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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Conserved and variable responses of the gut microbiome to resistant starch type 2.
TL;DR: The conserved responses of the gut microbiome among 13 human and 35 animal RS2 intervention studies are identified and significant variation found for this single dietary compound highlights the challenges in targeting the Gut microbiome to improve health with dietary interventions.
Journal ArticleDOI
Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome.
Janet E. Hill,Arianne Albert +1 more
TL;DR: Gardnerella vaginalis is a hallmark of vaginal dysbiosis, but it is found in the microbiomes of women with and without vaginal symptoms and those who do not have microbiologically defined diseases as mentioned in this paper.
Journal ArticleDOI
Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk.
Howard H.F. Tang,Howard H.F. Tang,Howard H.F. Tang,Anna Lang,Shu Mei Teo,Shu Mei Teo,Louise M. Judd,Ronald E. Gangnon,Michael D. Evans,Kristine E. Lee,Rose F. Vrtis,Patrick G. Holt,Robert F. Lemanske,Daniel J. Jackson,Kathryn E. Holt,Kathryn E. Holt,Michael Inouye,Michael Inouye,Michael Inouye,James E. Gern +19 more
TL;DR: In this article, the developmental trajectories of the nasal microbiome in early life and the composition of the microbiome during illnesses were related to risk of childhood asthma, and they correlated these with presence of asthma at 6, 8, 11, 13, and 18 years of age.
Journal ArticleDOI
Trait-based aerial dispersal of arbuscular mycorrhizal fungi.
TL;DR: Trait-based predictions indicate that nearly 1/3 of described species from diverse genera demonstrate the potential for aerial dispersal and the prevalence of Aerial dispersal in AM fungi is perhaps greater than previously indicated.
Journal ArticleDOI
Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria
Elizabeth N. Bess,Elizabeth N. Bess,Jordan E. Bisanz,Fauna Yarza,Annamarie Bustion,Barry E. Rich,Xingnan Li,Seiya Kitamura,Emily Waligurski,Qi Yan Ang,Diana L. Alba,Peter Spanogiannopoulos,Stephen Nayfach,Suneil K. Koliwad,Dennis W. Wolan,Adrian A. Franke,Peter J. Turnbaugh +16 more
TL;DR: A consortium of four human gut microbiota species, including Eggerthella lenta, can convert plant-derived lignans into bioactive enterolignans via a five-step pathway, providing mechanistic insight into the production of these protective metabolites.
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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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