The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
出版年份 2018 全文链接
标题
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
作者
关键词
-
出版物
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
Volume 84, Issue 7, Pages -
出版商
American Society for Microbiology
发表日期
2018-01-30
DOI
10.1128/aem.02627-17
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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。- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- A communal catalogue reveals Earth’s multiscale microbial diversity
- (2017) Luke R. Thompson et al. NATURE
- Variability of the Sheep Lung Microbiota
- (2016) Laura Glendinning 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
- Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification
- (2016) Josef Wagner et al. BMC MICROBIOLOGY
- Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens
- (2016) Wenjing Zhao et al. BMC MICROBIOLOGY
- 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
- Absolute quantification of microbial taxon abundances
- (2016) Ruben Props et al. ISME Journal
- Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
- (2016) Daryl M Gohl et al. NATURE BIOTECHNOLOGY
- 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
- A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
- (2016) Wenke Smets et al. SOIL BIOLOGY & BIOCHEMISTRY
- Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples
- (2016) Angela Glassing et al. Gut Pathogens
- Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method
- (2016) Henry A. Paz et al. Frontiers in Microbiology
- Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
- (2016) Patrick D. Schloss et al. PeerJ
- Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
- (2016) Alfonso Benítez-Páez et al. GigaScience
- Adjusting microbiome profiles for differences in microbial load by spike-in bacteria
- (2016) Frank Stämmler et al. Microbiome
- Human milk microbiota profiles in relation to birthing method, gestation and infant gender
- (2016) Camilla Urbaniak et al. Microbiome
- Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
- (2015) Jarmo Ritari et al. BMC GENOMICS
- The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
- (2015) J Paul Brooks et al. BMC MICROBIOLOGY
- Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
- (2015) Alma E. Parada et al. ENVIRONMENTAL MICROBIOLOGY
- Occurrence of Fungal DNA Contamination in PCR Reagents: Approaches to Control and Decontamination
- (2015) S. Czurda et al. JOURNAL OF CLINICAL MICROBIOLOGY
- Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeks
- (2015) Vanessa L. Hale et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Successful test launch for nanopore sequencing
- (2015) Nicholas J Loman et al. NATURE METHODS
- Improved data analysis for the MinION nanopore sequencer
- (2015) Miten Jain et al. NATURE METHODS
- Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR
- (2015) Bruce Humphrey et al. PLoS One
- Sinonasal Microbiome Sampling: A Comparison of Techniques
- (2015) Ahmed Bassiouni et al. PLoS One
- Sample storage conditions significantly influence faecal microbiome profiles
- (2015) Jocelyn M Choo et al. Scientific Reports
- Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences
- (2015) Brett Wagner Mackenzie et al. Frontiers in Microbiology
- Primer and platform effects on 16S rRNA tag sequencing
- (2015) Julien Tremblay et al. Frontiers in Microbiology
- De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
- (2015) Sarah L. Westcott et al. PeerJ
- 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice
- (2015) Alan W. Walker et al. Microbiome
- Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
- (2015) Yan He et al. Microbiome
- The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations
- (2015) Fiona Fouhy et al. PLoS One
- The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects
- (2015) Danyta I. Tedjo et al. PLoS One
- Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool
- (2015) Monika A. Gorzelak et al. PLoS One
- Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing
- (2015) Marcia L. Hart et al. PLoS One
- Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats
- (2014) E. Ramos-Morales et al. ANIMAL FEED SCIENCE AND TECHNOLOGY
- Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems
- (2014) Perrine Cruaud et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Comparison of methods for fecal microbiome biospecimen collection
- (2014) Christine Dominianni et al. BMC MICROBIOLOGY
- Limits to robustness and reproducibility in the demarcation of operational taxonomic units
- (2014) Thomas S. B. Schmidt et al. ENVIRONMENTAL MICROBIOLOGY
- Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
- (2014) Mikhail Tikhonov et al. ISME Journal
- How to Deal with PCR Contamination in Molecular Microbial Ecology
- (2014) Adèle Mennerat et al. MICROBIAL ECOLOGY
- rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
