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
Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community.
Nagalakshmi Haleyur,Esmaeil Shahsavari,Sohni Jain,Eman Koshlaf,Vivek B. Ravindran,Paul D. Morrison,A. Mark Osborn,Andrew S. Ball +7 more
TL;DR: Investigating the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia suggested that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process.
Journal ArticleDOI
Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma
Jakob Stokholm,Jonathan Thorsen,Martin J. Blaser,Martin J. Blaser,Morten Arendt Rasmussen,Mathis Hjort Hjelmsø,Shiraz A. Shah,Emil Dalgaard Christensen,Bo L. Chawes,Klaus Bønnelykke,Susanne Brix,Martin S. Mortensen,Asker Daniel Brejnrod,Asker Daniel Brejnrod,Gisle Vestergaard,Gisle Vestergaard,Urvish Trivedi,Søren J. Sørensen,Hans Bisgaard +18 more
TL;DR: Investigation of the effects of cesarean section delivery on gut microbial composition by 16S rRNA gene amplicon sequencing during the first year of life found that appropriate maturation of the gut microbiota could mitigate against the increased asthma risk associated with gut microbial changes due to cesaren section delivery.
Book ChapterDOI
Learning ecological networks from next-generation sequencing data
Corinne Vacher,Alireza Tamaddoni-Nezhad,Stefaniya Kamenova,Nathalie Peyrard,Yann Moalic,Régis Sabbadin,Loïc Schwaller,Julien Chiquet,M. Alex Smith,Jessica Vallance,Virgil Fievet,Boris Jakuschkin,David A. Bohan +12 more
TL;DR: Three case studies, in which species associations or interactions have been revealed with NGS and several currently available statistical and machine-learning approaches that could be used for reconstructing networks of direct interactions between species, based on the NGS co-occurrence data are reviewed.
Journal ArticleDOI
Isolation and analysis of microbial communities in soil, rhizosphere, and roots in perennial grass experiments
TL;DR: Methods presented here provide a complete set of steps for how to collect field samples, isolate, extract, quantify, amplify, and sequence DNA, and analyze microbial community diversity and composition in replicated field trials.
Journal ArticleDOI
Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats
TL;DR: Coloration by ruminal epithelial bacteria is age related and might participate in the anatomic and functional development of the rumen and the relationship between the microbiota and the host.
References
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