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 microbiome pattern reflects healthy ageing and predicts survival in humans
Tomasz Wilmanski,Christian Diener,Noa Rappaport,Sushmita Patwardhan,Jack Wiedrick,Jodi Lapidus,John C. Earls,Anat Zimmer,Gustavo Glusman,Max Robinson,James T. Yurkovich,Deborah M. Kado,Jane A. Cauley,Joseph M. Zmuda,Nancy E Lane,Andrew T. Magis,Jennifer C. Lovejoy,Leroy Hood,Sean M. Gibbons,Sean M. Gibbons,Eric S. Orwoll,Nathan D. Price +21 more
TL;DR: In this paper, the authors leverage three independent cohorts comprising over 9,000 individuals and find that compositional uniqueness is strongly associated with microbially produced amino acid derivatives circulating in the bloodstream.
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Current challenges and best-practice protocols for microbiome analysis.
Richa Bharti,Dominik G. Grimm +1 more
TL;DR: The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization.
Journal ArticleDOI
Lack of detection of a human placenta microbiome in samples from preterm and term deliveries.
Jacob S. Leiby,Kevin McCormick,Scott Sherrill-Mix,Erik L. Clarke,Lyanna R. Kessler,Louis J. Taylor,Casey E. Hofstaedter,Aoife M. Roche,Lisa M. Mattei,Kyle Bittinger,Michal A. Elovitz,Rita Leite,Samuel Parry,Frederic D. Bushman +13 more
TL;DR: The findings do not support the existence of a consistent placental microbiome, in either placenta from term deliveries or spontaneous preterm births.
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Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut.
Emma Guerin,Andrey N. Shkoporov,Stephen R. Stockdale,Stephen R. Stockdale,Adam G. Clooney,Feargal J. Ryan,Thomas D.S. Sutton,Lorraine A. Draper,Enrique González-Tortuero,R. Paul Ross,R. Paul Ross,Colin Hill +11 more
TL;DR: Comparing genomics and taxonomic analysis enabled a classification scheme of crAss-like phages from human fecal microbiomes into four candidate subfamilies composed of ten candidate genera, and mass spectrometry of a crAss -like phage capsid protein could be linked to metagenomic sequencing data, confirming crAss, like phage structural annotations.
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The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems.
Jesse R. Willis,Toni Gabaldón +1 more
TL;DR: This review surveys the main sequencing-based methodologies that are currently used to explore the oral microbiome and highlights major findings enabled by these approaches, and discusses future prospects in the field.
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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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