DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan,Paul J. McMurdie,Michael J. Rosen,Andrew W. Han,Amy Jo A. Johnson,Susan Holmes +5 more
TLDR
The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants.Abstract:
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.read more
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Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function.
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Stephanie L. Bond,Edouard Timsit,Matthew L. Workentine,Trevor W. Alexander,Renaud Léguillette +4 more
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Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells
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Oral microbiome composition, but not diversity, is associated with adolescent anxiety and depression symptoms
Carra A Simpson,Christina J. Adler,Mieke R du Plessis,E. Landau,Stuart G. Dashper,Eric C. Reynolds,Orli Schwartz,Julian G Simmons +7 more
TL;DR: Oral microbiome composition, but not diversity, was associated with adolescent anxiety and depression symptoms, and several host mood-microbial relationships were moderated by proposed mechanisms, including salivary cortisol and CRP.
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TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
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