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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Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut
Martin Frederik Laursen,Mikiyasu Sakanaka,Mikiyasu Sakanaka,Nicole von Burg,Urs M. Mörbe,Daniel Andersen,Janne Marie Moll,Ceyda T. Pekmez,Aymeric Rivollier,Kim F. Michaelsen,Christian Mølgaard,Mads Vendelbo Lind,Lars O. Dragsted,Takane Katayama,Takane Katayama,Henrik Lund Frandsen,Anne Marie Vinggaard,Martin Iain Bahl,Susanne Brix,William W. Agace,William W. Agace,Tine Rask Licht,Henrik Munch Roager,Henrik Munch Roager +23 more
TL;DR: In this paper, Bifidobacterium species associated with breastfeeding can convert aromatic amino acids (tryptophan, phenylalanine and tyrosine) into their respective aromatic lactic acids (indolelactic acid, phenyllactic acid and 4-hydroxyphenyllactic acids) via a previously unrecognized aromatic lactate dehydrogenase (ALDH).
Journal ArticleDOI
Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe.
Manuel Delgado-Baquerizo,Manuel Delgado-Baquerizo,Ellen L. Fry,David J. Eldridge,Franciska T. de Vries,Peter Manning,Kelly Hamonts,Jens Kattge,Gerhard Boenisch,Brajesh K. Singh,Richard D. Bardgett +10 more
TL;DR: It is reported that aboveground plant community attributes, such as diversity and cover, and functional traits can predict a unique portion of the variation in the diversity and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate.
Journal ArticleDOI
Mortierella elongata's roles in organic agriculture and crop growth promotion in a mineral soil
Fang Li,Fang Li,Lin Chen,Marc Redmile-Gordon,Jiabao Zhang,Jiabao Zhang,Congzhi Zhang,Ning Qi,Wei Li +8 more
Journal ArticleDOI
Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men.
Ilias Lagkouvardos,Karoline Kläring,Silke S. Heinzmann,Stefanie Platz,Birgit Scholz,Karl-Heinz Engel,Philippe Schmitt-Kopplin,Dirk Haller,Sascha Rohn,Thomas Skurk,Thomas Clavel +10 more
TL;DR: Flaxseeds increase enterolignan production but do not markedly alter fecal metabolome and dominant bacterial communities, which underline the possible role of members of the family Ruminococcaceae in the regulation of enterolIGNan production and blood lipids.
Journal ArticleDOI
Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome
Zhijian Huang,Shenzheng Zeng,Jinbo Xiong,Dongwei Hou,Renjun Zhou,Chengguang Xing,Dongdong Wei,Xisha Deng,Lingfei Yu,Hao Wang,Zhixuan Deng,Shaoping Weng,Satapornvanit Kriengkrai,Daliang Ning,Jizhong Zhou,Jianguo He +15 more
TL;DR: Solid evidence of the causality between IM dysbiosis and shrimp WFS is offered, which exemplify the ‘microecological Koch’s postulates’ (an intestinal microbiota Dysbiosis, a disease) in disease etiology, and inspire the cogitation on etiology from an ecological perspective.
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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