DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
出版年份 2019 全文链接
标题
DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
作者
关键词
Microbiome, Taxonomy annotation, OTU classification, 16S, Database, Accuracy, Dairy, Cheese, Milk, Whey, Teat, Starter
出版物
BMC GENOMICS
Volume 20, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2019-07-08
DOI
10.1186/s12864-019-5914-8
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
- (2018) Johan Bengtsson-Palme et al. BIOINFORMATICS
- Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis
- (2018) Teresita M. Porter et al. MOLECULAR ECOLOGY
- The human skin microbiome
- (2018) Allyson L. Byrd et al. NATURE REVIEWS MICROBIOLOGY
- Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems
- (2018) Marie Frétin et al. Scientific Reports
- Sequencing of the Cheese Microbiome and Its Relevance to Industry
- (2018) Bhagya. R. Yeluri Jonnala et al. Frontiers in Microbiology
- Taxonomy annotation and guide tree errors in 16S rRNA databases
- (2018) Robert Edgar PeerJ
- Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
- (2018) Robert C. Edgar PeerJ
- Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
- (2018) Nicholas A. Bokulich et al. Microbiome
- Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification
- (2018) Elisa Salvetti et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
- (2018) Jolinda Pollock et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Large plasmidome of dairy Lactococcus lactis subsp. lactis biovar diacetylactis FM03P encodes technological functions and appears highly unstable
- (2018) Oscar van Mastrigt et al. BMC GENOMICS
- IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
- (2018) Adithya Murali et al. Microbiome
- DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
- (2018) Ehsaneddin Asgari et al. BIOINFORMATICS
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Uncultivated microbes in need of their own taxonomy
- (2017) Konstantinos T Konstantinidis et al. ISME Journal
- 25 years of serving the community with ribosomal RNA gene reference databases and tools
- (2017) Frank Oliver Glöckner et al. JOURNAL OF BIOTECHNOLOGY
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups
- (2017) Simon Jon McIlroy et al. Database-The Journal of Biological Databases and Curation
- Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes
- (2017) Michelle A. Berry et al. Frontiers in Microbiology
- Overcoming hurdles in sharing microbiome data
- (2017) Nature Microbiology
- Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features
- (2017) Sander Wuyts et al. mSystems
- Unbiased probabilistic taxonomic classification for DNA barcoding
- (2016) Panu Somervuo et al. BIOINFORMATICS
- 16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform
- (2016) Fiona Fouhy et al. BMC MICROBIOLOGY
- DADA2: High-resolution sample inference from Illumina amplicon data
- (2016) Benjamin J Callahan et al. NATURE METHODS
- Phylogeny-aware identification and correction of taxonomically mislabeled sequences
- (2016) Alexey M. Kozlov et al. NUCLEIC ACIDS RESEARCH
- SPINGO: a rapid species-classifier for microbial amplicon sequences
- (2015) Guy Allard et al. BMC BIOINFORMATICS
- Comparing K-mer based methods for improved classification of 16S sequences
- (2015) Hilde Vinje et al. BMC BIOINFORMATICS
- Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
- (2015) Jarmo Ritari et al. BMC GENOMICS
- Microbial abundance and community structure in a melting alpine snowpack
- (2015) Anna Lazzaro et al. EXTREMOPHILES
- metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data
- (2015) Johan Bengtsson-Palme et al. Molecular Ecology Resources
- BacDive – The Bacterial Diversity Metadatabase in 2016
- (2015) Carola Söhngen et al. NUCLEIC ACIDS RESEARCH
- The International Nucleotide Sequence Database Collaboration
- (2015) Guy Cochrane et al. NUCLEIC ACIDS RESEARCH
- The global ocean microbiome
- (2015) M. A. Moran SCIENCE
- Structure and function of the global ocean microbiome
- (2015) S. Sunagawa et al. SCIENCE
- Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps
- (2015) Marco Meola et al. Frontiers in Microbiology
- riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics
- (2015) Matteo Ramazzotti et al. Frontiers in Genetics
- The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
- (2015) Alejandra Escobar-Zepeda et al. Frontiers in Genetics
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- jvenn: an interactive Venn diagram viewer
- (2014) Philippe Bardou et al. BMC BIOINFORMATICS
- Diversity, resistance and resilience of the bacterial communities at two alpine glacier forefields after a reciprocal soil transplantation
- (2014) Marco Meola et al. ENVIRONMENTAL MICROBIOLOGY
- Traditional cheeses: Rich and diverse microbiota with associated benefits
- (2014) Marie-Christine Montel et al. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
- Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
- (2014) A Murat Eren et al. ISME Journal
- Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
- (2014) Pablo Yarza et al. NATURE REVIEWS MICROBIOLOGY
- A meta-analysis of changes in bacterial and archaeal communities with time
- (2013) Ashley Shade et al. ISME Journal
- LPSN—list of prokaryotic names with standing in nomenclature
- (2013) Aidan C. Parte NUCLEIC ACIDS RESEARCH
- The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
- (2013) Pelin Yilmaz et al. NUCLEIC ACIDS RESEARCH
- Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data
- (2013) A. Murat Eren et al. Methods in Ecology and Evolution
- SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
- (2012) Elmar Pruesse et al. BIOINFORMATICS
- The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier
- (2012) Irene LG Newton et al. BMC MICROBIOLOGY
- A framework for human microbiome research
- (2012) NATURE
- The human microbiome: at the interface of health and disease
- (2012) Ilseung Cho et al. NATURE REVIEWS GENETICS
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- The Genus Lactobacillus: A Taxonomic Update
- (2012) Elisa Salvetti et al. Probiotics and Antimicrobial Proteins
- Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
- (2011) Patrick D. Schloss et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
- (2011) William A. Walters et al. BIOINFORMATICS
- Interactive metagenomic visualization in a Web browser
- (2011) Brian D Ondov et al. BMC BIOINFORMATICS
- Analysis of 16S rRNA environmental sequences using MEGAN
- (2011) Suparna Mitra et al. BMC GENOMICS
- Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories
- (2011) Ramon Rosselló-Móra ENVIRONMENTAL MICROBIOLOGY
- Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys
- (2011) Jeffrey J Werner et al. ISME Journal
- Biodiversity of air-borne microorganisms at Halley station, Antarctica
- (2010) David A. Pearce et al. EXTREMOPHILES
- V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences
- (2010) Martin Hartmann et al. JOURNAL OF MICROBIOLOGICAL METHODS
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- Database resources of the National Center for Biotechnology Information
- (2010) E. W. Sayers et al. NUCLEIC ACIDS RESEARCH
- Changes through time: integrating microorganisms into the study of succession
- (2010) Noah Fierer et al. RESEARCH IN MICROBIOLOGY
- Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome
- (2010) Carlos W Nossa WORLD JOURNAL OF GASTROENTEROLOGY
- Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys
- (2009) N. Youssef et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- 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
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Pyrosequencing analysis of the Oral Microflora of healthy adults
- (2009) B.J.F. Keijser et al. JOURNAL OF DENTAL RESEARCH
- Global Sequencing: A Review of Current Molecular Data and New Methods Available to Assess Microbial Diversity
- (2008) Richard Christen MICROBES AND ENVIRONMENTS
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
- (2008) J. R. Cole et al. NUCLEIC ACIDS RESEARCH
- Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
- (2008) A. Koeppel et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
- (2008) Susan M. Huse et al. PLoS Genetics
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