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
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming.
Kyle Hartman,Marcel G. A. van der Heijden,Marcel G. A. van der Heijden,Raphaël Wittwer,Samiran Banerjee,Jean Claude Walser,Klaus Schlaeppi +6 more
TL;DR: It is found that about 10% of variation in microbial communities was explained by the tested cropping practices, which presents the basis towards developing microbiota management strategies for smart farming.
Journal ArticleDOI
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
Jizhong Zhou,Jizhong Zhou,Jizhong Zhou,Zhili He,Yunfeng Yang,Ye Deng,Ye Deng,Susannah G. Tringe,Lisa Alvarez-Cohen,Lisa Alvarez-Cohen +9 more
TL;DR: A critical review and synthesis of the most commonly applied “open-format" and “closed-format” detection technologies for interrogating microbial communities and discusses their characteristics, advantages, and disadvantages within the context of environmental applications.
Posted ContentDOI
ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
TL;DR: ampvis2, an R package designed for analysis of microbial community data in OTU-table format with focus on simplicity, reproducibility, and sample metadata integration, with a minimal set of intuitive commands, which includes flexible heatmaps and simplified ordination.
Journal ArticleDOI
Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota.
Tingting Chen,Wenmin Long,Chenhong Zhang,Shuang Liu,Liping Zhao,Bruce R. Hamaker,Bruce R. Hamaker +6 more
TL;DR: It is shown that the dominance of Prevotella versus Bacteroides in fecal innocula, identified into two different enterotypes, differentially impacts in vitro fermentation profiles of SCFAs from fibers with different chemical structures.
Journal ArticleDOI
Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants
Roberto Berni Canani,Naseer Sangwan,Andrew T. Stefka,Rita Nocerino,Lorella Paparo,Rosita Aitoro,Antonio Calignano,Aly A. Khan,Jack A. Gilbert,Jack A. Gilbert,Cathryn R. Nagler +10 more
TL;DR: The data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.
References
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QIIME allows analysis of high-throughput community sequencing data.
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