ArticleNature microbiology2023
Probe-based bacterial single-cell RNA sequencing predicts toxin regulation.
Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed, 110 citations in OpenAlex.
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- A Microcapsule-Integrated smRandom-seq Platform Enables Fixation-Free Single Microbe RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Simultaneous measurements of translation rate and transcriptome uncovers linked regulation within an active bacterial cell population.Science advances · 2026Article
- Microbial single-cell transcriptomics links gut microbiota functional states to metabolic changes in male mice.Nature communications · 2026Article
- Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron.STAR protocols · 2026Article
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- Single-bacterium metabolome revealing heterogeneous cellular states in bacterial populations.Nature communications · 2026Article
- Review
- Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data.Statistics in medicine · 2026Article
- Single-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa.Nature communications · 2026Article
- Ultrasmall oral Saccharibacteria modulate gingival immunoactivation through type IV pili and TLR2-dependent endocytosis.Nature communications · 2026Article
- Illuminating the mechanism: gene expression responses to antimicrobial photodynamic therapy.BMC genomics · 2026Review
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- A Brief Review of Microbial Omics: Methods and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Single microorganism RNA sequencing of microbiomes using smRandom-Seq.Nature protocols · 2026Review
- Decoding the spatiotemporal heterogeneity of bacterial virulence gene expression using single-cell approaches.Frontiers in microbiology · 2026Review
- Clinical application of single-cell RNA sequencing in disease and therapy.Clinical and translational medicine · 2025Review
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 1 country.
Funding
Abstract
Clonal bacterial populations rely on transcriptional variation across individual cells to produce specialized states that increase fitness. Understanding all cell states requires studying isogenic bacterial populations at the single-cell level. Here we developed probe-based bacterial sequencing (ProBac-seq), a method that uses libraries of DNA probes and an existing commercial microfluidic platform to conduct bacterial single-cell RNA sequencing. We sequenced the transcriptome of thousands of individual bacterial cells per experiment, detecting several hundred transcripts per cell on average. Applied to Bacillus subtilis and Escherichia coli, ProBac-seq correctly identifies known cell states and uncovers previously unreported transcriptional heterogeneity. In the context of bacterial pathogenesis, application of the approach to Clostridium perfringens reveals heterogeneous expression of toxin by a subpopulation that can be controlled by acetate, a short-chain fatty acid highly prevalent in the gut. Overall, ProBac-seq can be used to uncover heterogeneity in isogenic microbial populations and identify perturbations that affect pathogenicity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.