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
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High-throughput sequencing analysis of bacterial community composition and quality characteristics in refrigerated pork during storage
Li Ning,Youxiong Zhang,Qingping Wu,Qihui Gu,Moutong Chen,Yinzhi Zhang,Xiulan Sun,Jumei Zhang +7 more
TL;DR: The predicted metabolic pathways, based o the data of 16S rDNA, indicated an abundant carbohydrate metabolism and amino metabolism in refrigerated pork, which provides insight into the determinants of shelf life.
Journal ArticleDOI
Archaea dominate oxic subseafloor communities over multimillion-year time scales
Aurèle Vuillemin,Scott D. Wankel,Ömer K. Coskun,Tobias Magritsch,Sergio Vargas,Emily R. Estes,Arthur J. Spivack,David C. Smith,Robert A. Pockalny,Richard W. Murray,Steven D'Hondt,William D. Orsi +11 more
TL;DR: This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.
Journal ArticleDOI
Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens.
Kaire Loit,Kalev Adamson,Mohammad Bahram,Rasmus Puusepp,Sten Anslan,Riinu Kiiker,Rein Drenkhan,Leho Tedersoo +7 more
TL;DR: MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms and other associated organisms from plant tissues following both amplicon-based and PCR-free metagenomics approaches, and it is demonstrated that the Sequel instrument is efficient for metabarcoding of complex samples, whereas MinION is not suited for this purpose.
Journal ArticleDOI
Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure
Eric J. C. Gálvez,Aida Iljazovic,Achim Gronow,Richard A. Flavell,Richard A. Flavell,Till Strowig +5 more
TL;DR: The results show that the impact of Nlrp6 and also of adaptive immunity on microbiota composition depends on community structure and primarily influences pathobionts but not commensals.
Journal ArticleDOI
Exploring potential bacterial and fungal biocontrol agents transmitted from seeds to sprouts of wheat
TL;DR: The results suggested that wheat seeds and sprouts might contain core bacteriome and mycobiome during the development from seeds to sprouts and could transmit in the plant tissues of wheat.
References
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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
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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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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.
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