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

Microbial single-cell sequencing technology enables unprecedented resolution of microbial ecosystems, revealing cellular heterogeneity, interactions, and genetic evolution.

• Why it matters: Microbial communities are diverse and dynamic, and bulk measurements miss key cellular states, interactions, and evolutionary changes.
• What they did: This review systematically compiles current microbial single-cell sequencing technologies, synthesizing their technical principles, strengths/limitations, and domain-specific challenges, and summarizes microbial spatial omics with imaging using sequencing and fluorescence in situ hybridization.
• The result: The synthesis clarifies how different single-cell and spatial approaches can be applied to study microbial ecosystems, guiding selection of methods that match specific technical constraints and research goals.

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