One cell at a time: droplet-based microbial cultivation, screening and sequencing

Beiyu Hu; Peng Xu; Liang Ma; Dongwei Chen; Jian Wang; Xin Dai; Li Huang; Wenbin Du

doi:10.1007/s42995-020-00082-8

One cell at a time: droplet-based microbial cultivation, screening and sequencing

Mar Life Sci Technol. 2021 Jan 19;3(2):169-188. doi: 10.1007/s42995-020-00082-8. eCollection 2021 May.

Authors

Beiyu Hu^{1

2}, Peng Xu³, Liang Ma⁴, Dongwei Chen¹, Jian Wang¹, Xin Dai^{1

2}, Li Huang^{1

2}, Wenbin Du^{1

4

2

5}

Affiliations

¹ State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China.
² College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China.
³ Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA.
⁴ Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China.
⁵ Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China.

Abstract

Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.

Keywords: Antibiotic resistance; Droplet microfluidics; Microbial cultivation; Single-cell screening; Single-cell sequencing; Uncultured microorganisms.

Publication types

Review