Construction and application of a microfluidic-droplet system for high-throughput screening of amylase-producing strains from jiuqu

Abstract

Amylases are crucial biocatalysts in brewing and bioindustries, yet isolating high-yielding producers from complex fermentation starters like Chinese Baijiu jiuqu remains slow and low-throughput. Here, we developed a high-throughput microfluidic droplet platform that integrates a fluorogenic starch substrate to enable single-cell compartmentalization and real-time phenotypic screening. When applied to three major aroma-types of jiuqu, the platform rapidly identified 38 amylase-producing strains within just 8 hours—drastically faster than traditional plate methods requiring several days. The top-performing isolate exhibited a hydrolysis halo-to-colony (H/C) ratio of 3.8 and a DNS-validated activity of 350 U mL⁻¹. Compared to conventional screening, this droplet-based approach significantly shortens the screening cycle, reduces reagent consumption, and enhances throughput and analytical accuracy, enabling direct genotype–phenotype linkage at the single-cell level. This work establishes an efficient pipeline for mining functional microbial resources and demonstrates significant potential for industrial enzyme discovery and strain improvement in traditional fermentation and beyond.