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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Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass
TL;DR: A new class of microbiome sequence processing tools, called amplicon sequence variant (ASV) methods, outperformed conventional methods and may allow more-robust computational identification of contaminants in samples representing low-biomass communities.
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PHAGE Study: Effects of Supplemental Bacteriophage Intake on Inflammation and Gut Microbiota in Healthy Adults.
Hallie P. Febvre,Sangeeta Rao,Melinda Gindin,Natalie D. M. Goodwin,Elijah Finer,Jorge S. Vivanco,Shen Lu,Daniel K. Manter,Taylor C. Wallace,Tiffany L. Weir +9 more
TL;DR: Together, these data demonstrate the potential of bacteriophages to selectively reduce target organisms without global disruption of the gut community.
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Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut
TL;DR: It is shown that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain, and phage-driven HGT is a key eco-evolutionary driving force of gut colonization—it accelerates evolution and promotes genetic diversity of commensal bacteria.
Journal ArticleDOI
Links between environment, diet, and the hunter-gatherer microbiome.
Gabriela K. Fragiadakis,Samuel A. Smits,Erica D. Sonnenburg,Will Van Treuren,Gregor Reid,Rob Knight,Alphaxard Manjurano,John Changalucha,Maria Gloria Dominguez-Bello,Jeff Leach,Justin L. Sonnenburg +10 more
TL;DR: Additional observations from the Hadza microbiota and their lifestyle and environment are presented, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the short-term effects of introducing agricultural products into the diet.
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The gut microbiome of nonhuman primates: Lessons in ecology and evolution.
Jonathan B. Clayton,Andres Gomez,Katherine R. Amato,Dan Knights,Dominic A. Travis,Ran Blekhman,Rob Knight,Steven R. Leigh,Steven R. Leigh,Rebecca M. Stumpf,Tiffany M. Wolf,Kenneth E. Glander,Francis Cabana,Timothy J. Johnson +13 more
TL;DR: It is highlighted how studying the gut microbiome of NHPs offers new insights into primate nutrition, physiology, and immune system function, as well as enhances the understanding of primate ecology and evolution.
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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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