Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TLDR
The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.Abstract:
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.read more
Citations
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A clinician's guide to microbiome analysis.
TL;DR: The major decision points confronting new entrants to the field or for those designing new projects in microbiome research are summarized and recommendations based on current technology options and the experience of sequencing platform choices are provided.
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Analysis of microbial compositions: a review of normalization and differential abundance analysis.
TL;DR: Some recent methods for differential abundance analysis are reviewed and described and their strengths and weaknesses are described.
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Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities.
TL;DR: Estimation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque, suggesting that not all protocols are suitable to study the salivary mycobiome.
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The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
Jennifer D. Rocca,Marie Simonin,Joanna R. Blaszczak,Joanna R. Blaszczak,Jessica G. Ernakovich,Sean M. Gibbons,Sean M. Gibbons,Firas S. Midani,Alex D. Washburne,Alex D. Washburne +9 more
TL;DR: It is found that stressor exposure significantly decreases microbiome alpha diversity and increases beta diversity (community dispersion) across a range of environments and stressor types.
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Gut Dysbiosis Associated With Hepatitis C Virus Infection.
Takako Inoue,Jiro Nakayama,Kei Moriya,Hideto Kawaratani,Rie Momoda,Kiyoaki Ito,Etsuko Iio,Shunsuke Nojiri,Kei Fujiwara,Masashi Yoneda,Hitoshi Yoshiji,Yasuhito Tanaka +11 more
TL;DR: HCV infection is associated with gut dysbiosis, even in patients with mild liver disease, and overgrowth of viridans streptococci can account for hyperammonemia in CH and LC.
References
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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
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantis,Philip Hugenholtz,Neils Larsen,Mark Rojas,Eoin L. Brodie,Keith Keller,Thomas Huber,Daniel Dalevi,Ping Hu,Gary L. Andersen +9 more
TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
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