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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Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to tubulointerstitial fibrosis.
Lin Chen,Dan-Qian Chen,Jing-Ru Liu,Jun Zhang,Nosratola D. Vaziri,Shougang Zhuang,Hua Chen,Ya-Long Feng,Yan Guo,Yan Guo,Ying-Yong Zhao +10 more
TL;DR: The findings suggest that restoring the function of the intestinal barrier could prevent kidney damage due to microbial imbalance in the gut, and contribute to the pathogenesis of inflammation and TIF.
Journal ArticleDOI
Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle.
TL;DR: Saponins have the ability to modulate the ruminal microbial community and ruminal metabolites and thus affect the rumen environment, however, the response seems to be dependent on the composition of the basal diet.
Journal ArticleDOI
Activated ATF6 Induces Intestinal Dysbiosis and Innate Immune Response to Promote Colorectal Tumorigenesis.
Olivia I. Coleman,Elena M. Lobner,Sandra Bierwirth,Adam Sorbie,Nadine Waldschmitt,Eva Rath,Emanuel Berger,Ilias Lagkouvardos,Thomas Clavel,Kathleen McCoy,Achim Weber,Mathias Heikenwalder,Klaus-Peter Janssen,Dirk Haller +13 more
TL;DR: In studies of nATF6IEC mice, sustained intestinal activation of ATF6 in the colon to promote dysbiosis and microbiota-dependent tumorigenesis is found.
Journal ArticleDOI
Understanding the anaerobic biodegradability of food waste: Relationship between the typological, biochemical and microbial characteristics.
TL;DR: It was demonstrated that some FW characteristics as the density, the volatile solids and the fibres content vary as a function of the typological composition and the storage of FW before collection seems to impact several biochemical characteristics and could improve the biodegradability of FW.
Journal ArticleDOI
Root Microbiota in Primary and Secondary Apical Periodontitis
Serge Bouillaguet,Daniel Manoil,Myriam Girard,Justine Simone Louis,Nadia Gaïa,Stefano Leo,Jacques Schrenzel,Vladimir Lazarevic +7 more
TL;DR: The identification of bacterial taxa differentially abundant in primary and secondary intraradicular infections may provide the basis for targeted therapeutic approaches aimed at reducing the incidence of apical periodontitis.
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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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