ArticleNature communications2023
Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 89 citations in OpenAlex.
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- iModulonMiner 2.0: multi-modality modularization of prokaryotic bulk, single-cell, and community omics data.Nucleic acids research · 2026Article
- Harnessing microfluidics for microbiology: from bacteria-host interactions to emerging cancer therapies.Communications biology · 2026Review
- Spatial Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Tissue by spRandom-seq.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- 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
- 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
- Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution.Trends in genetics : TIG · 2026Review
- Pre-treatment bacterial cell states shape antibiotic-induced transcriptional reprogramming and survival.Nature communications · 2026Article
- The gut-joint axis in osteoarthritis.Nature reviews. Rheumatology · 2026Review
- scDeepAPA: a deep learning framework for single-cell alternative polyadenylation identification.Briefings in bioinformatics · 2026Article
- Review
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 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
- Single-bacterial cell insights into mechanisms of ceftriaxone resistance in Neisseria subflava.Nature communications · 2026Article
- BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution.Briefings in bioinformatics · 2026Article
- Antibiotic Persistence Emerges from Cell-State-Driven Transcriptional Reprogramming.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.
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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.