Cargando…

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon

Amplicon sequencing of the 16S rRNA gene is the predominant method to quantify microbial compositions and to discover novel lineages. However, traditional short amplicons often do not contain enough information to confidently resolve their phylogeny. Here we present a cost‐effective protocol that am...

Descripción completa

Detalles Bibliográficos
Autores principales:	Martijn, Joran, Lind, Anders E., Schön, Max E., Spiertz, Ian, Juzokaite, Lina, Bunikis, Ignas, Pettersson, Olga V., Ettema, Thijs J. G.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley & Sons, Inc. 2019
Materias:	Research Articles
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849856/ https://www.ncbi.nlm.nih.gov/pubmed/31012228 http://dx.doi.org/10.1111/1462-2920.14636

Ejemplares similares

Complex archaea that bridge the gap between prokaryotes and eukaryotes
por: Spang, Anja, et al.
Publicado: (2015)

16S rRNA Amplicon Sequencing of Urban Prokaryotic Communities in the South Bronx River Estuary
por: Naro-Maciel, Eugenia, et al.
Publicado: (2020)

Detecting uber-operons in prokaryotic genomes
por: Che, Dongsheng, et al.
Publicado: (2006)

DOOR: a database for prokaryotic operons
por: Mao, Fenglou, et al.
Publicado: (2009)

Hikarchaeia demonstrate an intermediate stage in the methanogen-to-halophile transition
por: Martijn, Joran, et al.
Publicado: (2020)

The evolutionary origin of host association in the Rickettsiales
por: Schön, Max E., et al.
Publicado: (2022)

Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome
por: Kinoshita, Yuta, et al.
Publicado: (2021)

Transcriptome dynamics-based operon prediction in prokaryotes
por: Fortino, Vittorio, et al.
Publicado: (2014)

Position preference of essential genes in prokaryotic operons
por: Liu, Tao, et al.
Publicado: (2021)

Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence
por: Seol, Donghyeok, et al.
Publicado: (2022)

ProOpDB: Prokaryotic Operon DataBase
por: Taboada, Blanca, et al.
Publicado: (2012)

Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon
por: Cuscó, Anna, et al.
Publicado: (2019)

Draft Genome Sequence of “Candidatus Moanabacter tarae,” Representing a Novel Marine Verrucomicrobial Lineage
por: Vosseberg, Julian, et al.
Publicado: (2018)

PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
por: Schön, Max E, et al.
Publicado: (2020)

Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product
por: Sudjai, Aunthikarn, et al.
Publicado: (2022)

The distinctive signatures of promoter regions and operon junctions across prokaryotes
por: Janga, Sarath Chandra, et al.
Publicado: (2006)

Footprints of Optimal Protein Assembly Strategies in the Operonic Structure of Prokaryotes
por: Ewald, Jan, et al.
Publicado: (2015)

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution
por: Spang, Anja, et al.
Publicado: (2013)

16S rRNA gene amplicon dataset of prokaryotic communities from a subantarctic marine ecosystem: Ushuaia Bay and surrounding waters
por: Rodríguez-Flórez, Clara Natalia, et al.
Publicado: (2020)

A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea)
por: Onuț-Brännström, Ioana, et al.
Publicado: (2023)

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing
por: Parikh, Hardik I., et al.
Publicado: (2016)

Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing
por: Akpolat, Can, et al.
Publicado: (2021)

A novel method for accurate operon predictions in all sequenced prokaryotes
por: Price, Morgan N., et al.
Publicado: (2005)

AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses
por: Yi, Haidong, et al.
Publicado: (2020)

AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses
por: Huang, Le, et al.
Publicado: (2020)

Long-read amplicon denoising
por: Kumar, Venkatesh, et al.
Publicado: (2019)

High-quality genome sequences of uncultured microbes by assembly of read clouds
por: Bishara, Alex, et al.
Publicado: (2018)

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering
por: Franzén, Oscar, et al.
Publicado: (2015)

Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics
por: Arikawa, Koji, et al.
Publicado: (2023)

Enhanced Symbiotic Characteristics in Bacterial Genomes with the Disruption of rRNA Operon
por: Ahn, Hyeonju, et al.
Publicado: (2020)

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade
por: Viklund, Johan, et al.
Publicado: (2013)

Erratum to: Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering
por: Franzén, Oscar, et al.
Publicado: (2015)

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils
por: Zhao, Jun, et al.
Publicado: (2023)

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping
por: Olsen, Remi-Andre, et al.
Publicado: (2015)

Exploiting rRNA Operon Copy Number to Investigate Bacterial Reproductive Strategies
por: Roller, Benjamin R.K., et al.
Publicado: (2016)

rRNA operon multiplicity as a bacterial genome stability insurance policy
por: Fleurier, Sebastien, et al.
Publicado: (2022)

16S rRNA Gene Amplicon Profiling of Anaerobic Bulking-Associated Prokaryotic Microbiota in a Mesophilic Expanded Granular Sludge Bed Reactor for Beverage Wastewater Treatment
por: Yamada, Takeshi, et al.
Publicado: (2019)

Asgard archaea are the closest prokaryotic relatives of eukaryotes
por: Spang, Anja, et al.
Publicado: (2018)

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife
por: Galan, Maxime, et al.
Publicado: (2016)

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
por: Prodan, Andrei, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_lkft5v9t3mjokdm3c907n6d3i2