Polychip-A High-Throughput Droplet Microfluidics Platform for Interrogating Microbial Interactions

Microbial interactions are fundamental to ecology, health, and disease, yet high-throughput tools to study these complex relationships remain scarce. We introduce Polychip, a fully integrated, high-throughput droplet microfluidics platform that revolutionizes microbial interaction screening. By seamlessly combining six microfluidic operations onto a single chip, Polychip achieves 99.7% efficiency and accelerates screening by 11-14 times compared to traditional high-throughput liquid handling robotic methods, with minimal human input. Using the Polychip, we screened 2.24 × 10⁶ soil-extracted microorganisms against the multidrug-resistant (MDR) pathogen Pseudomonas aeruginosa. This process recovered 1.96 × 10⁴ hit droplets with an antimicrobial activity confirmation accuracy of 48%. Three environmental isolates (Stenotrophomonas sp.) exhibiting high potency and broad-spectrum antimicrobial activity were identified through this screen. Supernatants from these three environmental isolates suppressed growth of both gram-negative MDR pathogen Acinetobacter baumannii and gram-positive methicillin-resistant Staphylococcus aureus (MRSA). Through whole-genome sequencing, metabolic pathway analysis, and mass spectrometry, we identified the secreted compound as enterochelin. This demonstrates Polychip's unprecedented single-cell resolution and high throughput screening capability in rapidly discovering antimicrobial activities, opening new frontiers in combating resistant microbial pathogens, as well as more broadly advancing microbial ecology research.