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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Microbiome–metabolomics reveals gut microbiota associated with glycine-conjugated metabolites and polyamine metabolism in chronic kidney disease
Ya-Long Feng,Gang Cao,Dan-Qian Chen,Nosratola D. Vaziri,Lin Chen,Jun Zhang,Ming Wang,Yan Guo,Ying-Yong Zhao +8 more
TL;DR: The CKD-associated gut microbial dysbiosis is confirmed and a novel dietary and therapeutic strategy to improve the gut microbial Dysbiosis and the associated metabolomic disorders and retarded the progression of kidney disease in the rat model of CKD is identified.
Journal ArticleDOI
Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems.
Sen Li,Fengzhi Wu +1 more
TL;DR: Taken together, trifolium and mustard as the intercrops significantly increased cucumber continuous cropping soil bacterial and fungal communities diversity, and intercropping strongly changed the relationships of microbial taxa, though did not shape notably soil microbial communities structure.
Journal ArticleDOI
Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer
A. B. Moyes,A. B. Moyes,Lara M. Kueppers,Lara M. Kueppers,Jennifer Pett-Ridge,Dana L. Carper,Nick Vandehey,James P. O'Neil,A. Carolin Frank +8 more
TL;DR: It is proposed that foliar endophytes represent a low-cost, evolutionarily stable N2 -fixing strategy for long-lived conifers and this novel source of biological N2 fixation has fundamental implications for understanding forest N budgets.
Journal ArticleDOI
Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community
TL;DR: The virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies were characterized using next-generation sequencing methods and found no evidence of a core viral community across samples.
Journal ArticleDOI
Effects of past and current drought on the composition and diversity of soil microbial communities
TL;DR: Soils with a history of drought had higher overall bacterial alpha diversity at the end of the experimental drought, presumably because of adaptation of the bacterial community to drought conditions, and some bacterial taxa decreased in abundance more in the pre-droughted soils.
References
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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
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UCHIME improves sensitivity and speed of chimera detection
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