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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From metabarcoding to metaphylogeography: separating the wheat from the chaff.
TL;DR: Metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.
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NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis.
Wasin Poncheewin,Gerben D. A. Hermes,Jesse C. J. van Dam,Jasper J. Koehorst,Hauke Smidt,Peter J. Schaap +5 more
TL;DR: NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial and archaeal 16S ribosomal RNA (rRNA), eukaryotic 18S rRNA and Ribosomal intergenic transcribed spacer sequences.
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Soil microbial community responses to labile organic carbon fractions in relation to soil type and land use along a climate gradient
Paulina B. Ramírez,Sebastián Fuentes-Alburquenque,Beatriz Díez,Beatriz Díez,Ignacio T. Vargas,Carlos A. Bonilla +5 more
TL;DR: Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYNT FONDECYT 1161045 1150171======CONIGNYT Doctorado National Chile Scholarship, Government of Chile 21140873======
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PCR-based quantification of taxa-specific abundances in microbial communities: Quantifying and avoiding common pitfalls.
TL;DR: In conclusion, amplicon sequencing and qPCR of 16S rRNA genes are valuable tools to determine relative and absolute taxa-specific genome abundances, but results can deviate by several orders of magnitudes from the true values if the reviewed error sources are ignored.
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Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds.
TL;DR: The results suggest that an abundance of facultative anaerobes is a negative prognostic factor in the chronic wound microbiome, possibly due to the increased robustness of such communities to different metabolic environments.
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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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