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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Effects of oral probiotic supplements on vaginal microbiota during pregnancy: a randomised, double-blind, placebo-controlled trial with microbiome analysis
Shahid Husain,John Allotey,Zoe Drymoussi,Mark Wilks,Mark Wilks,Borja M. Fernandez-Felix,Angela Whiley,Angela Whiley,Julie Dodds,Shakila Thangaratinam,Christine McCourt,Erica M Prosdocimi,William G. Wade,B M de Tejada,Javier Zamora,Khalid S. Khan,Michael Millar,Michael Millar +17 more
TL;DR: To determine the effects on the vaginal microbiota of an oral probiotic preparation administered from early pregnancy, a large number of women were randomly assigned to receive either a probiotic or a dummy pill.
Journal ArticleDOI
Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils
TL;DR: S sandy soils of tundra is revealed as a source of novel acidobacterial diversity and an insight into the ecological preferences of different taxonomic groups within this phylum is provided.
Journal ArticleDOI
Modulation of cytokine patterns and microbiome during pregnancy in IBD
Janine van der Giessen,Dana Binyamin,Anna Belogolovski,S. Frishman,Kinneret Tenenbaum-Gavish,Eran Hadar,Yoram Louzoun,Maikel P. Peppelenbosch,Christien J. van der Woude,Omry Koren,Gwenny M. Fuhler +10 more
TL;DR: Serum proinflammatory cytokine levels markedly improve on conception in pregnant patients with IBD, and intestinal microbiome diversity of patientsWith IBD normalises during middle and late pregnancy, which concludes that pregnancy is safe and even potentially beneficial for patientswith IBD.
Journal ArticleDOI
Developing standards for the microbiome field.
Gregory C. A. Amos,Alastair Logan,Saba Anwar,Martin Fritzsche,Ryan Mate,Thomas Bleazard,Sjoerd Rijpkema +6 more
TL;DR: The development of the first reference reagents produced by the National Institute for Biological Standards and Control for microbiome analysis by next-generation sequencing can act as global working standards and will be evaluated as candidate World Health Organization International Reference Reagents.
Journal ArticleDOI
CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9.
TL;DR: A method for robust directed evolution using mutagenesis of large sequence spaces in their genomic contexts using error-prone PCR and Cas9-mediated genome integration of mutant libraries of large-sized donor variants into single or multiple genomic sites with efficiencies reaching 98-99%.
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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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