ArticlePLoS computational biology2011
PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 87 citations in OpenAlex.
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment.Frontiers in microbiology · 2023Article
- Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures.Antibiotics (Basel, Switzerland) · 2021Review
- Article
- Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring.Molecular ecology resources · 2019Article
- Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota.mBio · 2018Article
- The Emergency Medical Service Microbiome.Applied and environmental microbiology · 2018Review
- Microbiome overview in swine lungs.PloS one · 2017Article
- Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.Microbes and environments · 2016Review
- Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon.Scientific reports · 2016Article
- Review
- Article
- Application of computational methods in genetic study of inflammatory bowel disease.World journal of gastroenterology · 2016Review
- A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity.NPJ biofilms and microbiomes · 2016Article
- Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.Applied and environmental microbiology · 2016Article
- Phylogenetics and the human microbiome.Systematic biology · 2015Review
- Wine fermentation microbiome: a landscape from different Portuguese wine appellations.Frontiers in microbiology · 2015Article
- Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.BMC ecology · 2014Article
- Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.PloS one · 2014Article
- Unravelling the diversity of grapevine microbiome.PloS one · 2014Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?
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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.