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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House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs.
TL;DR: The results of this study suggest that the dominant species of sourdough LAB and yeasts dominated also the house microbiota.
Journal ArticleDOI
Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations
TL;DR: It is suggested that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils is highlighted.
Journal ArticleDOI
Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode.
M. Imran Hamid,M. Imran Hamid,Muzammil Hussain,Yunpeng Wu,Xiaoling Zhang,Meichun Xiang,Xingzhong Liu +6 more
TL;DR: Evidence is provided that plants shift the structural and functional composition of the rhizosphere microbiota to suppress pathogen infection in LTM cropping soils to dissuade pathogen infestation.
Journal ArticleDOI
Municipal solid waste landfills harbor distinct microbiomes
Blake W. Stamps,Christopher N. Lyles,Joseph M. Suflita,Jason R. Masoner,Isabelle M. Cozzarelli,Dana W. Kolpin,Bradley S. Stevenson +6 more
TL;DR: How leachate microbiomes are distinct from those of other natural or built environments is illustrated, and light is shed on the major selective forces responsible for this microbial diversity.
Journal ArticleDOI
The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition.
Lindsay E. O'Donnell,Douglas Robertson,Christopher J. Nile,Laura J. Cross,Marcello P. Riggio,Andrea Sherriff,David J. Bradshaw,Margaret Lambert,Jennifer Malcolm,Mark J. Buijs,Egija Zaura,Wim Crielaard,Bernd W. Brandt,Gordon Ramage +13 more
TL;DR: This is the first study to provide a detailed understanding of the oral microbiome of denture wearers and has provided evidence that DS development is more complex than simply a candidal infection.
References
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