ArticlePloS one2012
Reconstruction of ribosomal RNA genes from metagenomic data.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Urbanization and the Gut Microbiome: Insights From the Anna's Hummingbird (Calypte anna) in California.Integrative and comparative biology · 2025Article
- Genomic and Phenotypic Evaluation of Potential Probiotic Pediococcus Strains with Hypocholesterolemic Effect Isolated from Traditional Fermented Food.Probiotics and antimicrobial proteins · 2022Article
- MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes.mSystems · 2021Article
- Article
- Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets.PloS one · 2019Article
- Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface.Frontiers in microbiology · 2018Article
- Impacts of chemical gradients on microbial community structure.The ISME journal · 2017Article
- Planktonic Growth ofInternational journal of otolaryngology · 2017Article
- Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.Environmental microbiology · 2016Article
- Impact of methionine on a partial-nitritation biofilter.Environmental science and pollution research international · 2016Article
- Comparison of bacterial communities of conventional and A-stage activated sludge systems.Scientific reports · 2016Article
- Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome.Frontiers in microbiology · 2016Article
- Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads.BMC microbiology · 2015Article
- Reconstructing 16S rRNA genes in metagenomic data.Bioinformatics (Oxford, England) · 2015Article
- Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples.BMC bioinformatics · 2015Article
- Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome.Frontiers in microbiology · 2015Article
- High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.Nucleic acids research · 2013Article
- Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress.The ISME journal · 2013Article
- RNA-CODE: a noncoding RNA classification tool for short reads in NGS data lacking reference genomes.PloS one · 2013Article
- Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes.PloS one · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data. Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCR-based methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes.
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Registered trials
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