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 core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis.
TL;DR: The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow, and a novel definition of a dysbiotic quarter at individual cow level was introduced by analyzing the milk microbiota.
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Comparison of the oral microbiome in mouthwash and whole saliva samples
TL;DR: Results show that mouthwash samples perform similarly to saliva samples for analysis of the oral microbiome, and are also a resource suitable for human microbiome research.
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The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.
Emanuel Heitlinger,Emanuel Heitlinger,Susana Carolina Martins Ferreira,Dagmar Thierer,Heribert Hofer,Marion L. East +5 more
TL;DR: It is proposed that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryote in high-ranking than low-ranking animals.
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Effects of prescription antibiotics on soil- and root-associated microbiomes and resistomes in an agricultural context
Francisco Cerqueira,Anastasis Christou,Despo Fatta-Kassinos,Maria Vila-Costa,Josep M. Bayona,Benjamin Piña +5 more
TL;DR: The use of treated wastewater for crop irrigation is rapidly increasing to respond to the ever-growing demands for water and food resources, but this practice may contribute to the spread of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in agricultural settings, constituting a potential risk for human consumers.
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DNA metabarcoding reveals organisms contributing to particulate matter flux to abyssal depths in the North East Pacific ocean
TL;DR: This paper used DNA metabarcoding of 16S and 18S rRNA genes to investigate the community in sinking particulates collected over 9-months (November 2016-July 2017) at Station M, located within the California Current ecosystem.
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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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