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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Microbial community dynamics in anaerobic digesters treating conventional and vacuum toilet flushed blackwater.
TL;DR: It is demonstrated that different blackwater types enriched different microbial consortia, probably due to ammonia concentrations and sulfate loadings, which should be taken into consideration for practical applications.
Journal ArticleDOI
Very-Low-Calorie Ketogenic Diets With Whey, Vegetable, or Animal Protein in Patients With Obesity: A Randomized Pilot Study.
Sabrina Basciani,Elisabetta Camajani,Savina Contini,Agnese Persichetti,Renata Risi,Loris Bertoldi,Lidia Strigari,Giancarlo Prossomariti,Mikiko Watanabe,Stefania Mariani,Carla Lubrano,Alfredo Genco,Giovanni Spera,Lucio Gnessi +13 more
TL;DR: VLCKDs based on whey or vegetable protein have a safer profile and result in a healthier microbiota composition than those containing animal proteins, and are more effective in maintaining muscle performance.
Journal ArticleDOI
Naught all zeros in sequence count data are the same.
TL;DR: In this article, a conceptual framework outlining four types of processes that may give rise to zero values in sequence count data was developed and compared with different zero-handling models to identify the most differentially expressed sequences.
Journal ArticleDOI
Strain-level epidemiology of microbial communities and the human microbiome.
Yan Yan,Yan Yan,Long H. Nguyen,Eric A. Franzosa,Eric A. Franzosa,Curtis Huttenhower,Curtis Huttenhower +6 more
TL;DR: The distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs are summarized.
Journal ArticleDOI
Soil microbiomes associated with Verticillium wilt-suppressive broccoli and chitin amendments are enriched with potential biocontrol agents.
Patrik Inderbitzin,Judson A Ward,Alexandra Barbella,Natalie Solares,Dmitriy Izyumin,Prabir Burman,Dan O. Chellemi,Krishna V. Subbarao +7 more
TL;DR: This study demonstrates that substrate-mediated shifts in soil prokaryote communities are associated with the transition of Verticillium wilt-conducive soils to Verticills wilts-suppressive soils, and suggests that soils likely harbor numerous additional antagonists of fungal plant pathogens that contribute to the biological suppression of plant disease.
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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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