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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Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil
TL;DR: Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments.
Journal ArticleDOI
Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants
TL;DR: The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time.
Journal ArticleDOI
Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports
TL;DR: Zooplankton communities were distinct among coastlines and significantly divergent among marine, freshwater and estuarine habitats even at the family level, and biodiversity varied substantially across two seasons reaching a beta diversity of 0.9 in a sub-Arctic port exposed to high vessel traffic.
Journal ArticleDOI
Epithelial calcineurin controls microbiota-dependent intestinal tumor development
Kenneth Peuker,Kenneth Peuker,Stefanie Muff,Jun Wang,Jun Wang,Sven Künzel,Sven Künzel,Esther Bosse,Yvonne Zeissig,Yvonne Zeissig,Giuseppina Luzzi,Giuseppina Luzzi,Marijana Basic,Anne Strigli,Andrea Ulbricht,Arthur Kaser,Alexander Arlt,Triantafyllos Chavakis,Gijs R. van den Brink,Clemens Schafmayer,Jan Hendrik Egberts,Thomas Becker,Marco Bianchi,André Bleich,Christoph Röcken,Jochen Hampe,Jochen Hampe,Stefan Schreiber,John F. Baines,John F. Baines,Richard S. Blumberg,Sebastian Zeissig +31 more
TL;DR: It is demonstrated that calcineurin and NFAT factors are constitutively expressed by primary IECs and selectively activated in intestinal tumors as a result of impaired stratification of the tumor-associated microbiota and toll-like receptor signaling.
Journal ArticleDOI
Synergistic pretreatment of waste activated sludge using CaO2 in combination with microwave irradiation to enhance methane production during anaerobic digestion
Jie Wang,Yongmei Li +1 more
TL;DR: In this article, the effects of combined calcium peroxide (CaO2) and microwave pretreatment on anaerobic digestion of waste activated sludge, lab-scale experiments were conducted to measure the solubilization, biodegradation, and dewaterability of the waste activation sludge.
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
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QIIME allows analysis of high-throughput community sequencing data.
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