Synergistic Integration of Whole-Cell Biosensors and Droplet Microfluidics for High-Throughput Microbial Screening

High-throughput screening (HTS) is essential for developing microbial cell factories, yet traditional droplet microfluidics often struggles to detect nonfluorescent metabolites. This perspective explores the whole-cell biosensor-encapsulated droplet reactor-based microbial high-throughput screening system (WCB-DHTS) as a versatile solution, which decouples production from sensing to reduce metabolic stress. By using engineered sensor strains to convert target metabolite concentrations into fluorescence signals, this platform enables the detection of diverse products within picoliter-scale droplets. This paper details strategies for optimizing transcription factor (TF)-based biosensors, including protein engineering and dynamic range tuning. It further discusses microfluidic integration techniques, such as co-encapsulation and pico-injection. Finally, the perspective addresses current challenges like transmembrane transport and droplet randomness, offering insights into future dual-color normalization and de novo sensor design. This integrated system significantly accelerates the design–build–test–learn cycle for sustainable biomanufacturing.