Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms

Sci Rep. 2017 Jan 23;7:41192. doi: 10.1038/srep41192.


Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Separation / methods*
  • Chlamydomonas reinhardtii / genetics
  • DNA / analysis
  • DNA / isolation & purification
  • Genome
  • Genomics*
  • Microbiological Techniques*
  • Microfluidic Analytical Techniques*
  • Microfluidics
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / isolation & purification
  • Single-Cell Analysis / methods*


  • DNA