Cargando…

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

BACKGROUND: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to find...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ritari, Jarmo, Salojärvi, Jarkko, Lahti, Leo, de Vos, Willem M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2015
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676846/ https://www.ncbi.nlm.nih.gov/pubmed/26651617 http://dx.doi.org/10.1186/s12864-015-2265-y

Ejemplares similares

Evaluation of 16S rRNA Databases for Taxonomic Assignments Using a Mock Community
por: Park, Sang-Cheol, et al.
Publicado: (2018)

Tipping elements in the human intestinal ecosystem
por: Lahti, Leo, et al.
Publicado: (2014)

Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
por: Henderson, Gemma, et al.
Publicado: (2019)

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
por: Westcott, Sarah L., et al.
Publicado: (2015)

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
por: Almeida, Alexandre, et al.
Publicado: (2018)

Data-Driven Modeling for Species-Level Taxonomic Assignment From 16S rRNA: Application to Human Microbiomes
por: Gwak, Ho-Jin, et al.
Publicado: (2020)

Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
por: Bacci, Giovanni, et al.
Publicado: (2015)

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data
por: Lahti, Leo, et al.
Publicado: (2013)

TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage
por: Brandt, Bernd W., et al.
Publicado: (2012)

Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data
por: Agnihotry, Shikha, et al.
Publicado: (2020)

Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis
por: Jalanka, Jonna, et al.
Publicado: (2020)

Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database
por: Jones, Briony, et al.
Publicado: (2021)

Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies
por: Mugnai, Francesco, et al.
Publicado: (2023)

Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences
por: Ziemski, Michal, et al.
Publicado: (2021)

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
por: Yoon, Seok-Hwan, et al.
Publicado: (2017)

Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
por: Dueholm, Morten Simonsen, et al.
Publicado: (2020)

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
por: Kolmeder, Carolin A., et al.
Publicado: (2016)

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
por: Soergel, David A W, et al.
Publicado: (2012)

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region
por: Kosecka-Strojek, Maja, et al.
Publicado: (2019)

Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S–23S rRNA region
por: Kosecka-Strojek, Maja, et al.
Publicado: (2019)

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
por: Liu, Zongzhi, et al.
Publicado: (2008)

Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
por: Machida, Ryuji J., et al.
Publicado: (2017)

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
por: Nguyen, Nam-Phuong, et al.
Publicado: (2016)

Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
por: Durazzi, Francesco, et al.
Publicado: (2021)

MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
por: Liao, Chun-Chieh, et al.
Publicado: (2022)

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes
por: Yadav, Deepak, et al.
Publicado: (2019)

Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria
por: Okubo, Takashi, et al.
Publicado: (2012)

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets
por: Chaudhary, Nikhil, et al.
Publicado: (2015)

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments
por: Macheriotou, Lara, et al.
Publicado: (2019)

Intestinal Microbiota in Healthy U.S. Young Children and Adults—A High Throughput Microarray Analysis
por: Ringel-Kulka, Tamar, et al.
Publicado: (2013)

VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences
por: Mori, Hiroshi, et al.
Publicado: (2010)

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing
por: Numberger, Daniela, et al.
Publicado: (2019)

Correction to: MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
Publicado: (2022)

Application of 16S rRNA virtual RFLP for the discrimination of some closely taxonomic-related lactobacilli species
por: Laref, Nora, et al.
Publicado: (2022)

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples
por: López-Aladid, Ruben, et al.
Publicado: (2023)

Taxonomy annotation and guide tree errors in 16S rRNA databases
por: Edgar, Robert
Publicado: (2018)

Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples
por: Al-Hebshi, Nezar Noor, et al.
Publicado: (2015)

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
por: F. Escapa, Isabel, et al.
Publicado: (2020)

The Clinical Utility of Two High-Throughput 16S rRNA Gene Sequencing Workflows for Taxonomic Assignment of Unidentifiable Bacterial Pathogens in Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
por: Lao, Hiu-Yin, et al.
Publicado: (2022)

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy
por: Gao, Xiang, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_9ltndptgr210n0ihboj3fi9r93