ArticleBMC genomics2013
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease.Frontiers in physiology · 2022Pooled it
- Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.The Journal of nutritional biochemistry · 2020Trial
- Gut microbiota profiles in reactive and metastatic lymphadenopathy in colorectal cancer: a tumor location-stratified analysis.International journal of colorectal disease · 2026Article
- From soil to sequences: mechanisms and tools unravelling plant-rhizomicrobiome interactions.World journal of microbiology & biotechnology · 2026Review
- Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science.Metabolites · 2025Review
- Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.ISME communications · 2025Article
- Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly.BMC bioinformatics · 2023Article
- Immune priming prior to pathogen exposure sheds light on the relationship between host, microbiome and pathogen in disease.Royal Society open science · 2023Article
- Altered intestinal microbiota in children with bronchiolitis.Frontiers in microbiology · 2023Article
- An overview of technologies for MS-based proteomics-centric multi-omics.Expert review of proteomics · 2022Article
- Article
- Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods.Frontiers in microbiology · 2021Article
- Impact of Fermentable Protein, by Feeding High Protein Diets, on Microbial Composition, Microbial Catabolic Activity, Gut Health and beyond in Pigs.Microorganisms · 2020Review
- Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments.3 Biotech · 2020Review
- AnToxicology reports · 2020Article
- Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota.Microorganisms · 2019Article
- Systems biology perspective for studying the gut microbiota in human physiology and liver diseases.EBioMedicine · 2019Review
- Bioactive Synthetic-Bioinformatic Natural Product Cyclic Peptides Inspired by Nonribosomal Peptide Synthetase Gene Clusters from the Human Microbiome.Journal of the American Chemical Society · 2019Article
- Predictors Linking Obesity and the Gut Microbiome (the PROMISE Study): Protocol and Recruitment Strategy for a Cross-Sectional Study on Pathways That Affect the Gut Microbiome and Its Impact on Obesity.JMIR research protocols · 2019Article
- To assemble or not to resemble-A validated Comparative Metatranscriptomics Workflow (CoMW).GigaScience · 2019Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing (NGS) technologies can be applied in complex microbial ecosystems for metatranscriptome analysis by employing direct cDNA sequencing, which is known as RNA sequencing (RNA-seq). RNA-seq generates large datasets of great complexity, the comprehensive interpretation of which requires a reliable bioinformatic pipeline. In this study, we focus on the development of such a metatranscriptome pipeline, which we validate using Illumina RNA-seq datasets derived from the small intestine microbiota of two individuals with an ileostomy.
resultsThe metatranscriptome pipeline developed here enabled effective removal of rRNA derived sequences, followed by confident assignment of the predicted function and taxonomic origin of the mRNA reads. Phylogenetic analysis of the small intestine metatranscriptome datasets revealed a strong similarity with the community composition profiles obtained from 16S rDNA and rRNA pyrosequencing, indicating considerable congruency between community composition (rDNA), and the taxonomic distribution of overall (rRNA) and specific (mRNA) activity among its microbial members. Reproducibility of the metatranscriptome sequencing approach was established by independent duplicate experiments. In addition, comparison of metatranscriptome analysis employing single- or paired-end sequencing methods indicated that the latter approach does not provide improved functional or phylogenetic insights. Metatranscriptome functional-mapping allowed the analysis of global, and genus specific activity of the microbiota, and illustrated the potential of these approaches to unravel syntrophic interactions in microbial ecosystems.
conclusionsA reliable pipeline for metatransciptome data analysis was developed and evaluated using RNA-seq datasets obtained for the human small intestine microbiota. The set-up of the pipeline is very generic and can be applied for (bacterial) metatranscriptome analysis in any chosen niche.
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