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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A practical guide to DNA metabarcoding for entomological ecologists
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Stoichiometric controls of soil carbon and nitrogen cycling after long-term nitrogen and phosphorus addition in a mesic grassland in South Africa
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TL;DR: In this article, the authors investigated how long-term N and phosphorus (P) additions affect microbial community composition, and to what extent microbial homeostasis explains changes in different processes involved in soil C and N cycling in response to nutrient addition.
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A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome
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TL;DR: The authors determine the effects of fiber-deprived diet on the spatial structure of the murine colon microbiome, finding that the absence of dietary fiber and polysaccharides leads to local changes along the colon and deterioration of the mucus layer.
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The gut microbiota prime systemic antiviral immunity via the cGAS-STING-IFN-I axis.
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TL;DR: In this paper , the authors investigated how gut commensals modulate systemic immunity and response to viral infection and found that the microbiota-driven tonic IFN-I-response was dependent on cGAS-STING but not on TLR signaling or direct host-bacteria interactions.
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Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession
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TL;DR: It is proposed that the boundaries between successional stages (3–4 and 14–21 days after hatching) may be optimal times for microbiome interventions and the patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut.
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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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