ArticleNature communications2024
Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The global prevalence of biofilm-forming Enterococcus faecalis in clinical isolates: a systematic review and meta-analysis.BMC infectious diseases · 2025Pooled it
- A comprehensive review of regulatory mechanisms of novel enterotoxin genes inAnnals of medicine · 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
- Siderophore sharing protects clonalApplied and environmental microbiology · 2026Article
- Microbial single-cell transcriptomics links gut microbiota functional states to metabolic changes in male mice.Nature communications · 2026Article
- Environmental regulation of virulence in Vibrio cholerae: integrating multi-omics, predictive models, and comparative insights across emerging Vibrio species.Gut pathogens · 2026Review
- Current State of the Fight Against Antimicrobial Resistance: What Are the Different Strategies for Tomorrow?Antibiotics (Basel, Switzerland) · 2026Review
- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- Targeting metabolism to combat anticancer and antibacterial drug resistance.Trends in pharmacological sciences · 2026Review
- Differential sensitivity of leukocyte populations toInfection and immunity · 2026Article
- Comparative transcriptomics uncover differential regulatory mechanisms in MRSA and MSSA biofilms through RNA-sequencing.Folia microbiologica · 2026Article
- Infection responsive bio-nanoparticles as "molecular sprayer " for infection-repair integration via direct sterilization and macrophage polarization regulation.Bioactive materials · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- UnderstandingMicroorganisms · 2026Review
- BacQuant: A Scalable Automated Image Processing Pipeline for Quantifying Biofilm Aggregates.microPublication biology · 2026Article
- Cell-to-Cell and Patient-to-Patient Variability in Antimicrobial Resistance.Microorganisms · 2025Review
- Pathogen virulence genes: Advances, challenges and future directions in infectious disease research (Review).International journal of molecular medicine · 2025Review
- Single-cell lysis patterns morphogenesis of eDNA in the matrix ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
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Abstract
Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display metabolic and transcriptional diversity along with recalcitrance to antibiotics and host immune defenses. Here, we present an optimized bacterial single-cell RNA sequencing method, BaSSSh-seq, to study Staphylococcus aureus diversity during biofilm growth and transcriptional adaptations following immune cell exposure. BaSSSh-seq captures extensive transcriptional heterogeneity during biofilm compared to planktonic growth. We quantify and visualize transcriptional regulatory networks across heterogeneous biofilm subpopulations and identify gene sets that are associated with a trajectory from planktonic to biofilm growth. BaSSSh-seq also detects alterations in biofilm metabolism, stress response, and virulence induced by distinct immune cell populations. This work facilitates the exploration of biofilm dynamics at single-cell resolution, unlocking the potential for identifying biofilm adaptations to environmental signals and immune pressure.
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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.