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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Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database
Andrew Bissett,Anna Fitzgerald,Thys Meintjes,Pauline M. Mele,Frank Reith,Frank Reith,Paul G. Dennis,Martin F. Breed,Belinda Brown,Mark V. Brown,Joël Brugger,Margaret Byrne,Stefan Caddy-Retalic,Bernie Carmody,David J. Coates,Carolina Correa,Belinda C. Ferrari,Vadakattu V. S. R. Gupta,Kelly Hamonts,Kelly Hamonts,Asha Haslem,Philip Hugenholtz,Mirko Karan,Jason Koval,Andrew J. Lowe,Stuart Macdonald,Leanne McGrath,David Martin,Matthew J. Morgan,Kristin I. North,Chanyarat Paungfoo-Lonhienne,Elise Pendall,Lori A. Phillips,Rebecca Pirzl,Jeff R. Powell,Mark A. Ragan,Susanne Schmidt,Nicole P. Seymour,Ian Snape,John R. Stephen,Matthew Stevens,Matt Tinning,Kristen J. Williams,Yun Kit Yeoh,Carla M. Zammit,Andrew G. Young +45 more
TL;DR: The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale, becoming the first Australian soil microbial diversity database.
Journal ArticleDOI
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome
Imane Allali,Imane Allali,Jason W. Arnold,Jeffrey Roach,Maria B. Cadenas,Natasha Butz,Hosni M. Hassan,Matthew D. Koci,Anne Ballou,Mary Mendoza,Rizwana Ali,M. Andrea Azcarate-Peril +11 more
TL;DR: The three platforms compared were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions, demonstrating that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity.
Journal ArticleDOI
Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere
Charlotte I. Carlström,Christopher M. Field,Miriam Bortfeld-Miller,Barbara Müller,Shinichi Sunagawa,Julia A. Vorholt +5 more
TL;DR: The authors identify several keystone strains and show that priority effects drive phyllosphere community assembly, and indicate that individual strains of Proteobacteria and Actinobacteria have the greatest potential to affect community structure as keystone species.
Journal ArticleDOI
Climate warming leads to divergent succession of grassland microbial communities
Xue Guo,Jiajie Feng,Zhou Shi,Xishu Zhou,Xishu Zhou,Mengting Yuan,Mengting Yuan,Xuanyu Tao,Lauren Hale,Tong Yuan,Jianjun Wang,Yujia Qin,Aifen Zhou,Ying Fu,Liyou Wu,Zhili He,Joy D. Van Nostrand,Daliang Ning,Daliang Ning,Xueduan Liu,Yiqi Luo,Yiqi Luo,Yiqi Luo,James M. Tiedje,Yunfeng Yang,Yunfeng Yang,Jizhong Zhou +26 more
TL;DR: In this paper, the authors examined the temporal succession of soil microbes in a long-term climate change experiment at a tall-grass prairie ecosystem and found that experimental warming was found to significantly alter the community structure of bacteria and fungi.
Journal ArticleDOI
Mechanism and Effect of Temperature on Variations in Antibiotic Resistance Genes during Anaerobic Digestion of Dairy Manure.
TL;DR: The bacterial community succession was the dominant mechanism that influenced the variation in ARGs and integrons during anaerobic digestion and Thermophilic an aerobic digestion is recommended for the treatment and reuse of animal manure.
References
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