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
Bacterial rather than fungal community composition is associated with microbial activities and nutrient-use efficiencies in a paddy soil with short-term organic amendments
Junjie Guo,Wenbo Liu,Chen Zhu,Gongwen Luo,Yali Kong,Ning Ling,Min Wang,Jingyu Dai,Qirong Shen,Shiwei Guo +9 more
TL;DR: Soil microbial activities and nutrient-use efficiencies were dramatically changed along with the alteration of bacterial community composition, and soil organic carbon emerged as the major determinant of theacterial community composition.
Journal ArticleDOI
Protective Factors in the Intestinal Microbiome Against Clostridium difficile Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation.
Yeon Joo Lee,Arguello Es,Robert R. Jenq,Eric R. Littmann,Grace Kim,Liza Miller,Lilan Ling,Cesar J. Figueroa,Elizabeth Robilotti,Miguel-Angel Perales,Juliet N. Barker,Sergio Giralt,van den Brink Mrm,Eric G. Pamer,Ying Taur,Ying Taur +15 more
TL;DR: In this article, the authors examined the microbiota composition of allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients to identify bacterial colonizers that confer protection against CDI after engraftment.
Journal ArticleDOI
Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes.
TL;DR: These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.
Journal ArticleDOI
Analysis of gut microbiota and the effect of lauric acid against necrotic enteritis in Clostridium perfringens and Eimeria side-by-side challenge model
TL;DR: Investigation of gut microbiota changes in chickens challenged with netB-positive Clostridium perfringens strain and/or the predisposing Eimeria species and fed diets with fishmeal supplementation demonstrated that microbial communities in the jejunum were distinct from those in the cecum, and the microbial community change was more significant inJejunum.
Journal ArticleDOI
Dietary quality and the colonic mucosa–associated gut microbiome in humans
Yanhong Liu,Nadim J. Ajami,Hashem B. El-Serag,Clark Hair,Clark Hair,David Y. Graham,David Y. Graham,David Y. Graham,Donna L. White,Liang Chen,Liang Chen,Zhensheng Wang,Sarah Plew,Sarah Plew,Jennifer R. Kramer,Jennifer R. Kramer,Jennifer R. Kramer,Rhonda A. Cole,Rhonda A. Cole,Ruben Hernaez,Jason K. Hou,Nisreen Husain,Nisreen Husain,Maria Jarbrink-Sehgal,Maria Jarbrink-Sehgal,Fasiha Kanwal,Gyanprakash A. Ketwaroo,Gyanprakash A. Ketwaroo,Yamini Natarajan,Yamini Natarajan,Rajesh Shah,Rajesh Shah,Rajesh Shah,Maria Velez,Maria Velez,Niharika Mallepally,Joseph F. Petrosino,Li Jiao +37 more
TL;DR: A lower score for total HEI-2005 was significantly associated with reduced relative abundance of potentially beneficial bacteria but increased potentially harmful bacteria in the colonic mucosa of endoscopically normal individuals.
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