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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Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure
TL;DR: The succession of the bacterial community appeared to have a greater influence on the variation of ARGs during composting than the presence of antibiotics, and thus the compost product should be considered as an important reservoir for ARGs.
Journal ArticleDOI
Targeting zonulin and intestinal epithelial barrier function to prevent onset of arthritis
Narges Tajik,Michael Frech,Oscar Schulz,Fabian Schälter,Sébastien Lucas,Vugar Azizov,Kerstin Dürholz,Franziska Steffen,Yasunori Omata,Andreas Rings,Marko Bertog,Aroldo Rizzo,Aida Iljazovic,Marijana Basic,Arnd Kleyer,Stephan Culemann,Gerhard Krönke,Yubin Luo,Klaus Überla,Udo S. Gaipl,Benjamin Frey,Till Strowig,Kerstin Sarter,Stephan C. Bischoff,Stefan Wirtz,Juan D. Cañete,Francesco Ciccia,Georg Schett,Mario M. Zaiss +28 more
TL;DR: It is shown that both mice and humans with autoimmune arthritis can have dysbiosis and barrier leakiness prior to major signs of inflammatory arthritis, and treatment of mice with a zonulin antagonist can limit collagen-induced arthritis.
Journal ArticleDOI
Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.
Ricardo J. Eloy Alves,Bui Quang Minh,Bui Quang Minh,Tim Urich,Arndt von Haeseler,Christa Schleper +5 more
TL;DR: A taxonomy of AOA is defined based on a resolved amoA phylogeny and emergent global patterns in AOA diversity are described, revealing global environmental patterns that challenge many earlier generalisations.
Journal ArticleDOI
Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease
Wu Xiong,Wu Xiong,Rong Li,Yi Ren,Chen Liu,Qingyun Zhao,Huasong Wu,Alexandre Jousset,Alexandre Jousset,Qirong Shen +9 more
TL;DR: Comparisons of microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease in a vanilla long-term continuous cropping system indicate that fungal communities may be important in the development of soil suppressiveness against vanilla FUSarium wilts disease.
Journal ArticleDOI
Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia.
Ruben Garrido-Oter,Ryohei Thomas Nakano,Nina Dombrowski,Nina Dombrowski,Ka Wai Ma,Alice C. McHardy,Paul Schulze-Lefert +6 more
TL;DR: In this article, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order.
References
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