Advances in single-cell sequencing technology in microbiome research

Yinhang Wu; Jing Zhuang; Yifei Song; Xinyi Gao; Jian Chu; Shuwen Han

doi:10.1016/j.gendis.2023.101129

Advances in single-cell sequencing technology in microbiome research

Genes Dis. 2023 Sep 28;11(4):101129. doi: 10.1016/j.gendis.2023.101129. eCollection 2024 Jul.

Authors

Yinhang Wu^{1

2

3}, Jing Zhuang^{1

2

3}, Yifei Song¹, Xinyi Gao⁴, Jian Chu^{1

2

3}, Shuwen Han^{1

2

3}

Affiliations

¹ Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang 313000, China.
² Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, Zhejiang 313000, China.
³ The Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 313000, China.
⁴ Zhejiang Provincial People's Hospital and Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310000, China.

Abstract

With the rapid development of histological techniques and the widespread application of single-cell sequencing in eukaryotes, researchers desire to explore individual microbial genotypes and functional expression, which deepens our understanding of microorganisms. In this review, the history of the development of microbial detection technologies was revealed and the difficulties in the application of single-cell sequencing in microorganisms were dissected as well. Moreover, the characteristics of the currently emerging microbial single-cell sequencing (Microbe-seq) technology were summarized, and the prospects of the application of Microbe-seq in microorganisms were distilled based on the current development status. Despite its mature development, the Microbe-seq technology was still in the optimization stage. A retrospective study was conducted, aiming to promote the widespread application of single-cell sequencing in microorganisms and facilitate further improvement in the technology.

Keywords: Bacterial antibiotic resistance; Host immunity; Host-phage interaction; Microbial single-cell sequencing; Microorganisms; Single cell; Single-cell sequencing technology.

Publication types

Review