Simple and multiplexed tracking of bacterial growth in double emulsion droplets

Abstract Droplet-based microfluidics enable researchers to observe phenotypic heterogeneity within complex biological mixtures through parallel encapsulation of individual samples followed by imaging. Observing or quantifying dynamic heterogeneity remains challenging due to complexities associated with trapping and tracking many individual droplets. Current approaches for time-lapse imaging require specialized devices with droplet traps that limit accessibility and throughput. Here, using readily available materials and software, we demonstrate a simple method for stabilizing and monitoring many, individual droplets for up to 12 hours. We leveraged our method to track bacterial growth within droplets in a high-throughput manner. Our method allows tracking the changes and variation in growth rate within and across droplets, revealing heterogeneity in growth patterns hidden in batch assays. Improving the affordability and throughput of time-dependent phenotyping assays helps to advance biological discovery and biotechnology innovation.