Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start

David Conchouso, Amani Al-Ma'abadi, Hayedeh Behzad, Mohammed Alarawi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Katsuhiko Mineta*, Takashi Gojobori

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant due to the complex and multidisciplinary nature of the field. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (>50,000 cells/day) for mining and bioprospecting metagenomic data.

Original languageEnglish
Pages (from-to)504-518
Number of pages15
JournalGenomics, Proteomics and Bioinformatics
Issue number3
Publication statusPublished - 2021 Jun


  • Biotechnology
  • Droplet microfluidics
  • Droplet sorter
  • Metagenomics
  • Single cell

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Computational Mathematics


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