ArticleScientific reports2019
Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 40 citations in OpenAlex.
- An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut.Cell · 2026Article
- Enriching Bacteria-Specific RNA From Host Samples Before NGS With Transcript-Capture.Bio-protocol · 2026Article
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- Unravelling bacterial complexity at high resolution with single-cell transcriptomics.Nature microbiology · 2026Review
- Bacterial reporter-paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Hybrid capture RNA-seq defines temporal gene expression inbioRxiv : the preprint server for biology · 2026Article
- Transcript-Capture sequencing enriches mRNA ofNAR molecular medicine · 2026Article
- Transcript-Capture sequencing enriches mRNA ofbioRxiv : the preprint server for biology · 2025Article
- Advances in Single-Cell Sequencing for Infectious Diseases: Progress and Perspectives.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Actively expressed microbiota in mucosal biopsies of treatment-naïve ulcerative colitis patients.Gut microbes reports · 2025Article
- Urinary tract infections and catheter-associated urinary tract infections caused byMicrobiology and molecular biology reviews : MMBR · 2024Review
- Dissecting host-microbe interactions with modern functional genomics.Current opinion in microbiology · 2024Review
- Transcriptome analysis ofmBio · 2024Article
- Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry.The Japanese dental science review · 2023Review
- High-throughput functional genomics: A (myco)bacterial perspective.Molecular microbiology · 2023Review
- Probe-based bacterial single-cell RNA sequencing predicts toxin regulation.Nature microbiology · 2023Article
- Article
- Pseudomonas aeruginosa Promotes Persistence of Stenotrophomonas maltophilia via Increased Adherence to Depolarized Respiratory Epithelium.Microbiology spectrum · 2023Article
- Article
- Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion.Communications biology · 2022Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dual transcriptional profiling of host and bacteria during infection is challenging due to the low abundance of bacterial mRNA. We report Pathogen Hybrid Capture (PatH-Cap), a method to enrich for bacterial mRNA and deplete bacterial rRNA simultaneously from dual RNA-seq libraries using transcriptome-specific probes. By addressing both the differential RNA content of the host relative to the infecting bacterium and the overwhelming abundance of uninformative structural RNAs (rRNA, tRNA) of both species in a single step, this approach enables analysis of very low-input RNA samples. By sequencing libraries before (pre-PatH-Cap) and after (post-PatH-Cap) enrichment, we achieve dual transcriptional profiling of host and bacteria, respectively, from the same sample. Importantly, enrichment preserves relative transcript abundance and increases the number of unique bacterial transcripts per gene in post-PatH-Cap libraries compared to pre-PatH-Cap libraries at the same sequencing depth, thereby decreasing the sequencing depth required to fully capture the transcriptional profile of the infecting bacteria. We demonstrate that PatH-Cap enables the study of low-input samples including single eukaryotic cells infected by 1-3 Pseudomonas aeruginosa bacteria and paired host-pathogen temporal gene expression analysis of Mycobacterium tuberculosis infecting macrophages. PatH-Cap can be applied to the study of a range of pathogens and microbial species, and more generally, to lowly-abundant species in mixed populations.
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