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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Tree species identity surpasses richness in affecting soil microbial richness and community composition in subtropical forests
Liang Chen,Wenhua Xiang,Huili Wu,Shuai Ouyang,Bo Zhou,Yelin Zeng,Yongliang Chen,Yakov Kuzyakov,Yakov Kuzyakov,Yakov Kuzyakov +9 more
TL;DR: In this paper, the authors examined the effects of tree species richness and the presence of certain influential tree species on soil bacterial and fungal communities in Chinese subtropical forests, using high-throughput Illumina sequencing for microbial identification.
Journal ArticleDOI
Synbiotics Alter Fecal Microbiomes, But Not Liver Fat or Fibrosis, in a Randomized Trial of Patients With Nonalcoholic Fatty Liver Disease
Eleonora Scorletti,Eleonora Scorletti,Eleonora Scorletti,Paul R. Afolabi,Paul R. Afolabi,Elizabeth A. Miles,Debbie E. Smith,Debbie E. Smith,Amal Almehmadi,Albandri Alshathry,Caroline E. Childs,Stefania Del Fabbro,Josh Bilson,Josh Bilson,Helen Moyses,Geraldine F. Clough,Jaswinder K. Sethi,Jaswinder K. Sethi,Janisha Patel,Mark Wright,David J. Breen,Charles Peebles,Angela Darekar,Richard Aspinall,Andrew Fowell,Joanna Dowman,Valerio Nobili,Valerio Nobili,Giovanni Targher,Nathalie M. Delzenne,Laure B. Bindels,Philip C. Calder,Philip C. Calder,Christopher D. Byrne,Christopher D. Byrne +34 more
TL;DR: In a randomized trial of patients with NAFLD, 1 y administration of a synbiotic combination (probiotic and prebiotic) altered fecal microbiomes but did not reduce liver fat content or markers of liver fibrosis.
Journal ArticleDOI
A20 controls intestinal homeostasis through cell-specific activities
Lars Vereecke,Sara Vieira-Silva,Thomas Billiet,Johan H. van Es,Conor Mc Guire,Karolina Slowicka,Mozes Sze,Maaike van den Born,Gert De Hertogh,Hans Clevers,Jeroen Raes,Paul Rutgeerts,Severine Vermeire,Rudi Beyaert,Geert van Loo +14 more
TL;DR: Despite absence of spontaneous intestinal inflammation in intestinal epithelial cell (IEC) specific A20 knockout mice, it is found additional myeloid-specific A20 deletion to synergistically drive intestinal pathology through cell-specific mechanisms.
Journal ArticleDOI
High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes
TL;DR: In this paper, the authors carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing.
Journal ArticleDOI
Macroecology to Unite All Life, Large and Small.
Ashley Shade,Robert R. Dunn,Robert R. Dunn,Shane A. Blowes,Petr Keil,Brendan J. M. Bohannan,Martina Herrmann,Kirsten Küsel,Jay T. Lennon,Nathan J. Sanders,Nathan J. Sanders,David Storch,David Storch,Jonathan M. Chase +13 more
TL;DR: It is argued that it is time to bridge the gap in microbial ecology and macroecology, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity.
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
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Search and clustering orders of magnitude faster than BLAST
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Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
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