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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Alteration of the fecal microbiota in North-Eastern Han Chinese population with sporadic Parkinson's disease.
TL;DR: The gut microbiota composition of 10 patients with sporadic PD and over 65 age and 10 matched controls was analyzed to explore fecal microbiota compositions in North-eastern Han sporadic PD patients and will provide a foundation to improve the understanding of PD.
Journal ArticleDOI
Suppression of soil-borne Fusarium pathogens of peanut by intercropping with the medicinal herb Atractylodes lancea
TL;DR: The results support the idea that intercropping with A. lancea or use of its effective components has a strong potential for managing soil-borne fungal diseases.
Journal ArticleDOI
Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities
Manuel Delgado-Baquerizo,Manuel Delgado-Baquerizo,Andrew Bissett,David J. Eldridge,Fernando T. Maestre,Ji-Zheng He,Ji-Zheng He,Jun-Tao Wang,Kelly Hamonts,Yu-Rong Liu,Brajesh K. Singh,Noah Fierer,Noah Fierer +12 more
TL;DR: Analysing data from more than 1,000 sites globally, the authors show that palaeoclimatic legacies explain a greater amount of variation in bacterial community richness and composition than current climate.
Journal ArticleDOI
Quantifying long-term recurrence in planktonic microbial eukaryotes.
Caterina R. Giner,Vanessa Balagué,Anders K. Krabberød,Isabel Ferrera,Albert Reñé,Esther Garcés,Josep M. Gasol,Ramiro Logares,Ramiro Logares,Ramon Massana +9 more
TL;DR: This work links long-term whole community dynamics with that of individual OTUs and taxonomic groups, indicating that recurrent and non-recurrent changes characterize the dynamics of microbial assemblages.
Journal ArticleDOI
Biochar Induces Changes to Basic Soil Properties and Bacterial Communities of Different Soils to Varying Degrees at 25 mm Rainfall: More Effective on Acidic Soils
TL;DR: Results from this study revealed that it is necessary to formulate biochar and fertilizer application schemes based on different soil types and the interactions between acidic soil bacterial communities and measured soil parameters including pH, organic matter were found to be statistically significant.
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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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.
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