Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.
A. Murat Eren,Lois Maignien,Woo Jun Sul,Leslie G. Murphy,Sharon L. Grim,Hilary G. Morrison,Mitchell L. Sogin +6 more
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TLDR
Oligotyping is described, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches.Citations
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Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +6 more
TL;DR: In this article, a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation is described and validated, which addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Susannah J. Salter,Michael J. Cox,Elena M. Turek,Szymon T. Calus,William O.C.M. Cookson,Miriam F. Moffatt,Paul Turner,Paul Turner,Julian Parkhill,Nicholas J. Loman,Alan W. Walker,Alan W. Walker +11 more
TL;DR: It is demonstrated that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass.
Journal ArticleDOI
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis.
TL;DR: It is argued that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that ASVs should replace OTUs as the standard unit of marker-gene analysis and reporting.
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Best practices for analysing microbiomes.
Rob Knight,Alison Vrbanac,Bryn C. Taylor,Alexander A. Aksenov,Chris Callewaert,Chris Callewaert,Justine W. Debelius,Antonio Gonzalez,Tomasz Kosciolek,Laura-Isobel McCall,Daniel McDonald,Alexey V. Melnik,James T. Morton,Jose Navas,Robert A. Quinn,Jon G. Sanders,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Anupriya Tripathi,Zhenjiang Zech Xu,Jesse R. Zaneveld,Qiyun Zhu,J. Gregory Caporaso,Pieter C. Dorrestein,Pieter C. Dorrestein +25 more
TL;DR: This Review focuses on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis.
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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Jethro S. Johnson,Daniel Spakowicz,Bo-Young Hong,Lauren M. Petersen,Patrick Demkowicz,Lei Chen,Shana R. Leopold,Blake M. Hanson,Hanako O. Agresta,Mark Gerstein,Erica Sodergren,George M. Weinstock +11 more
TL;DR: The authors explore the potential of the 16S gene for discriminating bacterial taxa and show that full-length sequencing combined with appropriate clustering of intragenomic sequence variation can provide accurate representation of bacterial species in microbiome datasets.
References
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Analysis of relative gene expression data using real-time quantitative pcr and the 2(-delta delta c(t)) method
TL;DR: The 2-Delta Delta C(T) method as mentioned in this paper was proposed to analyze the relative changes in gene expression from real-time quantitative PCR experiments, and it has been shown to be useful in the analysis of realtime, quantitative PCR data.
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A mathematical theory of communication
TL;DR: This final installment of the paper considers the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now.
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QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
Journal ArticleDOI
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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