ArticleBMC genomics2020
Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 34 citations in OpenAlex.
- Bulk transcriptomics of peripheral blood mononuclear cells delineates systems-level immune dysregulation in pediatric dengue infection.NPJ systems biology and applications · 2026Article
- DepStep: An Efficient One-Step rRNA Depletion Workflow for RNA Sequencing in Non-model Organisms.Bio-protocol · 2026Article
- Optimization of Metagenomic Library Construction for Influenza A Virus and SARS-CoV-2: Systematic Comparison of rRNA Depletion Strategies and Fragmentation Orders.Diagnostics (Basel, Switzerland) · 2026Article
- Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.Nature microbiology · 2026Article
- Illuminating the mechanism: gene expression responses to antimicrobial photodynamic therapy.BMC genomics · 2026Review
- Plant Growth-Promoting Rhizobacteria and Bacterial Biocontrol Agents in Tomato Disease Management: Mechanisms, Applications, and Omics Perspectives.Global challenges (Hoboken, NJ) · 2025Review
- Biomineralized gold nanoparticles along with endophytic bacterial taxa in needles of Norway spruce (Picea abies).Environmental microbiome · 2025Article
- Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.Frontiers in immunology · 2025Review
- Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA fromMicrobial genomics · 2024Article
- Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity.Nature structural & molecular biology · 2024Article
- Dual RNA-seq in filarial nematodes andFrontiers in microbiology · 2024Article
- Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures.mSystems · 2023Article
- Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry.The Japanese dental science review · 2023Review
- Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti.The ISME journal · 2023Article
- Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation.Biological procedures online · 2023Article
- PPNet: Identifying Functional Association Networks by Phylogenetic Profiling of Prokaryotic Genomes.Microbiology spectrum · 2023Article
- Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage.Antibiotics (Basel, Switzerland) · 2022Article
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters.Microorganisms · 2021Review
- RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.PLoS genetics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell. Moreover, bacterial cells frequently contain 100-fold lower quantities of RNA compared to mammalian cells, which further complicates mRNA sequencing from non-cultivable and non-model bacterial species. To overcome these limitations, we report EMBR-seq (Enrichment of mRNA by Blocked rRNA), a method that efficiently depletes 5S, 16S and 23S rRNA using blocking primers to prevent their amplification.
resultsEMBR-seq results in 90% of the sequenced RNA molecules from an E. coli culture deriving from mRNA. We demonstrate that this increased efficiency provides a deeper view of the transcriptome without introducing technical amplification-induced biases. Moreover, compared to recent methods that employ a large array of oligonucleotides to deplete rRNA, EMBR-seq uses a single or a few oligonucleotides per rRNA, thereby making this new technology significantly more cost-effective, especially when applied to varied bacterial species. Finally, compared to existing commercial kits for bacterial rRNA depletion, we show that EMBR-seq can be used to successfully quantify the transcriptome from more than 500-fold lower starting total RNA.
conclusionsEMBR-seq provides an efficient and cost-effective approach to quantify global gene expression profiles from low input bacterial samples.
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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.