Microbial single-cell sequencing technologies: Principles, applications, and spatial integration

The advent of microbial single-cell sequencing technology provides unprecedented resolution to study microbial ecosystems, revealing cellular heterogeneity, interactions, and genetic evolution of microorganisms. This review systematically compiles current microbial single-cell sequencing technologies, providing a detailed synthesis of their underlying technical principles, illuminating the strengths and limitations of various approaches. In-depth summaries of the technical challenges they encounter in different microbial domains and their practical applications are provided. Finally, we summarized the emerging field of microbial spatial omics, with a particular focus on advanced imaging techniques utilizing sequencing and fluorescence in situ hybridization.