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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Decoding Wheat Endosphere–Rhizosphere Microbiomes in Rhizoctonia solani–Infested Soils Challenged by Streptomyces Biocontrol Agents
Ricardo Araujo,Ricardo Araujo,Christopher A. Dunlap,Steve Barnett,Steve Barnett,Christopher M. M. Franco +5 more
TL;DR: It may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.
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Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease.
Nicholas S. Rhoades,Tasha Barr,Sara M. Hendrickson,Kamm Prongay,Andrew J. Haertel,Leanne Gill,Laura Garzel,Katrine Whiteson,Mark K. Slifka,Ilhem Messaoudi +9 more
TL;DR: The composition of the microbial community could provide a phenotypic marker of an infant’s susceptibility to diarrheal disease, and these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.
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Making the Most of Trait-Based Approaches for Microbial Ecology.
TL;DR: This work uses case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.
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Diversity of gut microbiomes in marine fishes is shaped by host‐related factors
Qi Huang,Ronia Chung-tin Sham,Yu Deng,Yan Ping Mao,Yan Ping Mao,Chunxiao Wang,Tong Zhang,Kenneth M.Y. Leung,Kenneth M.Y. Leung +8 more
TL;DR: Investigations on the co‐evolution of fish gut microbiomes and their hosts, the physiological functions of gut microorganisms and the development of probiotics for improving the nutrition and health of aquaculture fish species are paved the way.
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Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome.
Florencia A. Tettamanti Boshier,Sujatha Srinivasan,Anthony Lopez,Noah G. Hoffman,Sean Proll,David N. Fredricks,Joshua T. Schiffer,Joshua T. Schiffer +7 more
TL;DR: Inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome when the relative abundance of a species is >10%, and are a reasonable proxy of species-specificqPCR values, particularly when bacteria are present at a higher relative abundance.
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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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