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
Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation
Kei E. Fujimura,Alexandra R. Sitarik,Suzanne Havstad,Din L. Lin,Sophia R. Levan,Douglas Fadrosh,Ariane R. Panzer,Brandon LaMere,Elze Rackaityte,Nicholas W. Lukacs,Ganesa Wegienka,Homer A. Boushey,Dennis R. Ownby,Edward M. Zoratti,Albert M. Levin,Christine Cole Johnson,Susan V. Lynch +16 more
TL;DR: It is suggested that neonatal gut microbiome dysbiosis might promote CD4+ T cell dysfunction associated with childhood atopy, and the effect of NGM3 fecal water on relativeCD4+CD25+FOXP3+ cell abundance.
Journal ArticleDOI
Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
Lingfei Hu,Christelle A. M. Robert,Selma Cadot,Xi Zhang,Meng Ye,Beibei Li,Daniele Manzo,Noémie Chervet,Thomas Steinger,Marcel G. A. van der Heijden,Marcel G. A. van der Heijden,Klaus Schlaeppi,Matthias Erb +12 more
TL;DR: The results reveal a mechanism by which plants determine the composition of rhizosphere microbiota, plant performance and plant-herbivore interactions of the next generation by modifying root-associated microbiota.
Journal ArticleDOI
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics.
Juan Jovel,Jordan Patterson,Weiwei Wang,Naomi Hotte,Sandra O'Keefe,Troy Mitchel,Troy Perry,Dina Kao,Andrew Mason,Karen L. Madsen,Gane Ka-Shu Wong +10 more
TL;DR: The two main approaches for analyzing the microbiome, 16S ribosomal RNA gene amplicons and shotgun metagenomics, are illustrated with analyses of libraries designed to highlight their strengths and weaknesses and several methods for taxonomic classification of bacterial sequences are discussed.
Journal ArticleDOI
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
Maggie R. Wagner,Derek S. Lundberg,Tijana Glavina del Rio,Susannah G. Tringe,Jeffery L. Dangl,Thomas Mitchell-Olds +5 more
TL;DR: This large-scale field experiment disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard to demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
Journal ArticleDOI
Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome
TL;DR: Feeding pattern and time of harvest are important parameters when assessing the microbiome's contribution to host metabolism and likely represent a mechanism by which the gut microbiome affects host metabolism.
References
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