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Open AccessJournal ArticleDOI

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan, +5 more
- 01 Jul 2016 - 
- Vol. 13, Iss: 7, pp 581-583
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.

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Plasma levels of trimethylamine-N-oxide can be increased with 'healthy' and 'unhealthy' diets and do not correlate with the extent of atherosclerosis but with plaque instability.

Yen Chin Koay, +15 more
- 21 Jan 2021 - 
TL;DR: Dietary-induced changes in the microbiome, of both 'healthy' and 'unhealthy' diets, can cause an increase in the plasma level of trimethylamine-N-oxide, and a mouse model of plaque instability demonstrates an association of TMAO plasma levels with atherosclerotic plaque instability, which confirms TmaO as being a marker of cardiovascular risk.
Journal ArticleDOI

Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment

Margherita Musella, +10 more
- 15 May 2020 - 
TL;DR: The structural variation of the microbiota of Mytilus galloprovincialis at the tissue scale is characterized, also exploring the connection with the microbial ecosystem of the surrounding water, highlighting the putative importance of mussel microbiota for different aspects of host physiology, with ultimate repercussions on mussel health and productivity.
Journal ArticleDOI

Optimization of organics to nutrients (COD:N:P) ratio for aerobic granular sludge treating high-strength organic wastewater

Rania Ahmed Hamza, +4 more
- 10 Feb 2019 - 
TL;DR: The bacterial behavior in consuming the organics was altered under nutrient-deficient conditions, where faster degradation rates were observed as the amounts of nutrients decreased, with higher relative abundance of heterotrophs and diazotrophic bacterial populations.
Journal ArticleDOI

Impact of oral metronidazole treatment on the vaginal microbiota and correlates of treatment failure.

Marijn C. Verwijs, +4 more
- 01 Feb 2020 - 
TL;DR: Metronidazole alone may not cure women with high G. vaginalis relative abundance, potentially due to biofilm presence, and women withhigh pathobionts concentration, and these women may benefit from additional biofilm-disrupting and/or pathOBiont-targeting treatments.
Journal ArticleDOI

Blueberry proanthocyanidins and anthocyanins improve metabolic health through a gut microbiota-dependent mechanism in diet-induced obese mice.

Arianne Morissette, +17 more
- 31 Mar 2020 - 
TL;DR: Results show that blueberry PAC and ANT polyphenols can reduce diet-induced body weight and improve insulin sensitivity, and that at least part of these beneficial effects are explained by modulation of the gut microbiota.
References
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Curtis Huttenhower, +253 more
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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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Trending Questions (2)
The income and spending of senior high school students?

The provided paper is about the DADA2 software package for modeling and correcting Illumina-sequenced amplicon errors. It does not provide any information about the income and spending of senior high school students.

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How can I best normalise my samples from amplicon data?

The paper does not provide information on how to best normalize samples from amplicon data. The paper focuses on the DADA2 software package for modeling and correcting Illumina-sequenced amplicon errors.

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