Cargando…

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

BACKGROUND: The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. RESULTS: Here, we report that many hierarchical and greedy clustering methods produce...

Descripción completa

Detalles Bibliográficos
Autores principales:	He, Yan, Caporaso, J Gregory, Jiang, Xiao-Tao, Sheng, Hua-Fang, Huse, Susan M, Rideout, Jai Ram, Edgar, Robert C, Kopylova, Evguenia, Walters, William A, Knight, Rob, Zhou, Hong-Wei
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438525/ https://www.ncbi.nlm.nih.gov/pubmed/25995836 http://dx.doi.org/10.1186/s40168-015-0081-x

Ejemplares similares

Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
por: He, Yan, et al.
Publicado: (2015)

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
por: Bokulich, Nicholas A., et al.
Publicado: (2018)

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
por: Rideout, Jai Ram, et al.
Publicado: (2016)

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
por: Walters, William A., et al.
Publicado: (2011)

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
por: McDonald, Daniel, et al.
Publicado: (2012)

Open-Source Sequence Clustering Methods Improve the State Of the Art
por: Kopylova, Evguenia, et al.
Publicado: (2016)

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
por: Fouquier, Jennifer, et al.
Publicado: (2016)

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies
por: Chase, John H., et al.
Publicado: (2015)

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
por: Rideout, Jai Ram, et al.
Publicado: (2014)

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking
por: Bokulich, Nicholas A., et al.
Publicado: (2016)

The Ecology of Microbial Communities Associated with Macrocystis pyrifera
por: Michelou, Vanessa K., et al.
Publicado: (2013)

Correction: The Ecology of Microbial Communities Associated with Macrocystis pyrifera
por: Michelou, Vanessa K., et al.
Publicado: (2013)

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)
por: Ottesen, Andrea R, et al.
Publicado: (2013)

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
por: Asnicar, Francesco, et al.
Publicado: (2020)

Defining seasonal marine microbial community dynamics
por: Gilbert, Jack A, et al.
Publicado: (2012)

The Western English Channel contains a persistent microbial seed bank
por: Caporaso, J Gregory, et al.
Publicado: (2012)

Temporal variability is a personalized feature of the human microbiome
por: Flores, Gilberto E, et al.
Publicado: (2014)

An Introduction to Applied Bioinformatics: a free, open, and interactive text.
por: Bolyen, Evan, et al.
Publicado: (2018)

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions
por: Parfrey, Laura Wegener, et al.
Publicado: (2011)

q2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
por: Bokulich, Nicholas A., et al.
Publicado: (2018)

Nitrogen Cycling Microbial Diversity and Operational Taxonomic Unit Clustering: When to Prioritize Accuracy Over Speed
por: Egenriether, Sada, et al.
Publicado: (2022)

On the Linear Stability of Crystals in the Schrödinger–Poisson Model
por: Komech, A., et al.
Publicado: (2016)

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
por: Shade, Ashley, et al.
Publicado: (2014)

Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes
por: Das Kangabam, Rajiv, et al.
Publicado: (2020)

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
por: Amir, Amnon, et al.
Publicado: (2017)

From molecules to dynamic biological communities
por: McDonald, Daniel, et al.
Publicado: (2013)

Which is more important for classifying microbial communities: who's there or what they can do?
por: Xu, Zhenjiang, et al.
Publicado: (2014)

Functional and Taxonomic Diversity of Anaerobes in Supraglacial Microbial Communities
por: Pittino, Francesca, et al.
Publicado: (2023)

The Neglected Microbial Components of Commercial Probiotic Formulations
por: Fiore, Walter, et al.
Publicado: (2020)

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
por: Caporaso, J Gregory, et al.
Publicado: (2012)

Reconciliation between operational taxonomic units and species boundaries
por: Mysara, Mohamed, et al.
Publicado: (2017)

WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences
por: Metwally, Ahmed A., et al.
Publicado: (2016)

k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank
por: Bernard, Guillaume, et al.
Publicado: (2018)

Assessing alignment-based taxonomic classification of ancient microbial DNA
por: Eisenhofer, Raphael, et al.
Publicado: (2019)

Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil
por: Dong, Weiling, et al.
Publicado: (2021)

Retaining Patients in Care: An Important but Neglected Challenge
por: Hodgins, Stephen
Publicado: (2019)

Emerging and Neglected Viruses of Zoonotic Importance in Croatia
por: Vilibic-Cavlek, Tatjana, et al.
Publicado: (2021)

The neglected importance of high-endemic ESBL sites
por: Henriksen, Thor-Henrik, et al.
Publicado: (2022)

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
por: Joos, Lisa, et al.
Publicado: (2020)

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome
por: Li, Kelvin, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_dmhkgcb9rh8ijiom2obmhbdf99