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Updated: Aug 5, 2026
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
Microbial single-cell sequencing technologies: Principles, applications, and spatial integration
Fei Xu1, Fangyu Mo1, Babatunde O Kehinde2
1Hainan Institute, Zhejiang University, Sanya 572025, China; Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.
Biotechnology Advances
|July 30, 2026
Summary
Microbial single-cell sequencing offers new insights into microbial ecosystems by revealing cellular details. This review synthesizes technologies, challenges, and applications, including spatial omics.
Area of Science:
- Microbiology
- Genomics
- Molecular Biology
Background:
- Microbial ecosystems are complex and traditionally studied at a population level.
- Single-cell sequencing (SCS) technology enables the study of microbial heterogeneity, interactions, and evolution at an unprecedented resolution.
- Understanding individual microbial cells is crucial for fields ranging from environmental science to medicine.
Purpose of the Study:
- To systematically review and synthesize current microbial single-cell sequencing technologies.
- To provide a detailed understanding of the technical principles, strengths, and limitations of various SCS approaches.
- To discuss the challenges and practical applications of SCS across different microbial domains and introduce the emerging field of microbial spatial omics.
Main Methods:
- Systematic literature review of microbial single-cell sequencing technologies.
- Analysis of underlying technical principles, strengths, and limitations of different SCS methods.
- Exploration of technical challenges and practical applications in diverse microbial environments.
- Summary of advancements in microbial spatial omics, including imaging techniques.
Main Results:
- Microbial SCS technologies provide high-resolution data on cellular heterogeneity, interactions, and genetic evolution.
- Various SCS approaches have distinct technical principles, strengths, and limitations that influence their applicability.
- Significant technical challenges exist in applying SCS across different microbial domains, impacting data acquisition and interpretation.
- Emerging microbial spatial omics techniques, combining sequencing with advanced imaging, offer new avenues for studying microbial communities in situ.
Conclusions:
- Microbial single-cell sequencing is a transformative technology for dissecting microbial ecosystems.
- A comprehensive understanding of SCS technologies, their challenges, and applications is essential for researchers.
- The integration of SCS with spatial omics and advanced imaging holds great promise for future microbial research.
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