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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Journal ArticleDOI
Root microbiota dynamics of perennial Arabis alpina are dependent on soil residence time but independent of flowering time.
Nina Dombrowski,Klaus Schlaeppi,Matthew T. Agler,Stéphane Hacquard,Eric Kemen,Ruben Garrido-Oter,Ruben Garrido-Oter,Jörg Wunder,George Coupland,Paul Schulze-Lefert +9 more
TL;DR: The robustness of the root microbiota against the onset and perpetual flowering of A. alpina is revealed, whereas, after microbiota acquisition during vegetative growth, the established root-associated bacterial assemblage is structurally robust to perturbations caused by flowering and drastic changes in plant stature.
Journal ArticleDOI
Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge
Jan C. Plaizier,S. Li,Anne Mette Danscher,Hooman Derakshani,Pia Haubro Andersen,Ehsan Khafipour +5 more
TL;DR: Although the composition of the bacterial community of the feces was affected by the SARA challenge, bacterial taxa in the feces that can be used for accurate and non-invasive diagnosis of SARA could not be identified.
Journal ArticleDOI
Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS)
Sophie A. Poeker,Annelies Geirnaert,Laura Berchtold,Anna Greppi,Lukasz Krych,Robert E. Steinert,Tomas de Wouters,Christophe Lacroix +7 more
TL;DR: The data suggest that the metabolic profile of SCFA profile may be the most suitable and robust read-out to characterize microbiota-modulating effects of a DF and highlights importance to understand the inter-individual response to a prebiotic treatment for mechanistic understanding and human application.
Journal ArticleDOI
Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest
Joseph E. Knelman,Emily B. Graham,N. A. Trahan,Steven K. Schmidt,Diana R. Nemergut,Diana R. Nemergut +5 more
TL;DR: In this article, the authors examined the effect of a common post-fire colonizer plant species, Corydalis aurea, on soil chemistry, microbial biomass, soil enzyme activity and bacterial community structure one year after a major forest wildfire in Colorado, USA, in severely burned and lightly burned soils.
Journal ArticleDOI
Rapid identification of the botanical and entomological sources of honey using DNA metabarcoding.
TL;DR: Although this method was generally successful in determining both plant and insect sources, honeys rich in polyphenolic compounds or subject to crystallization were recalcitrant to analysis, so further research is required to combat honey adulteration and mislabeling.
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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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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