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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Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations.
Stefan Lambert,Margot Tragin,Jean-Claude Lozano,Jean-François Ghiglione,Daniel Vaulot,François-Yves Bouget,Pierre E. Galand +6 more
TL;DR: The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.
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Reductionist synthetic community approaches in root microbiome research.
Yong-Xin Liu,Yuan Qin,Yang Bai +2 more
TL;DR: The emergence, current achievements, and future opportunities for using SynCom experiments in plant microbiome research, with a focus on plant root-associated bacteria are summarized.
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Population-level inferences from environmental DNA—Current status and future perspectives
Eva Egelyng Sigsgaard,Mads Reinholdt Jensen,Inger Eleanor Winkelmann,Peter Rask Møller,Michael Møller Hansen,Philip Francis Thomsen +5 more
TL;DR: An overview of the achievements of eDNA‐based population genetics to date, and the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information are outlined.
Journal ArticleDOI
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Kelly D. Goodwin,Luke R. Thompson,Luke R. Thompson,Bernardo Duarte,Tim Kahlke,Andrew R. Thompson,João Carlos Marques,Isabel Caçador +7 more
TL;DR: DNA sequencing of bioindicators promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.
Journal ArticleDOI
Community dynamics of free-living and particle-attached bacteria following a reservoir Microcystis bloom
TL;DR: The analyses showed that PA bacterial communities were generally more diverse and appeared to be more responsive to routinely measured environmental variables than FL bacteria, suggesting that Microcystis blooms had a facilitative influence on specific bacteria by mediating the transitions from free-living to particle-attached lifestyles.
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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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