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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Journal ArticleDOI
Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China
Hao Guan,Yan Yanhong,Li Xiaoling,Li Xiaomei,Shuai Yang,Guangyan Feng,Qifan Ran,Yimin Cai,Ying Li,Xinquan Zhang +9 more
TL;DR: It is confirmed that microbial community of silages in hot and humid area is unique and climatic factors ultimately affect the fermentation quality through influencing microbial community.
Journal ArticleDOI
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores.
Jon G. Sanders,Annabel C. Beichman,Joe Roman,Joe Roman,Jarrod J. Scott,David R. Emerson,James J. McCarthy,Peter R. Girguis +7 more
TL;DR: It is demonstrated that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.
Journal ArticleDOI
The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity
Citlali Fonseca-García,Devin Coleman-Derr,Devin Coleman-Derr,Devin Coleman-Derr,Etzel Garrido,Axel Visel,Axel Visel,Axel Visel,Susannah G. Tringe,Susannah G. Tringe,Susannah G. Tringe,Laila P. Partida-Martinez +11 more
TL;DR: Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cactu holobiont.
Journal ArticleDOI
Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction
Xin Zhou,Jing Li,Junli Guo,Bin Geng,Wen-Jie Ji,Qian Zhao,Jinlong Li,Xin-Lin Liu,Jun-Xiang Liu,Zhao-Zeng Guo,Wei Cai,Yongqiang Ma,Dong Ren,Jun Miao,Shao-Bo Chen,Zhuoli Zhang,Junru Chen,Jiuchang Zhong,Wenbin Liu,Minghui Zou,Yu-Ming Li,Jun Cai +21 more
TL;DR: These results provide the first evidence that cardiovascular outcomes post-MI are driven by intestinal microbiota translocation into systemic circulation and new therapeutic strategies targeting to protect the gut barrier and eliminate gut bacteria translocation may reduce or even prevent cardiovascular events post- MI.
Journal ArticleDOI
Open-Source Sequence Clustering Methods Improve the State Of the Art
Evguenia Kopylova,Jose A. Navas-Molina,Céline Mercier,Zhenjiang Zech Xu,Frédéric Mahé,Yan He,Hongwei Zhou,Torbjørn Rognes,Torbjørn Rognes,J. Gregory Caporaso,Rob Knight +10 more
TL;DR: The performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options in QIIME, hierarchical clustering methods in mothur, and USEARCH’s most recent clustering algorithm, UPARSE are evaluated.
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
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Journal ArticleDOI
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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QIIME allows analysis of high-throughput community sequencing data.
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