficiencies and application potentials in microbial synthetic biology.

Key words: droplet-based microfluidics, single-cell analysis, cell factory, high-throughput screening, direct evolution

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