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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The Gut-Eye Axis: Lessons Learned from Murine Models.
Jason L. Floyd,Maria B. Grant +1 more
TL;DR: Some evidence is described that supports the possible role of a dysbiotic gut microbiota in the onset and exacerbation of ocular diseases, primarily diabetic retinopathy, age-related macular degeneration, choroidal neovascularization, and uveitis.
Journal ArticleDOI
Microbiome and Longevity: High Abundance of Longevity-Linked Muribaculaceae in the Gut of the Long-Living Rodent Spalax leucodon
Mustafa Sibai,Ebru Altuntaş,Berna Yıldırım,Gürkan Öztürk,Suleyman Yildirim,Turan Demircan,Turan Demircan +6 more
TL;DR: The gut and skin bacterial structure of Spalax for the first time is reported and the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in SpalAX fecal samples.
Journal ArticleDOI
Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis.
Bettina Glasl,Caitlin E. Smith,Caitlin E. Smith,Caitlin E. Smith,David G. Bourne,David G. Bourne,David G. Bourne,Nicole S. Webster,Nicole S. Webster,Nicole S. Webster +9 more
TL;DR: Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment, and recommended meticulous control of host- genotype effects in coral microbiome research.
Journal ArticleDOI
Biological pretreatment with Trametes versicolor to enhance methane production from lignocellulosic biomass: A metagenomic approach
TL;DR: High-cellulolytic white-rot fungi and 16S rRNA gene amplicon sequencing revealed a more diverse microbial community in the fungal-pretreated anaerobic digesters, which affected VFA production, cellulose degradation and eventually methane yield in an affirmative way.
Journal ArticleDOI
Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation
Xiaoxu Sun,Rui Xu,Yiran Dong,Fangbai Li,Wan Tao,Tianle Kong,Miaomiao Zhang,Lang Qiu,Xiaoyu Wang,Weimin Sun +9 more
TL;DR: The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth and indicates that they could also facilitate plant growth since a number of plant growth-promoting genes were encoded.
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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