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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Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat
François-Étienne Sylvain,Aleicia Holland,Sidki Bouslama,Émie Audet-Gilbert,Camille Lavoie,Adalberto Luis Val,Nicolas Derome +6 more
TL;DR: The results suggest that the variable skin mucus community is a relevant target for the development of microbial biomarkers of environmental status, while the more conserved gut microbiome is better suited to study long-term host-microbe interactions over evolutionary time scales.
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Freshwater monitoring by nanopore sequencing
Lara Urban,Andre Holzer,J. Jotautas Baronas,Michael B Hall,Philipp Braeuninger-Weimer,Michael J Scherm,Daniel J Kunz,Daniel J Kunz,Surangi N. Perera,Daniel E. Martin-Herranz,Edward T. Tipper,Susannah J. Salter,Maximilian R Stammnitz +12 more
TL;DR: The MinION as mentioned in this paper is a pocket-sized device that can sequence genetic information on-the-go and can be used to detect bacterial species present in rivers, which has been used to monitor water quality in remote areas.
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Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere
Jeffrey A. Kimbrel,Ty J. Samo,Christopher S. Ward,Daniel Nilson,Michael P. Thelen,Anthony J. Siccardi,Anthony J. Siccardi,Paul V. Zimba,Todd W. Lane,Xavier Mayali +9 more
TL;DR: Algal-associated bacterial communities are controlled by algal host, culture conditions, and the initial inoculum composition of the algal microbiome, and this knowledge can inform the engineering of more productive algal systems.
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Microbial niches in raw ingredients determine microbial community assembly during kimchi fermentation.
Hye Seon Song,Tae Woong Whon,Juseok Kim,Se Hee Lee,Joon Yong Kim,Yeon Bee Kim,Hak Jong Choi,Jin Kyu Rhee,Seong Woon Roh +8 more
TL;DR: The results suggest that the raw ingredient microbial habitat niches selectively affect microbial community assembly patterns and processes during kimchi fermentation.
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Impact of land uses, drought, flood, wildfire, and cascading events on water quality and microbial communities: A review and analysis
TL;DR: In this article, the authors provide a review of the potential impacts of climate-related extreme events (i.e., drought, flood, and wildfires) on different water quality indicators and the potential impact of cascading extreme events on dynamics of water quality behavior.
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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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