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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Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Jethro S. Johnson,Daniel Spakowicz,Bo-Young Hong,Lauren M. Petersen,Patrick Demkowicz,Lei Chen,Shana R. Leopold,Blake M. Hanson,Hanako O. Agresta,Mark Gerstein,Erica Sodergren,George M. Weinstock +11 more
TL;DR: The authors explore the potential of the 16S gene for discriminating bacterial taxa and show that full-length sequencing combined with appropriate clustering of intragenomic sequence variation can provide accurate representation of bacterial species in microbiome datasets.
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Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
TL;DR: This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data, a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces.
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The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?
Fabien Magne,Martin Gotteland,Lea Gauthier,Alejandra Zazueta,Susana A. Pesoa,Paola Navarrete,Ramadass Balamurugan +6 more
TL;DR: It is currently difficult to associate the Firmicutes/Bacteroidetes ratio with a determined health status and more specifically to consider it as a hallmark of obesity.
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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application
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Emergent simplicity in microbial community assembly.
Joshua E. Goldford,Joshua E. Goldford,Nanxi Lu,Djordje Bajić,Sylvie Estrela,Mikhail Tikhonov,Mikhail Tikhonov,Alicia Sánchez-Gorostiaga,Daniel Segrè,Pankaj Mehta,Alvaro Sanchez,Alvaro Sanchez +11 more
TL;DR: Monitoring the assembly of hundreds of soil- and plant-derived microbiomes in well-controlled minimal synthetic media shows that the community-level function and the coarse-grained taxonomy of the resulting communities are highly predictable and governed by nutrient availability, despite substantial species variability.
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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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