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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Journal ArticleDOI
Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.
Guoyan Zhao,Tommi Vatanen,Tommi Vatanen,Lindsay Droit,Arnold Park,Aleksandar Kostic,Tiffany W. Poon,Hera Vlamakis,Heli Siljander,Heli Siljander,Taina Härkönen,Taina Härkönen,Anu Maaria Hämäläinen,Aleksandr Peet,Aleksandr Peet,Vallo Tillmann,Vallo Tillmann,Jorma Ilonen,David Wang,Mikael Knip,Ramnik J. Xavier,Ramnik J. Xavier,Herbert W. Virgin +22 more
TL;DR: It was found that the intestinal viromes of cases were less diverse than those of controls and eukaryotic viruses and bacteriophage contigs that are associated with the presence or absence of autoimmunity and disease-associated viral bacteriophile contigs were statistically linked to specific components of the bacterial microbiome.
Book ChapterDOI
16S rRNA Gene Analysis with QIIME2.
Michael W. Hall,Robert G. Beiko +1 more
TL;DR: This chapter demonstrates how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis and walks through an example data set extracted from the guts of bumblebees to show how QIime2 can transform raw sequences into taxonomic bar plots, phylogenetic trees, principal co-ordinates analyses, and other visualizations of microbial diversity.
Journal ArticleDOI
Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota.
Allen Van Deynze,Pablo Zamora,Pierre-Marc Delaux,Cristobal Heitmann,Dhileepkumar Jayaraman,Shanmugam Rajasekar,Danielle Graham,Junko Maeda,Donald Gibson,Kevin D. Schwartz,Alison M. Berry,Srijak Bhatnagar,Guillaume Jospin,Aaron E. Darling,Richard Jeannotte,Javier Lopez,Bart C. Weimer,Jonathan A. Eisen,Howard Yana Shapiro,Jean-Michel Ané,Alan B. Bennett +20 more
TL;DR: Analysis of the mucilage microbiota of an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity.
Journal ArticleDOI
Cervicovaginal microbiota and local immune response modulate the risk of spontaneous preterm delivery.
Michal A. Elovitz,Pawel Gajer,Valerie Riis,Amy Brown,Michael S. Humphrys,Johanna B. Holm,Jacques Ravel +6 more
TL;DR: In this paper, a nested case control study on 107 well-phenotyped cases of spontaneous preterm birth (sPTB) and 432 women delivering at term using innovative Bayesian modeling of cervicovaginal microbiota, seven bacterial taxa were significantly associated with increased risk of sPTB, with a stronger effect in African American women.
Journal ArticleDOI
Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis.
TL;DR: The purpose of this review is to present the most common and emerging DNA‐based methods used to generate data for biodiversity and biomonitoring studies, with particular attention to the DNA metabarcoding method.
References
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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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