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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CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.
Phuc Leo H. Vo,Carlotta Ronda,Sanne E. Klompe,Ethan E. Chen,Christopher Acree,Harris H. Wang,Samuel H. Sternberg +6 more
TL;DR: A substantially improved version of the Tn7-like transposon from Vibrio cholerae is introduced, which uses a Type I-F CRISPR-Cas system for programmable, RNA-guided transposition and establishes INTEGRATE as a versatile tool for multiplexed, kilobase-scale genome engineering.
Journal ArticleDOI
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.
Bing Ma,Pawel Gajer,Sarah E. Brown,Michael S. Humphrys,Johanna B. Holm,L. Elaine Waetjen,Rebecca M. Brotman,Jacques Ravel +7 more
TL;DR: VALENCIA provides a much-needed solution for the robust and reproducible assignment of vaginal community state types and validated the broad applicability of VALENCIA for the classification of vaginal microbial communities by using it to classify three test datasets.
Journal ArticleDOI
Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation.
Jonathan L. Golob,Steven A. Pergam,Steven A. Pergam,Sujatha Srinivasan,Tina L. Fiedler,Congzhou Liu,Kristina Garcia,Marco Mielcarek,Daisy Ko,Sarah Aker,Sara Marquis,Tillie Loeffelholz,Anna Plantinga,Michael C. Wu,Kevin Celustka,Alex Morrison,Maresa C. Woodfield,David N. Fredricks,David N. Fredricks +18 more
TL;DR: Low alpha diversity in stool microbiota at neutrophil recovery associates with increased severe graft-versus-host disease (GVHD), greater abundance of oral Actinobacteria or Firmicutes, and decreased abundance of intestinal Lachnospiraceae in stool bacteria at neutrophic recovery associated with increase severe GVHD.
Journal ArticleDOI
Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.
TL;DR: The literature supports the idea that most oral microbes are site specialists, and a clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.
Journal ArticleDOI
Disentangling the mechanisms shaping the surface ocean microbiota
Ramiro Logares,Ramiro Logares,Ina M. Deutschmann,Pedro C. Junger,Caterina R. Giner,Caterina R. Giner,Anders K. Krabberød,Thomas Schmidt,Laura Rubinat-Ripoll,Mireia Mestre,Mireia Mestre,Mireia Mestre,Guillem Salazar,Guillem Salazar,Clara Ruiz-González,Marta Sebastián,Marta Sebastián,Colomban de Vargas,Silvia G. Acinas,Carlos M. Duarte,Josep M. Gasol,Josep M. Gasol,Ramon Massana +22 more
TL;DR: The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes, suggesting that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration.
References
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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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