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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Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats
Eva Egelyng Sigsgaard,Felipe Torquato,Tobias Guldberg Frøslev,Alec B. M. Moore,Johan Molgard Sorensen,Pedro Range,Radhouane Ben-Hamadou,Steffen S. Bach,Peter Rask Møller,Philip Francis Thomsen +9 more
TL;DR: The results confirm that seawater samples contain habitat‐characteristic molecular signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and regional conservation and management.
Journal ArticleDOI
Enteral Nutrition in Pediatric Patients Undergoing Hematopoietic SCT Promotes the Recovery of Gut Microbiome Homeostasis.
Federica D’Amico,Elena Biagi,Simone Rampelli,Jessica Fiori,Daniele Zama,Matteo Soverini,Monica Barone,Davide Leardini,Edoardo Muratore,Arcangelo Prete,Roberto Gotti,Andrea Pession,Riccardo Masetti,Patrizia Brigidi,Silvia Turroni,Marco Candela +15 more
TL;DR: The prompt recovery of a structural and functional eubiotic GM layout post-HSCT only in EN subjects is observed, thus possibly reducing the risk of systemic infections and GvHD onset.
Journal ArticleDOI
Vancomycin relieves mycophenolate mofetil-induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity.
Michael R. Taylor,Michael R. Taylor,Michael R. Taylor,Kyle L. Flannigan,Hannah Rahim,Hannah Rahim,Hannah Rahim,Amina Mohamud,Amina Mohamud,Amina Mohamud,Ian A. Lewis,Simon A. Hirota,Steven C. Greenway +12 more
TL;DR: It is found that consumption of MMF alters the composition of the gut microbiota, selecting for bacteria expressing the enzyme β-glucuronidase (GUS) and leading to an up-regulation of GUS activity in the gut of mice and symptomatic humans.
Journal ArticleDOI
Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome
TL;DR: The current sequencing and bioinformatic methods for producing taxonomic and functional profiles, recent studies utilizing and comparing these technologies, and the existing challenges and limitations of these data are discussed.
Journal ArticleDOI
Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia.
TL;DR: It is concluded that distinct bacterial metacommunities inhabited the nasopharynx and trachea of healthy feedlot cattle and those with BP, which may have provided colonization resistance against bacterial respiratory pathogens.
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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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