Probe-based bacterial single-cell RNA sequencing predicts toxin regulation.

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Clonal bacterial populations exhibit transcriptional variation for specialized cell states and increased fitness.
• Studying isogenic bacterial populations at the single-cell level is crucial for understanding diverse cell states.

Purpose of the Study:

• To develop a novel method for bacterial single-cell RNA sequencing.
• To analyze transcriptional heterogeneity in bacterial populations.
• To investigate the impact of environmental factors on bacterial pathogenicity.

Main Methods:

• Developed probe-based bacterial sequencing (ProBac-seq).
• Utilized DNA probes and a microfluidic platform for single-cell RNA sequencing.
• Sequenced transcriptomes of thousands of individual bacterial cells.

Main Results:

• ProBac-seq successfully sequenced transcriptomes of thousands of bacterial cells, detecting hundreds of transcripts per cell.
• Applied to Bacillus subtilis and Escherichia coli, ProBac-seq identified known cell states and uncovered novel transcriptional heterogeneity.
• Analysis of Clostridium perfringens revealed heterogeneous toxin expression in a subpopulation, modulated by acetate.

Conclusions:

• ProBac-seq is an effective method for uncovering transcriptional heterogeneity in isogenic microbial populations.
• The method can identify perturbations affecting bacterial pathogenicity, as demonstrated with Clostridium perfringens.
• Understanding single-cell transcriptional states is key to deciphering bacterial adaptation and virulence.