ArticlePloS one2008
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
138 citing papers in PubMed, 1 synthesis or guideline pooled it, 398 citations in OpenAlex.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- Review
- Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?Molecular ecology · 2025Article
- Unraveling the assembly mechanisms and differentiated ecological functions of protist cell-associated and free-living bacterial communities during twoMicrobiology spectrum · 2025Article
- No-tillage systems promote bacterial photosynthetic gene expression in low carbon, semi-arid surface soils.Applied and environmental microbiology · 2025Article
- The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.PeerJ · 2025Article
- Freshwater plastisphere: a review on biodiversity, risks, and biodegradation potential with implications for the aquatic ecosystem health.Frontiers in microbiology · 2024Review
- Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency.Environmental microbiology reports · 2023Article
- The oral microbiome in the pathophysiology of cardiovascular disease.Nature reviews. Cardiology · 2023Review
- Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly.BMC bioinformatics · 2023Article
- The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points.Microbial ecology · 2023Article
- Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment.Ecotoxicology (London, England) · 2021Article
- Global Distribution and Richness ofFrontiers in microbiology · 2021Article
- Antimicrobial Resistance in Veterinary Medicine: An Overview.International journal of molecular sciences · 2020Review
- Bacterial metagenome analysis of Mytilus galloprovincialis collected from Istanbul and Izmir coastal stations of Turkey.Environmental monitoring and assessment · 2020Article
- Quantitative models of nitrogen-fixing organisms.Computational and structural biotechnology journal · 2020Review
- Copepod-Associated Gammaproteobacterial Alkaline Phosphatases in the North Atlantic Subtropical Gyre.Frontiers in microbiology · 2020Article
- Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data.PloS one · 2020Article
- Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil.Journal, genetic engineering & biotechnology · 2019Article
- Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom.Applied and environmental microbiology · 2019Article
78 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundSequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environmental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural communities. METHODOLOGY/PRINCIPAL
findingsWe present a study of a complex marine metatranscriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology. Eight samples, four DNA and four mRNA, were processed from two time points in a controlled coastal ocean mesocosm study (Bergen, Norway) involving an induced phytoplankton bloom producing a total of 323,161,989 base pairs. Our study confirms the finding of the first published metatranscriptomic studies of marine and soil environments that metatranscriptomics targets highly expressed sequences which are frequently novel. Our alternative methodology increases the range of experimental options available for conducting such studies and is characterized by an exceptional enrichment of mRNA (99.92%) versus ribosomal RNA. Analysis of corresponding metagenomes confirms much higher levels of assembly in the metatranscriptomic samples and a far higher yield of large gene families with >100 members, approximately 91% of which were novel. CONCLUSIONS/SIGNIFICANCE: This study provides further evidence that metatranscriptomic studies of natural microbial communities are not only feasible, but when paired with metagenomic data sets, offer an unprecedented opportunity to explore both structure and function of microbial communities--if we can overcome the challenges of elucidating the functions of so many never-seen-before gene families.
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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.