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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Wild Bee Pollen Usage and Microbial Communities Co-vary Across Landscapes.
TL;DR: Understanding of how flowering plant community composition affects not only the pollen usage of a generalist bee but also its associated microbial communities is further understood.
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No evidence for a placental microbiome in human pregnancies at term
Irene Sterpu,Emma Fransson,Luisa W. Hugerth,Juan Du,Marcela Pereira,Liqin Cheng,Sebastian Alexandru Radu,Lorena Calderón-Pérez,Yinghua Zha,Pia Angelidou,Alexandra A. L. Pennhag,Fredrik Boulund,Annika Scheynius,Lars Engstrand,Eva Wiberg-Itzel,Ina Schuppe-Koistinen,Ina Schuppe-Koistinen +16 more
TL;DR: No evidence to support the existence of a placental microbiome is found in a cross-sectional study comparing samples from two groups of full-term births using PCR amplification and sequencing techniques and bacterial culture experiments.
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Red Wine Consumption Associated With Increased Gut Microbiota α-Diversity in 3 Independent Cohorts
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Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition.
Courtney R. A. Toth,Lisa M. Gieg +1 more
TL;DR: The results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and the roles of community members and candidate phyla in the authors' cultures that may be involved in hydrocarbon transformation to methane in oil systems are proposed.
Journal ArticleDOI
Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity
Aleksei A. Korzhenkov,Stepan V. Toshchakov,Rafael Bargiela,Huw Gibbard,Manuel Ferrer,Alina V. Teplyuk,David L. Jones,David L. Jones,Ilya V. Kublanov,Peter N. Golyshin,Olga V. Golyshina +10 more
TL;DR: This study showed a high abundance of archaea in this extremely acidic mine-impacted environment, and identified a separate clustering of globally occurring acidophilic members of TMEG that collectively belong to a distinct order within Thermoplasmata with yet unclear functional roles in the 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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