Microdroplet-based system for culturing of environmental microorganisms using FNAP-sort

Droplet microfluidics has emerged as a powerful technology for improving the culturing efficiency of environmental microorganisms. However, its widespread adoption has been limited due to considerable technical challenges, especially related to identification and manipulation of individual growth-positive droplets. Here, we combined microfluidic droplet technology with on-chip fluorescent nucleic acid probe in droplets for bacterial sorting (FNAP-sort) for recovery of growth-positive droplets and droplet microdispensing to establish an end-to-end workflow for isolation and culturing of environmental microbes. As a proof-of-concept, we demonstrate the ability of our technique to yield high-purity cultures of rare microorganisms from a representative complex environmental microbiome. As our system employs off-the-shelf commercially available equipment, we believe that it can be readily adopted by others and may thus find widespread use toward culturing the high proportion of as-of-yet uncultured microorganisms in different biomes.

Automated summary

The technique combines microfluidic droplet technology with fluorescent nucleic acid probes to efficiently recover growth-positive droplets, establishing a comprehensive workflow for isolation and culturing of environmental microbes. The system uses off-the-shelf commercially available equipment, making it easily adoptable for widespread use in culturing previously uncultured microorganisms.