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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Fecal microbiota transplant rescues mice from human pathogen mediated sepsis by restoring systemic immunity.
Sangman M. Kim,Sangman M. Kim,Jennifer R. DeFazio,Jennifer R. DeFazio,Sanjiv Hyoju,Kishan Sangani,Robert Keskey,Monika A. Krezalek,Nikolai N. Khodarev,Naseer Sangwan,Naseer Sangwan,Scott Christley,Katharine G. Harris,Ankit Malik,Alexander Zaborin,Romain Bouziat,Diana Rose E. Ranoa,Mara Wiegerinck,Jordan D. Ernest,Baddr A. Shakhsheer,Irma D. Fleming,Ralph R. Weichselbaum,Dionysios A. Antonopoulos,Dionysios A. Antonopoulos,Jack A. Gilbert,Jack A. Gilbert,Luis B. Barreiro,Luis B. Barreiro,Olga Zaborina,Bana Jabri,John C. Alverdy +30 more
TL;DR: Fecal microbiota transplant (FMT) can rescue mice from lethal sepsis of pathogens isolated from stool of a critically ill patient and show that FMT reverses the immunosuppressive effect induced by the pathogen community.
Journal ArticleDOI
Revegetation rewilds the soil bacterial microbiome of an old field.
TL;DR: It is demonstrated that metabarcoding of eDNA is effective at demonstrating the return of the native bacterial community in an old field following native plant revegetation, and provides an effective way of monitoring changes in bacterial communities that would otherwise go unchecked with conventional monitoring of restoration projects.
Journal ArticleDOI
Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar.
TL;DR: Principal component analysis and cluster analyses revealed the high correlation between the dynamics of bacterial community and metabolites in solid-state acetic acid fermentation.
Journal ArticleDOI
Effect of bioaugmented inoculation on microbiota dynamics during solid-state fermentation of Daqu starter using autochthonous of Bacillus, Pediococcus, Wickerhamomyces and Saccharomycopsis
TL;DR: The results reinforced the microbiota dynamic stability during the solid-state fermentation process of Daqu, and might aid in controlling the traditional Daqu manufacturing process.
Journal ArticleDOI
Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula.
TL;DR: This is the first description of fungi from the Plastisphere within the Southern Hemisphere, and highlights the need to further investigate the potential impacts of plastic associated fungi on other organisms and marine ecosystems.
References
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