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
Citations
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A longitudinal big data approach for precision health
Sophia Miryam Schüssler-Fiorenza Rose,Sophia Miryam Schüssler-Fiorenza Rose,Kévin Contrepois,Kegan J. Moneghetti,Kegan J. Moneghetti,Kegan J. Moneghetti,Wenyu Zhou,Tejaswini Mishra,Samson Mataraso,Orit Dagan-Rosenfeld,Ariel B. Ganz,Jessilyn Dunn,Daniel Hornburg,Shannon Rego,Dalia Perelman,Sara Ahadi,M. Reza Sailani,Yanjiao Zhou,Shana R. Leopold,Jieming Chen,Melanie Ashland,Jeffrey W. Christle,Jeffrey W. Christle,Monika Avina,Patricia Limcaoco,Camilo Ruiz,Marilyn Tan,Atul J. Butte,George M. Weinstock,George M. Slavich,Erica Sodergren,Tracey McLaughlin,Francois Haddad,Francois Haddad,Michael Snyder,Michael Snyder +35 more
TL;DR: The ability of deep longitudinal profiling to make health-related discoveries, identify clinically relevant molecular pathways and affect behavior in a prospective longitudinal cohort enriched for risk of type 2 diabetes mellitus is explored.
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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades
Nicholas D. Youngblut,Georg H. Reischer,William A. Walters,Nathalie Schuster,Chris Walzer,Gabrielle Stalder,Ruth E. Ley,Andreas H. Farnleitner,Andreas H. Farnleitner +8 more
TL;DR: The authors isolate evolutionary and ecological drivers of gut microbiomes from wild mammals, birds, reptiles, amphibians, and fish to provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.
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Host variables confound gut microbiota studies of human disease.
Ivan Vujkovic-Cvijin,Jack Sklar,Jack Sklar,Lingjing Jiang,Loki Natarajan,Rob Knight,Yasmine Belkaid +6 more
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Root exudates drive the soil-borne legacy of aboveground pathogen infection
Jun Yuan,Jun Zhao,Tao Wen,Mengli Zhao,Rong Li,Pim Goossens,Qiwei Huang,Yang Bai,Jorge M. Vivanco,George A. Kowalchuk,Roeland L. Berendsen,Qirong Shen +11 more
TL;DR: The data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.
Journal ArticleDOI
Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women
Benjamin J. Callahan,Daniel B. DiGiulio,Daniel B. DiGiulio,Daniela S. Aliaga Goltsman,Christine L. Sun,Elizabeth K. Costello,Pratheepa Jeganathan,Joseph R. Biggio,Ronald J. Wong,Maurice L. Druzin,Gary M. Shaw,David K. Stevenson,Susan Holmes,David A. Relman,David A. Relman +14 more
TL;DR: It is argued that the vaginal microbiota is better represented by the quantitative frequencies of these key taxa than by classifying communities into five community state types, and that previous conflicting results may reflect the different risk profile of women of black race.
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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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