ArticleScientific reports2016
Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 47 citations in OpenAlex.
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- An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions.Plant methods · 2024Article
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- Dual RNA-seq in filarial nematodes andFrontiers in microbiology · 2024Article
- Carotenoids in Health as Studied by Omics-Related Endpoints.Advances in nutrition (Bethesda, Md.) · 2023Review
- Metatranscriptomic analysis of the gut microbiome of black soldier fly larvae reared on lignocellulose-rich fiber diets unveils key lignocellulolytic enzymes.Frontiers in microbiology · 2023Article
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- Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications.NPJ microgravity · 2021Article
- Best practices on the differential expression analysis of multi-species RNA-seq.Genome biology · 2021Review
- The Genome of "Frontiers in microbiology · 2021Article
- Large scale genome reconstructions illuminate Wolbachia evolution.Nature communications · 2020Article
- Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells.BMC genomics · 2020Article
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- Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis.Microbial cell (Graz, Austria) · 2019Article
- Multispecies Transcriptomics Data Set of Brugia malayi, ItsMicrobiology resource announcements · 2018Article
- Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
Despite numerous advances in genomics and bioinformatics, technological hurdles remain to examine host-microbe transcriptomics. Sometimes the transcriptome of either or both can be ascertained merely by generating more sequencing reads. However, many cases exist where bacterial mRNA needs to be enriched further to enable cost-effective sequencing of the pathogen or endosymbiont. While a suitable method is commercially available for mammalian samples of this type, development of such methods has languished for invertebrate samples. Furthermore, a common method across multiple taxa would facilitate comparisons between bacteria in invertebrate vectors and their vertebrate hosts. Here, a method is described to concurrently remove polyadenylated transcripts, prokaryotic rRNA, and eukaryotic rRNA, including those with low amounts of starting material (e.g. 100 ng). In a Wolbachia-Drosophila system, this bacterial mRNA enrichment yielded a 3-fold increase in Wolbachia mRNA abundance and a concomitant 3.3-fold increase in the percentage of transcripts detected. More specifically, 70% of the genome could be recovered by transcriptome sequencing compared to 21% in the total RNA. Sequencing of similar bacterial mRNA-enriched samples generated from Ehrlichia-infected canine cells covers 93% of the Ehrlichia genome, suggesting ubiquitous transcription across the entire Ehrlichia chaffeensis genome. This technique can potentially be used to enrich bacterial mRNA in many studies of host-microbe interactions.
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