Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
Authors
Keywords
-
Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 21, Issue 1, Pages 298
Publisher
MDPI AG
Online
2020-01-03
DOI
10.3390/ijms21010298
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Laboratory contamination over time during low‐biomass sample analysis
- (2019) Laura S. Weyrich et al. Molecular Ecology Resources
- Ultra-deep, long-read nanopore sequencing of mock microbial community standards
- (2019) Samuel M Nicholls et al. GigaScience
- High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution
- (2019) Benjamin J Callahan et al. NUCLEIC ACIDS RESEARCH
- Updating the 97% identity threshold for 16S ribosomal RNA OTUs
- (2018) Robert C Edgar BIOINFORMATICS
- Nanopore sequencing and assembly of a human genome with ultra-long reads
- (2018) Miten Jain et al. NATURE BIOTECHNOLOGY
- The Third Revolution in Sequencing Technology
- (2018) Erwin L. van Dijk et al. TRENDS IN GENETICS
- Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
- (2018) Andrea D. Tyler et al. Scientific Reports
- BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
- (2018) Alexander Payne et al. BIOINFORMATICS
- Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences
- (2018) Adrian López-García et al. Frontiers in Microbiology
- Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation
- (2017) Sergey Koren et al. GENOME RESEARCH
- Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family
- (2017) Seema Alnajar et al. INFECTION GENETICS AND EVOLUTION
- A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies
- (2017) Yu Cao et al. Frontiers in Microbiology
- Campylobacter fetus meningitis confirmed by a 16S rRNA gene analysis using the MinION nanopore sequencer, South Korea, 2016
- (2017) Jangsup Moon et al. Emerging Microbes & Infections
- Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
- (2017) Alfonso Benítez-Páez et al. GigaScience
- Bacteria as emerging indicators of soil condition
- (2016) Syrie M. Hermans et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
- (2016) Bo Yang et al. BMC BIOINFORMATICS
- A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
- (2016) Rosalinda D’Amore et al. BMC GENOMICS
- Quality filtering of Illumina index reads mitigates sample cross-talk
- (2016) Erik Scott Wright et al. BMC GENOMICS
- Coinfections of Zika and Chikungunya Viruses in Bahia, Brazil, Identified by Metagenomic Next-Generation Sequencing
- (2016) Silvia I. Sardi et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Real-time, portable genome sequencing for Ebola surveillance
- (2016) Joshua Quick et al. NATURE
- Fast and sensitive mapping of nanopore sequencing reads with GraphMap
- (2016) Ivan Sović et al. Nature Communications
- Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach
- (2016) Saskia Decuypere et al. PLoS Neglected Tropical Diseases
- Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
- (2016) Alfonso Benítez-Páez et al. GigaScience
- Development of a Novel Long-Range 16S rRNA Universal Primer Set for Metagenomic Analysis of Gastrointestinal Microbiota in Newborn Infants
- (2016) Hye-Jin Ku et al. JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
- Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
- (2015) Tasuya Unno JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
- High-Throughput Sequencing Technologies
- (2015) Jason A. Reuter et al. MOLECULAR CELL
- A complete bacterial genome assembled de novo using only nanopore sequencing data
- (2015) Nicholas J Loman et al. NATURE METHODS
- Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens
- (2015) Ramya Srinivasan et al. PLoS One
- Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform
- (2015) Lucas Sinclair et al. PLoS One
- Design and evaluation of universal 16S rRNA gene primers for high-throughput sequencing to simultaneously detect DAMO microbes and anammox bacteria
- (2015) Yong-Ze Lu et al. WATER RESEARCH
- Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses
- (2015) Mohd Mohd Shaufi et al. Gut Pathogens
- Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
- (2015) Alexander L. Greninger et al. Genome Medicine
- Primer and platform effects on 16S rRNA tag sequencing
- (2015) Julien Tremblay et al. Frontiers in Microbiology
- Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer
- (2015) Andy Kilianski et al. GigaScience
- The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline
- (2015) Jérôme Lluch et al. PLoS One
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
- (2014) Martin Laurence et al. PLoS One
- Identification and classification of seafood-borne pathogenic and spoilage bacteria: 16S rRNA sequencing versus MALDI-TOF MS fingerprinting
- (2013) Karola Böhme et al. ELECTROPHORESIS
- The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
- (2013) Pelin Yilmaz et al. NUCLEIC ACIDS RESEARCH
- The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
- (2013) Tomáš Větrovský et al. PLoS One
- Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
- (2013) Stephen J. Salipante et al. PLoS One
- Performance comparison of benchtop high-throughput sequencing platforms
- (2012) Nicholas J Loman et al. NATURE BIOTECHNOLOGY
- Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
- (2012) Nicholas A Bokulich et al. NATURE METHODS
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Detection and identification of bacteria in clinical samples by 16S rRNA gene sequencing: comparison of two different approaches in clinical practice
- (2011) C. Jenkins et al. JOURNAL OF MEDICAL MICROBIOLOGY
- Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?
- (2011) Asli I. Özen et al. MICROBIAL ECOLOGY
- Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
- (2011) Martin Kircher et al. NUCLEIC ACIDS RESEARCH
- The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
- (2010) David L. Kirchman et al. ENVIRONMENTAL MICROBIOLOGY
- Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
- (2010) Marcus J. Claesson et al. NUCLEIC ACIDS RESEARCH
- Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
- (2009) P. D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model
- (2009) Luiz FW Roesch et al. ISME Journal
- Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories
- (2008) P.C.Y. Woo et al. CLINICAL MICROBIOLOGY AND INFECTION
- A renaissance for the pioneering 16S rRNA gene
- (2008) Susannah G Tringe et al. CURRENT OPINION IN MICROBIOLOGY
- Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing
- (2008) Anders F. Andersson et al. PLoS One
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started