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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Antidiabetic Potential of Green Seaweed Enteromorpha prolifera Flavonoids Regulating Insulin Signaling Pathway and Gut Microbiota in Type 2 Diabetic Mice.
TL;DR: The results indicated that EPW3 possessed great therapeutic potential as adjuvant therapy for type 2 diabetes, as indicated by activation of the IRS1/PI3K/AKT and inhibition of the JNK1/2 insulin pathway in liver.
Journal ArticleDOI
Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots.
Petr Kohout,Markéta Charvátová,Martina Štursová,Tereza Mašínová,Michal Tomšovský,Petr Baldrian +5 more
TL;DR: It is found that the termination of photosynthate flow through tree roots into soil is associated with profound changes in soil, both in decomposition processes and fungal community composition, and there is some evidence that root endophytic fungi may have an important role in the early stages of this process.
Journal ArticleDOI
Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.).
TL;DR: The coexistence of these indigenous bacterial and fungal taxa in sprouts, roots, and stems indicated their transmission during the development from sprouts to mature plants.
Journal ArticleDOI
Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau
TL;DR: The findings suggest that the aboveground vegetation diversity and soil nutrients were improved with the increased thinning intensity after 11years, indicating a dependence of the soil microbial community composition on soil nutrients.
Journal ArticleDOI
Next generation sequencing data of a defined microbial mock community
Esther Singer,Bill Andreopoulos,Robert M. Bowers,Janey Lee,Shweta Deshpande,Jennifer Chiniquy,Doina Ciobanu,Hans-Peter Klenk,Matthew Zane,Christopher Daum,Alicia Clum,Jan Fang Cheng,Alex Copeland,Tanja Woyke +13 more
TL;DR: The next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes, is reported, enabling extensive benchmarking and comparative evaluation of bioinformatics tools without the need to simulate data.
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
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.
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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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