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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Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model
TL;DR: The present study comprehensively describes the symbiotic relationship between the rumen microbiota and the host in lambs after starter feeding and demonstrates that the microbiome-driven generation of acetate and butyrate mediated the growth-related genes’ regulation of thegrowth-associated signalling pathway in the ruminal epithelium.
Journal ArticleDOI
A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice
TL;DR: It is demonstrated that higher amount of B. wadsworthia caused systemic inflammatory response in SPF mice, which adds new evidence to the pathogenicity of this bacterium and implied its potential role to the chronic inflammation related metabolic diseases like diabetes.
Journal ArticleDOI
Simultaneous nitrification, denitrification and phosphorus removal in a sequencing batch reactor (SBR) under low temperature
TL;DR: It was confirmed that polyphosphate accumulating organisms (PAOs) were dominant in microbial communities revealed by fluorescence in situ hybridization and 16S rRNA amplicon sequencing and denitrifying phosphorus removal by PAOs through nitrite pathway was found to be the main reason for the high efficiency of this SNDPR process.
Journal ArticleDOI
Regional-scale in-depth analysis of soil fungal diversity reveals strong pH and plant species effects in Northern Europe
Leho Tedersoo,Sten Anslan,Sten Anslan,Mohammad Bahram,Mohammad Bahram,Rein Drenkhan,Karin Pritsch,Franz Buegger,Allar Padari,Niloufar Hagh-Doust,Vladimir S. Mikryukov,Daniyal Gohar,Rasekh Amiri,Indrek Hiiesalu,Reimo Lutter,Raul Rosenvald,Elisabeth Rähn,Kalev Adamson,Tiia Drenkhan,Hardi Tullus,Katrin Jürimaa,Ivar Sibul,Eveli Otsing,Sergei Põlme,Marek Metslaid,Kaire Loit,Ahto Agan,Rasmus Puusepp,Inge Varik,Urmas Kõljalg,Urmas Kõljalg,Kessy Abarenkov +31 more
TL;DR: It is found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups, and the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
Journal ArticleDOI
Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples.
Jennifer J. Barb,Andrew J. Oler,Hyungsuk Kim,Natalia I. Chalmers,Gwenyth R. Wallen,Ann K. Cashion,Peter J. Munson,Nancy J. Ames +7 more
TL;DR: This paper examines a new process using seven hypervariable or V regions of the 16S rRNA (six amplicons: V2, V3, V4, V6-7, V8, and V9) processed simultaneously on the Ion Torrent Personal Genome Machine and shows that the methods used are valid.
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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