ArticleNature microbiology2023
Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection.
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 68 papers, 1 of them a synthesis that pooled it.
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Who cites it
68 citing papers in PubMed, 1 synthesis or guideline pooled it.
- From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.Briefings in bioinformatics · 2025Pooled it
- iModulonMiner 2.0: multi-modality modularization of prokaryotic bulk, single-cell, and community omics data.Nucleic acids research · 2026Article
- CBASS limits bacteriophage production while maintaining cell viability in Pseudomonas aeruginosa.Cell host & microbe · 2026Article
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- A Microcapsule-Integrated smRandom-seq Platform Enables Fixation-Free Single Microbe RNA Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A scalable, low-cost, sample hashing workflow for multiomic single-cell analysis using the Seq-Well SNature protocols · 2026Review
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Bacterial surface display enables lysis-independent joint host-pathogen single-cell profiling.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
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Single-bacterium RNA-seq protocol to uncover heterogeneous expression of coding and noncoding genes in Bacteroides thetaiotaomicron.STAR protocols · 2026Article
- Pre-treatment bacterial cell states shape antibiotic-induced transcriptional reprogramming and survival.Nature communications · 2026Article
- Single-phage profiling illuminates viral individuality during bacterial cell fate determination.Nature communications · 2026Article
- 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
- Microbial diversity as a foundation for biological AI : Learning biology from evolution's largest dataset.EMBO reports · 2026Article
- CBASS limits bacteriophage production while maintaining cell viability inbioRxiv : the preprint server for biology · 2026Article
8 more citing papers are in PubMed but not listed here.
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Abstract
Bacterial populations are highly adaptive. They can respond to stress and survive in shifting environments. How the behaviours of individual bacteria vary during stress, however, is poorly understood. To identify and characterize rare bacterial subpopulations, technologies for single-cell transcriptional profiling have been developed. Existing approaches show some degree of limitation, for example, in terms of number of cells or transcripts that can be profiled. Due in part to these limitations, few conditions have been studied with these tools. Here we develop massively-parallel, multiplexed, microbial sequencing (M3-seq)-a single-cell RNA-sequencing platform for bacteria that pairs combinatorial cell indexing with post hoc rRNA depletion. We show that M3-seq can profile bacterial cells from different species under a range of conditions in single experiments. We then apply M3-seq to hundreds of thousands of cells, revealing rare populations and insights into bet-hedging associated with stress responses and characterizing phage infection.
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