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:Â
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
Citations
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Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Stefan Janssen,Daniel McDonald,Antonio Gonzalez,Jose A. Navas-Molina,Lingjing Jiang,Zhenjiang Zech Xu,Kevin Winker,Deborah M. Kado,Eric S. Orwoll,Mark J. Manary,Siavash Mirarab,Rob Knight +11 more
TL;DR: The SATé-enabled phylogenetic placement (SEPP) technique explicitly against 16S V4 sequence fragments is benchmarked and it is shown that it outperforms the conceptually problematic but often-used practice of reconstructing de novo phylogenies.
Journal ArticleDOI
Disease Suppressive Soils: New Insights from the Soil Microbiome.
TL;DR: A number of hypotheses about the nature and ecology of microbial populations and communities of suppressive soils are proposed and the potential and limitations of new molecular techniques that can provide novel ways of testing these hypotheses are outlined.
Journal ArticleDOI
Gut-microbiota-targeted diets modulate human immune status.
Hannah C Wastyk,Gabriela K. Fragiadakis,Dalia Perelman,Dylan Dahan,Bryan D. Merrill,Feiqiao Brian Yu,Madeline Topf,Carlos Gonzalez,Will Van Treuren,Shuo Han,Jennifer L. Robinson,Joshua E. Elias,Erica D. Sonnenburg,Christopher D. Gardner,Justin L. Sonnenburg +14 more
TL;DR: In this paper, a 17-week randomized, prospective study (n = 18/arm) combined with -omics measurements of microbiome and host, including extensive immune profiling, was conducted to determine how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults.
Journal ArticleDOI
New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract.
Isabel F. Escapa,Isabel F. Escapa,Tsute Chen,Tsute Chen,Yanmei Huang,Yanmei Huang,Prasad Gajare,Floyd E. Dewhirst,Floyd E. Dewhirst,Katherine P. Lemon,Katherine P. Lemon +10 more
TL;DR: The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostrils microbiome, highlighting the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function.
Journal ArticleDOI
Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism
Alexander Duscha,Barbara Gisevius,Sarah Hirschberg,Nissan Yissachar,Gabriele I. Stangl,Eva Eilers,Eva Eilers,Verian Bader,Stefanie Haase,Johannes Kaisler,Christina David,Ruth Schneider,Riccardo Troisi,Daniel Zent,Tobias Hegelmaier,Nikolaos Dokalis,Sara Gerstein,Sara Del Mare-Roumani,Sivan Amidror,Ori Staszewski,Gereon Poschmann,Kai Stühler,Frank Hirche,András Balogh,Stefan Kempa,Pascal Träger,Mario M. Zaiss,Jacob Bak Holm,Megan G. Massa,Henrik Nielsen,Andreas Faissner,Carsten Lukas,Sören Gatermann,Markus Scholz,Horst Przuntek,Marco Prinz,Sofia K. Forslund,Konstanze F. Winklhofer,Dominik N. Müller,Ralf A. Linker,Ralf Gold,Aiden Haghikia +41 more
TL;DR: It is suggested that PA can serve as a potent immunomodulatory supplement to MS drugs and as an add-on to MS immunotherapy.
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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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