Journal ArticleDOI
Practical innovations for high-throughput amplicon sequencing.
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Improvements for sequencing 16S ribosomal RNA (rRNA) amplicons, a cornerstone technique in metagenomics, are described through unique tagging of template molecules before PCR, which substantially enriching microbial sequences without introducing bias.Abstract:
We describe improvements for sequencing 16S ribosomal RNA (rRNA) amplicons, a cornerstone technique in metagenomics. Through unique tagging of template molecules before PCR, amplicon sequences can be mapped to their original templates to correct amplification bias and sequencing error with software we provide. PCR clamps block amplification of contaminating sequences from a eukaryotic host, thereby substantially enriching microbial sequences without introducing bias.read more
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“Bioinformatics” 특집을 내면서
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Journal ArticleDOI
Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
Sarah L. Lebeis,Sarah L. Lebeis,Sur Herrera Paredes,Derek S. Lundberg,Natalie W. Breakfield,Jase Gehring,Meredith McDonald,Stephanie Malfatti,Tijana Glavina del Rio,Corbin D. Jones,Susannah G. Tringe,Jeffery L. Dangl +11 more
TL;DR: It is established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome, and selection from the available microbial communities to sculpt the root microbiome.
Journal ArticleDOI
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
Maggie R. Wagner,Derek S. Lundberg,Tijana Glavina del Rio,Susannah G. Tringe,Jeffery L. Dangl,Thomas Mitchell-Olds +5 more
TL;DR: This large-scale field experiment disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard to demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
Journal ArticleDOI
Assembly and ecological function of the root microbiome across angiosperm plant species.
Connor R. Fitzpatrick,Julia K. Copeland,Pauline W. Wang,David S. Guttman,Peter M. Kotanen,Marc T. J. Johnson +5 more
TL;DR: It is demonstrated that variation among 30 angiosperm species, which have diverged for up to 140 million years, affects root bacterial diversity and composition and the causes of variation in root microbiomes are emphasized.
Journal ArticleDOI
Conducting a microbiome study.
Julia K. Goodrich,Sara C. Di Rienzi,Angela C. Poole,Omry Koren,William A. Walters,J. Gregory Caporaso,J. Gregory Caporaso,Rob Knight,Rob Knight,Ruth E. Ley +9 more
TL;DR: A Primer for researchers from diverse disciplines interested in conducting microbiome research discusses factors to be considered in the design, execution, and data analysis of microbiome studies.
References
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TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
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Journal ArticleDOI
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
Clustal W and Clustal X version 2.0
Mark A. Larkin,Gordon Blackshields,Nigel P. Brown,R. Chenna,Paul A. McGettigan,Hamish McWilliam,Franck Valentin,Iain M. Wallace,Andreas Wilm,Rodrigo Lopez,J.D. Thompson,Toby J. Gibson,Desmond G. Higgins +12 more
TL;DR: The Clustal W and ClUSTal X multiple sequence alignment programs have been completely rewritten in C++ to facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems.
Journal ArticleDOI
FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies
Tanja Magoc,Steven L. Salzberg +1 more
TL;DR: FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
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