Induced Droplet Ovalisation (IDO): Image-based microfluidic method for high-throughput and label-free characterization of microbial proteolytic strains from wastewater sludge

Traditional bacterial isolation methods are costly, labour-intensive, and often fail to detect rare or slow-growing taxa. In contrast, droplet-based microfluidic assays have emerged as powerful alternatives. Here, we describe a novel, label-free microfluidic assay for screening microbial proteolytic activity based on oil-induced droplet ovalization. This method outperformed two traditional isolation techniques in terms of performance, time, and overall cost-efficiency. We present Induced Droplet Ovalisation (IDO): a droplet-based protocol that combines single-cell encapsulation with automated image analysis. Using a custom-made microfluidic device and bespoke image-processing scripts, our system efficiently detects microbial proteolytic activity by monitoring droplet deformability. This approach significantly reduces the time and resources required to study proteolytic consortia, offering an automated, easy-to-implement, and label-free alternative to conventional screening. Our device achieves high-throughput screening (HTS) at 0.2 kHz while significantly reducing the cultivation medium volume used compared to traditional methods. Furthermore, in-droplet microbial recovery is enhanced by two orders of magnitude, enabling the enumeration of significantly more colonies compared to traditional screenings. Beyond microbiological applications, this versatile platform serves as a powerful tool for studying hydrogel degradation and polymerization dynamics, extending its applicability across research and industry.