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
Acid mine drainage affects the diversity and metal resistance gene profile of sediment bacterial community along a river.
Xiaohui Zhang,Song Tang,Song Tang,Song Tang,Mao Wang,Weimin Sun,Yuwei Xie,Hui Peng,Aimin Zhong,Hongling Liu,Xiaowei Zhang,Hongxia Yu,John P. Giesy,Markus Hecker +13 more
TL;DR: These findings offer initial insight into the distribution patterns of sediment bacterial community structure, diversity and MRGs along a lotic ecosystem contaminated by AMD, and the factors that affect them.
Journal ArticleDOI
Probiotic yogurt and acidified milk similarly reduce postprandial inflammation and both alter the gut microbiota of healthy, young men.
Kathryn J Burton,Marta Rosikiewicz,Grégory Pimentel,Ueli Bütikofer,Ueli von Ah,Marie-Jeanne Voirol,Antony Croxatto,Sébastien Aeby,Jocelyne Drai,Philip G. McTernan,Gilbert Greub,François P. Pralong,Guy Vergères,Nathalie Vionnet +13 more
TL;DR: Probiotic yogurt and acidified milk similarly reduce postprandial inflammation that is associated with a HFM while inducing distinct changes in the gut microbiota of healthy men, which could be relevant for dietary treatments that target 'low-grade' inflammation.
Journal ArticleDOI
Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota.
TL;DR: It is found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface, and it is suggested that, in large-scale molecular studies of hundreds of insect specimens,surface sterilization may not be worth the time and effort involved.
Journal ArticleDOI
Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study.
Janice Crespo-Salgado,Janice Crespo-Salgado,V. Matti Vehaskari,V. Matti Vehaskari,Tyrus Stewart,Tyrus Stewart,Michael J. Ferris,Michael J. Ferris,Qiang Zhang,Guangdi Wang,Eugene Blanchard,Christopher M. Taylor,Mahmoud Kallash,Larry A. Greenbaum,Diego Aviles,Diego Aviles +15 more
TL;DR: The data suggests that no significant correlation exists between the alpha diversity of the intestinal microbiota and CRP, D-lactate, or uremic toxins.
Journal ArticleDOI
Mealworm frass as a potential biofertilizer and abiotic stress tolerance-inductor in plants
Jorge Poveda,Alejandro Jiménez-Gómez,Zaki Saati-Santamaría,R Usategui-Martín,Raúl Rivas,Raúl Rivas,Paula García-Fraile +6 more
TL;DR: Frass produced by the insect Tenebrio molitor, due to its nutritional content and associated microbiota, can be potentially used as a biofertilizer in organic farming, however, this potential dramatically varies according to the insect's diet.
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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QIIME allows analysis of high-throughput community sequencing data.
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