Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start.
10.1016/j.gpb.2021.03.010
- Author:
David CONCHOUSO
1
,
2
,
3
;
Amani AL-MA'ABADI
3
,
4
;
Hayedeh BEHZAD
3
,
4
;
Mohammed ALARAWI
3
,
4
;
Masahito HOSOKAWA
5
,
6
,
7
;
Yohei NISHIKAWA
5
,
8
;
Haruko TAKEYAMA
5
,
6
,
8
,
9
;
Katsuhiko MINETA
4
,
10
;
Takashi GOJOBORI
4
,
11
Author Information
1. Department of Industrial and Mechanical Engineering, Universidad de las Américas Puebla, Puebla 72810, Mexico
2. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
3. Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
4. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
5. Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan
6. Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan
7. Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.
8. Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan.
9. Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
10. Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Electronic address: katsuhiko.mineta@kaust.edu.sa.
11. Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia. Electronic address: takashi.gojobori@kaust.edu.sa.
- Publication Type:Journal Article
- Keywords:
Biotechnology;
Droplet microfluidics;
Droplet sorter;
Metagenomics;
Single cell
- From:
Genomics, Proteomics & Bioinformatics
2021;19(3):504-518
- CountryChina
- Language:English
-
Abstract:
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.
