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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A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow
Diana M. Proctor,Diana M. Proctor,Diana M. Proctor,Julia Fukuyama,Peter M. Loomer,Peter M. Loomer,Gary C. Armitage,Stacey Lee,Nicole M Davis,Mark I. Ryder,Susan Holmes,David A. Relman,David A. Relman +12 more
TL;DR: It is shown that regardless of tissue type, surface-associated bacterial communities vary along an ecological gradient from the front to the back of the mouth, and that on exposed tooth surfaces, the gradient is pronounced on lingual compared to buccal surfaces.
Journal ArticleDOI
Homogeneous selection dominates the microbial community assembly in the sediment of the Three Gorges Reservoir
TL;DR: The co-occurrence network showed that keystone species were more important than prevalent abundant species in interspecies interactions, and homogeneous selection plays a leading role in the assembly of the microbial communities.
Journal ArticleDOI
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity.
Robert C. Kaplan,Robert C. Kaplan,Zheng Wang,Mykhaylo Usyk,Daniela Sotres-Alvarez,Martha L. Daviglus,Neil Schneiderman,Gregory A. Talavera,Marc D. Gellman,Bharat Thyagarajan,Jee-Young Moon,Yoshiki Vázquez-Baeza,Daniel McDonald,Jessica Williams-Nguyen,Michael C. Wu,Kari E. North,Justin P. Shaffer,Christopher C. Sollecito,Qibin Qi,Carmen R. Isasi,Tao Wang,Rob Knight,Robert D. Burk +22 more
TL;DR: The analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.
Journal ArticleDOI
Environmental temperature alters the digestive performance and gut microbiota of a terrestrial amphibian.
TL;DR: The relationship between environmental temperature and digestive performance in red-backed salamanders may be mediated by temperature-induced changes in the abundance of chitin-digesting gut microbiota, suggesting that gut microbiota may mediate the relationship between temperature and digestion in ectotherms.
Journal ArticleDOI
Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults.
Jonathan N.V. Martinson,Nicholas V. Pinkham,Garrett W. Peters,Hanbyul Cho,Jeremy Heng,Mychiel Rauch,Susan C. Broadaway,Seth T. Walk +7 more
TL;DR: There is evidence that there is little “stability” within resident clonal populations of the common gut microbiome bacterial family, Enterobacteriaceae, and the results question the biological relevance of apparent stability at higher taxonomic levels.
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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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