ArticleScientific reports2017
Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- A Universal, Cost-Effective, and Efficient rRNA Depletion Method for Bacterial mRNA Enrichment.Biochemical genetics · 2026Article
- Transcriptomic and RNA Modification Landscape of Severe Fever with Thrombocytopenia Syndrome Virus Revealed by Nanopore Direct RNA Sequencing.Microorganisms · 2026Article
- A comparative analysis of mRNA enrichment strategies and guidance for improving their efficiency.Scientific reports · 2025Article
- Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.Microbial genomics · 2024Article
- Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.Nucleic acids research · 2024Article
- An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.Plant methods · 2024Article
- Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation.Biological procedures online · 2023Article
- Foliage of Tropical Trees and Shrubs and Their Secondary Metabolites Modify In Vitro Ruminal Fermentation, Methane and Gas Production without a Tight Correlation with the Microbiota.Animals : an open access journal from MDPI · 2022Article
- Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont.Marine biotechnology (New York, N.Y.) · 2022Article
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria.NPJ biofilms and microbiomes · 2022Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
- RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.PLoS genetics · 2021Article
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Cross-species RNA-seq for deciphering host-microbe interactions.Nature reviews. Genetics · 2021Review
- Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis.Microbial ecology · 2021Article
- Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary.Animal microbiome · 2021Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom.Frontiers in microbiology · 2021Article
- RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques.iScience · 2020Article
- Response of Pseudomonas aeruginosa to the Innate Immune System-Derived Oxidants Hypochlorous Acid and Hypothiocyanous Acid.Journal of bacteriology · 2020Article
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4 authors.
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Abstract
Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, comparative evaluation of bacterial rRNA depletion methods has remained limited. Moreover, no such study has utilized RNA derived from bacterial biofilms, which have potentially higher rRNA:mRNA ratios and higher rRNA carryover during RNA-seq analysis. Presently, we evaluated the efficiency of three subtractive hybridization-based kits in depleting rRNA from samples derived from biofilm, as well as planktonic cells of the opportunistic human pathogen Pseudomonas aeruginosa. Our results indicated different rRNA removal efficiency for the three procedures, with the Ribo-Zero kit yielding the highest degree of rRNA depletion, which translated into enhanced enrichment of non-rRNA transcripts and increased depth of RNA-seq coverage. The results indicated that, in addition to improving RNA-seq sensitivity, efficient rRNA removal enhanced detection of low abundance transcripts via qPCR. Finally, we demonstrate that the Ribo-Zero kit also exhibited the highest efficiency when P. aeruginosa/Staphylococcus aureus co-culture RNA samples were tested.
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