- (2014) Steven F. Stoddard et al. NUCLEIC ACIDS RESEARCH
- The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing
- (2014) Nicholas A. Kennedy et al. PLoS One
- Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes
- (2014) Martin Laurence et al. PLoS One
- Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR
- (2014) Jérémy Desneux et al. MicrobiologyOpen
- CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
- (2014) Florent E Angly et al. Microbiome
- An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
- (2014) Douglas W Fadrosh et al. Microbiome
- Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
- (2014) Agata Wesolowska-Andersen et al. Microbiome
- Cell Size Distributions of Soil Bacterial and Archaeal Taxa
- (2013) Maria C. Portillo et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
- (2013) James J. Kozich et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Dryland soil microbial communities display spatial biogeographic patterns associated with soil depth and soil parent material
- (2013) Blaire Steven et al. FEMS MICROBIOLOGY ECOLOGY
- Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant
- (2013) Nest McKain et al. JOURNAL OF MICROBIOLOGICAL METHODS
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- (2013) Morgan G I Langille et al. NATURE BIOTECHNOLOGY
- Ribosomal Database Project: data and tools for high throughput rRNA analysis
- (2013) James R. Cole 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
- Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
- (2013) Benjamin E. R. Rubin et al. PLoS One
- The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies
- (2013) Jonas Ghyselinck et al. PLoS One
- Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities
- (2013) Gemma Henderson et al. PLoS One
- Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform
- (2013) Erin B Fichot et al. Microbiome
- Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
- (2012) Feng Guo et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- 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
- Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
- (2012) Martin Iain Bahl et al. FEMS MICROBIOLOGY LETTERS
- Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
- (2012) J Gregory Caporaso et al. ISME Journal
- PCR inhibitors - occurrence, properties and removal
- (2012) C. Schrader et al. JOURNAL OF APPLIED MICROBIOLOGY
- Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities
- (2012) Jae-Hyung Ahn et al. JOURNAL OF MICROBIOLOGY
- Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates
- (2012) Nastassia V. Patin et al. MICROBIAL ECOLOGY
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
- (2012) Steven W. Kembel et al. PLoS Computational Biology
- 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
- UCHIME improves sensitivity and speed of chimera detection
- (2011) Robert C. Edgar et al. BIOINFORMATICS
- The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples
- (2011) Johanna Maukonen et al. FEMS MICROBIOLOGY ECOLOGY
- Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
- (2011) B. J. Haas et al. GENOME RESEARCH
- Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys
- (2011) Jeffrey J Werner et al. ISME Journal
- Getting pharmaceutical R&D back on target
- (2011) Mark E Bunnage Nature Chemical Biology
- An Efficient Strategy for Broad-Range Detection of Low Abundance Bacteria without DNA Decontamination of PCR Reagents
- (2011) Shy-Shin Chang et al. PLoS One
- Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity
- (2011) Pei-Ying Hong et al. PLoS One
- Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
- (2011) Patrick D. Schloss et al. PLoS One
- Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering
- (2011) W. J. Sul et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The under-recognized dominance of Verrucomicrobia in soil bacterial communities
- (2011) Gaddy T. Bergmann et al. SOIL BIOLOGY & BIOCHEMISTRY
- Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method
- (2010) Jin-Ya Wu et al. BMC MICROBIOLOGY
- Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
- (2010) Christian L. Lauber et al. FEMS MICROBIOLOGY LETTERS
- Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis
- (2010) Anne Salonen et al. JOURNAL OF MICROBIOLOGICAL METHODS
- An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications
- (2010) Sophie Champlot et al. PLoS One
- The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
- (2010) Patrick D. Schloss PLoS Computational Biology
- 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
- Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
- (2009) Victor Kunin et al. ENVIRONMENTAL MICROBIOLOGY
- Evaluation of time profile reconstruction from complex two-color microarray designs
- (2008) Ana C Fierro et al. BMC BIOINFORMATICS
- Real-Time DNA Sequencing from Single Polymerase Molecules
- (2008) J. Eid et al. SCIENCE
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