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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Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model.
Pedro J. Torres,Bryan Ho,Pablo Arroyo,Lillian Sau,Annie Chen,Scott T. Kelley,Varykina G. Thackray +6 more
TL;DR: Results suggest that dysbiosis of the gut microbiome may play a causal role in PCOS and that modulation of the Gut microbiome may be a potential treatment option for PCOS.
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Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA.
Angelo F. Bernardino,Fabiano Sviatopolk-Mirsky Pais,Louisi S Oliveira,Fabricio A. Gabriel,Tiago Osório Ferreira,Hermano M. Queiroz,Ana Carolina de Azevedo Mazzuco +6 more
TL;DR: It is suggested that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.
Journal ArticleDOI
Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
Edoardo Piombo,Ahmed Abdelfattah,Samir Droby,Michael Wisniewski,Davide Spadaro,Leonardo Schena +5 more
TL;DR: In this article, the authors present the current status of high-throughput sequencing (HTS) diagnostics of fungal and bacterial plant pathogens, discuss the challenges that need to be addressed, and provide direction for the development of methods for the detection of a restricted number of related taxa or all of the microorganisms present in a sample.
Journal ArticleDOI
Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings.
Xiaoxu Sun,Tianle Kong,Max M. Häggblom,Max Kolton,Fangbai Li,Yiran Dong,Huang Yuqing,Baoqin Li,Weimin Sun +8 more
TL;DR: Findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.
Journal ArticleDOI
Dichotomous development of the gut microbiome in preterm infants
Thao Ho,Maureen Groer,Bradley Kane,Alyson L. Yee,Benjamin A. Torres,Jack A. Gilbert,Jack A. Gilbert,Akhil Maheshwari,Akhil Maheshwari +8 more
TL;DR: Vaginal birth and antenatal steroids were identified as predictors of Gammaproteobacteria abundance in the early (≤ 2 weeks) and later (3rd and 4th weeks) stool samples, respectively, important in understanding the development of the gut microbiome in premature infants.
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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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