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 diversity along a 2600 km river continuum
Domenico Savio,Lucas Sinclair,Umer Zeeshan Ijaz,Juraj Parajka,Georg H. Reischer,Georg H. Reischer,Philipp Stadler,Alfred Paul Blaschke,Günter Blöschl,Robert L. Mach,Alexander K. T. Kirschner,Andreas H. Farnleitner,Andreas H. Farnleitner,Alexander Eiler +13 more
TL;DR: A comprehensive dataset detailing the bacterioplankton diversity along the midstream of the Danube River and its tributaries is presented, revealing that bacterial richness and evenness gradually declined downriver in both the free‐living and particle‐associated bacterial communities.
Journal ArticleDOI
Taxonomic structure and functional association of foxtail millet root microbiome.
Tao Jin,Yayu Wang,Yueying Huang,Jin Xu,Pengfan Zhang,Nian Wang,Xin Liu,Haiyan Chu,Guang Liu,Honggang Jiang,Yuzhen Li,Jing Xu,Karsten Kristiansen,Liang Xiao,Yunzeng Zhang,Gengyun Zhang,Guohua Du,Houbao Zhang,Hongfeng Zou,Zhang Haifeng,Zhuye Jie,Suisha Liang,Huijue Jia,Jingwang Wan,Dechun Lin,Jinying Li,Guangyi Fan,Huanming Yang,Jian Wang,Yang Bai,Xun Xu +30 more
TL;DR: The results demonstrated that host plants enrich specific bacteria and functions in the rhizoplane in foxtail millet root bacterial community, and may serve as a valuable knowledge foundation for bio-fertilizer development in agriculture.
Journal ArticleDOI
Kombucha tea fermentation: Microbial and biochemical dynamics.
Somnath Chakravorty,Semantee Bhattacharya,Antonis Chatzinotas,Writachit Chakraborty,Debanjana Bhattacharya,Ratan Gachhui +5 more
TL;DR: The data indicate that the microbial community structure and dynamics play an important role in the biochemistry of the fermentation of the beverage and a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations.
Journal ArticleDOI
Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations.
TL;DR: Deep 16S amplicon sequencing is used to investigate bacterial community characteristics in a fluvo-aquic soil treated for 24 years with inorganic fertilizers and organics and provides certain theoretical support for selection of rational fertilization strategies.
Journal ArticleDOI
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
TL;DR: This study demonstrates that de novo methods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
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