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Related Experiment Video

Updated: Nov 25, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Microbial single-cell RNA sequencing by split-pool barcoding.

Anna Kuchina¹, Leandra M Brettner^2,3, Luana Paleologu^4,5

¹Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA.

Science (New York, N.Y.)

|December 18, 2020

Summary

This summary is machine-generated.

We developed microSPLiT, a novel single-cell RNA sequencing method for bacteria. This technique resolves gene expression heterogeneity in microbial communities, enabling detailed analysis of bacterial transcriptional states.

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Last Updated: Nov 25, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

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Published on: May 23, 2018

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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Published on: August 29, 2014

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

Area of Science:

Microbiology
Genomics
Molecular Biology

Background:

Single-cell RNA sequencing (scRNA-seq) is crucial for eukaryotic gene expression analysis.
Existing scRNA-seq methods are not suitable for bacterial cells.
Understanding bacterial transcriptional heterogeneity is vital for microbiology.

Purpose of the Study:

To introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for bacteria.
To enable the resolution of heterogeneous transcriptional states in bacteria.
To create a comprehensive gene expression atlas for bacterial communities.

Main Methods:

Development of microSPLiT, a novel high-throughput scRNA-seq technique.
Application of microSPLiT to over 25,000 Bacillus subtilis cells across various growth stages.
Analysis of gene expression profiles at the single-cell level.

Main Results:

Successfully applied microSPLiT to both Gram-negative and Gram-positive bacteria.
Generated a detailed gene expression atlas of Bacillus subtilis, revealing changes in metabolism and lifestyle.
Identified known rare states like competence and prophage induction, alongside novel heterogeneous gene expression states.

Conclusions:

MicroSPLiT is a powerful tool for high-throughput single-cell gene expression analysis in bacteria.
The method allows for the study of bacterial transcriptional heterogeneity previously inaccessible.
MicroSPLiT opens new avenues for analyzing complex bacterial communities, including natural microbiota.