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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High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing.
Søren Michael Karst,Ryan M. Ziels,Rasmus Hansen Kirkegaard,Emil A. Sørensen,Daniel McDonald,Qiyun Zhu,Rob Knight,Mads Albertsen +7 more
TL;DR: In this article, a high-throughput amplicon sequencing approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing, yielding high-accuracy single-molecule consensus sequences of large genomic regions.
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Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities.
Tim N. Enke,Tim N. Enke,Manoshi S. Datta,Julia A. Schwartzman,Nathan Cermak,Désirée Schmitz,Julien Barrere,Alberto Pascual-García,Otto X. Cordero +8 more
TL;DR: The results suggest that the assembly of heterotrophic communities that degrade complex organic materials follows simple design principles that could be exploited to engineerheterotrophic microbiomes.
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Sex-specific effects of microbiome perturbations on cerebral Aβ amyloidosis and microglia phenotypes
Hemraj B. Dodiya,Thomas Kuntz,Shabana M. Shaik,Caroline Baufeld,Jeffrey A. Leibowitz,Xulun Zhang,Neil Gottel,Xiaoqiong Zhang,Oleg Butovsky,Jack A. Gilbert,Sangram S. Sisodia +10 more
TL;DR: The microbiome plays a causal role in modulating Aβ burden and microglia phenotypes and an antibiotic cocktail leads to reductions in brain amyloidosis, altered morphology, and gene expression inmicroglia of male but not female transgenic mice that exhibit Aβ deposits.
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Fungal diversity regulates plant-soil feedbacks in temperate grassland
Marina Semchenko,Jonathan W. Leff,Jonathan W. Leff,Yudi M. Lozano,Sirgi Saar,Sirgi Saar,John Davison,Anna V. Wilkinson,Benjamin G. Jackson,William J. Pritchard,Jonathan R. De Long,Simon Oakley,Kelly E. Mason,Nick Ostle,Elizabeth M. Baggs,David W. Johnson,Noah Fierer,Noah Fierer,Richard D. Bardgett +18 more
TL;DR: This study shows that plant species with resource-acquisitive traits, such as high shoot nitrogen concentrations and thin roots, attract diverse communities of putative fungal pathogens and specialist saprotrophs, and a lower diversity of mycorrhizal fungi, resulting in strong plant growth suppression on soil occupied by the same species.
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Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis.
Zhenhua Wu,Shimeng Huang,Tiantian Li,Na Li,Dandan Han,Bing Zhang,Zhenjiang Zech Xu,Shiyi Zhang,Jiaman Pang,Shilan Wang,Guolong Zhang,Jiangchao Zhao,Junjun Wang +12 more
TL;DR: In this article, the effect of EGCG delivery on the DSS-induced murine colitis was explored and it was shown that anti-inflammatory effect and colonic barrier integrity were enhanced by oral, but not rectal, EGCGs.
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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