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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Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat.
TL;DR: The results suggest that the symbiotic relationships between ground-dwelling beetles and these microbes are widespread, and that the community structure of this family is related to the evolutionary change in beetle ecology.
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Comammox Nitrospira Species Dominate in an Efficient Partial Nitrification–Anammox Bioreactor for Treating Ammonium at Low Loadings
Yung Hsien Shao,Jer Horng Wu +1 more
TL;DR: In this paper, a bench-scale bioreactor with continuous stirring was operated for more than 1000 days with limited oxygen supply to achieve efficient nitrogen removal (70.1 ± 2.7%) at a low ammonium loading of 35.2 mg-N/L/day.
Journal ArticleDOI
Revealing changes in the microbiome of Symbiodiniaceae under thermal stress.
Emma F. Camp,Tim Kahlke,Matthew R. Nitschke,Matthew R. Nitschke,Deepa Varkey,Deepa Varkey,Nerissa L. Fisher,Lisa Fujise,Samantha Goyen,David J. Hughes,Caitlin A. Lawson,Mickael Ros,Stephen Woodcock,Kun Xiao,William Leggat,David J. Suggett +15 more
TL;DR: This study examined the physiological response to heat stress by Symbiodiniaceae isolates with well-described thermal tolerances, and combined these observations with matched changes in bacterial composition and abundance through 16S rRNA metabarcoding to highlight the complexity of Symbiodinaceae-bacteria interactions.
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Relationships among wood‐boring beetles, fungi, and the decomposition of forest biomass
James Skelton,Michelle A. Jusino,Michelle A. Jusino,Paige S. Carlson,Katherine E. Smith,Katherine E. Smith,Mark T. Banik,Daniel L. Lindner,Jonathan M. Palmer,Jiri Hulcr +9 more
TL;DR: The results indicate ambrosia beetles introduce diverse fungal communities that do not extensively decay wood, but instead reduce decay rates by competing with wood decay fungi.
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Characteristics and mechanisms of H2S production in anaerobic digestion of food waste.
TL;DR: In this study, a lab-scale FWAD batch test was applied for 20 days under 35 °C and sulfides were found to be the dominant form of sulfur (accounting for 20-70% of total sulfur) in the mixed fermentation liquor in fermentation batch.
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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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