ArticleBioinformatics (Oxford, England)2015
Reconstructing 16S rRNA genes in metagenomic data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
84 citing papers in PubMed.
- Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder.Scientific reports · 2019Trial
- Diversity, ecology, cell biology and evolution of the Asgard archaea.Nature reviews. Microbiology · 2026Review
- Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.Microbiology spectrum · 2026Article
- Analysis of Intestinal Microbiota Differences and Functional Prediction Between Sichuan-Tibetan Black Pigs and Landrace Pigs.Microorganisms · 2026Article
- CoSMIC: A hybrid approach for large-scale, high-resolution microbial profiling of novel niches.PloS one · 2026Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.mSystems · 2025Article
- Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information.Nature communications · 2025Article
- Multidisciplinary methodologies used in the study of cable bacteria.FEMS microbiology reviews · 2025Review
- GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities.The ISME journal · 2025Article
- Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.Frontiers in microbiology · 2025Article
- Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genusFrontiers in microbiology · 2025Article
- Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant.Applied and environmental microbiology · 2024Article
- Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.Microbiome · 2024Article
- Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.Nature communications · 2024Article
- Metagenomics reveals the genetic diversity between sublineages of UCYN-A and their algal host plastids.ISME communications · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources.Nature communications · 2023Article
- Effect of salinity on genes involved in the stress response in mangrove soils.Antonie van Leeuwenhoek · 2023Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledMetagenomic data, which contains sequenced DNA reads of uncultured microbial species from environmental samples, provide a unique opportunity to thoroughly analyze microbial species that have never been identified before. Reconstructing 16S ribosomal RNA, a phylogenetic marker gene, is usually required to analyze the composition of the metagenomic data. However, massive volume of dataset, high sequence similarity between related species, skewed microbial abundance and lack of reference genes make 16S rRNA reconstruction difficult. Generic de novo assembly tools are not optimized for assembling 16S rRNA genes. In this work, we introduce a targeted rRNA assembly tool, REAGO (REconstruct 16S ribosomal RNA Genes from metagenOmic data). It addresses the above challenges by combining secondary structure-aware homology search, zproperties of rRNA genes and de novo assembly. Our experimental results show that our tool can correctly recover more rRNA genes than several popular generic metagenomic assembly tools and specially designed rRNA construction tools. AVAILABILITY AND IMPLEMENTATION: The source code of REAGO is freely available at https://github.com/chengyuan/reago.
Indexed as
Identifiers
What OpenQuestion holds
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.