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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Comparative analysis of gut microbiota of mosquito communities in central Illinois.
TL;DR: These findings expand the range of mosquito species whose gut microbiota has been characterized and sets the foundation for further studies to determine the influence of these microbiota on vector susceptibility to pathogens.
Journal ArticleDOI
Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine.
Hong Xutao,Jing Chen,Lin Liu,Huan Wu,Tan Haiqin,Guangfa Xie,Qian Xu,Huijun Zou,Wenjing Yu,Lan Wang,Nan Qin +10 more
TL;DR: Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by the finding that wine spoilage resulted from a high proportion of genus Lactobacillus.
Journal ArticleDOI
Feedstock determines biochar-induced soil priming effects by stimulating the activity of specific microorganisms
TL;DR: In this article, an 80-day soil-biochar incubation experiment was carried out to investigate biochar-induced soil priming effects by adopting isotopic techniques, and the intensity of PE was largely determined by the feedstock and was closely related to the proportion of cellulose and lignin in it.
Journal ArticleDOI
Effects of Nitrogen and Phosphorus Inputs on Soil Bacterial Abundance, Diversity, and Community Composition in Chinese Fir Plantations.
Wang Qing,Cong Wang,WeiWei Yu,Ali Turak,Chen Diwen,Huang Ying,Ao Junhua,Jiang Yong,Zhengrui Huang +8 more
TL;DR: Soil pH and mineral N availability appeared to have a cooperative effect on bacterial abundance and community structure, with soil pH being the key influencing factor by canonical correspondence analysis.
Journal ArticleDOI
Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response.
Igor Y. Oshkin,Igor Y. Oshkin,David A. C. Beck,Andrew Lamb,Veronika Tchesnokova,Gabrielle Benuska,Tami L. McTaggart,Marina G. Kalyuzhnaya,Svetlana N. Dedysh,Mary E. Lidstrom,Ludmila Chistoserdova +10 more
TL;DR: The results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe.
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
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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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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