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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Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease.
TL;DR: It is demonstrated for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
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Gut microbiota structure differs between honeybees in winter and summer
TL;DR: Overall, this study reveals that the gut microbiota of winter bees is remarkably different from foragers and nurses, and shows that diet is a major contributor to the observed differences in bacterial loads.
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Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.
TL;DR: It is found that for broadscale α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results, and while there are good reasons to employ ESVs, the authors need not question the validity of results based on OTUs.
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Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments.
Lisa Karstens,Mark Asquith,Sean Davin,Damien A. Fair,W. Thomas Gregory,Alan J. Wolfe,Jonathan Braun,Shannon K. McWeeney +7 more
TL;DR: A mock microbial community dilution series is introduced as a positive control and four computational strategies that can identify contaminants in 16S rRNA gene sequencing experiments in order to remove them from downstream analyses are evaluated.
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Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.
TL;DR: Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling approach that enables the identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques.
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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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