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
More filters
Journal ArticleDOI
Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus
TL;DR: It is indicated that plant-associated fungal communities are more strongly influenced by host genetic factors and plant breeding than bacterial communities, a finding that could influence strategies for optimizing microbial communities to improve crop yields.
Journal ArticleDOI
Design of synthetic bacterial communities for predictable plant phenotypes.
Sur Herrera Paredes,Tianxiang Gao,Theresa F. Law,Omri M. Finkel,Tatiana S. Mucyn,Paulo José Pereira Lima Teixeira,Isai Salas González,Meghan E. Feltcher,Matthew J. Powers,Elizabeth A. Shank,Corbin D. Jones,Vladimir Jojic,Jeffery L. Dangl,Gabriel Castrillo +13 more
TL;DR: It is demonstrated that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host and that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
Journal ArticleDOI
Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data.
Didier Debroas,Isabelle Domaizon,Jean-François Humbert,Ludwig Jardillier,Cécile Lepère,Anne Oudart,Najwa Taib +6 more
TL;DR: Publicly available 18S barcoding data was used to define biases that may limit analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems, and it was showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems.
Journal ArticleDOI
High-resolution mycobiota analysis reveals dynamic intestinal translocation preceding invasive candidiasis
Bing Zhai,Mihaela Ola,Thierry Rolling,Thierry Rolling,Nicholas L. Tosini,Sari Joshowitz,Eric R. Littmann,Luigi A Amoretti,Emily Fontana,Roberta J. Wright,Edwin Miranda,Charlotte A Veelken,Sejal Morjaria,Sejal Morjaria,Jonathan U. Peled,Jonathan U. Peled,Marcel R.M. van den Brink,Marcel R.M. van den Brink,N. Esther Babady,Geraldine Butler,Ying Taur,Ying Taur,Tobias M. Hohl,Tobias M. Hohl +23 more
TL;DR: In this article, the authors integrated an optimized bioinformatics pipeline with high-resolution mycobiota sequencing and comparative genomic analyses of fecal and blood specimens from recipients of allogeneic hematopoietic cell transplant.
Journal ArticleDOI
Nitrogen removal by granular nitritation-anammox in an upflow membrane-aerated biofilm reactor.
TL;DR: The results demonstrate that the nitritation-anammox UMABR could potentially be used for nitrogen removal from mainstream in some specific regions with relatively warm temperature.
References
More filters
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.
Related Papers (5)
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