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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Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn
Magdalena J. Mayr,Magdalena J. Mayr,Matthias Zimmermann,Matthias Zimmermann,Jason Dey,Andreas Brand,Andreas Brand,Bernhard Wehrli,Bernhard Wehrli,Helmut Bürgmann +9 more
TL;DR: It is shown that the methanotroph assemblage grows fast enough to limit methane outgassing to the atmosphere during lake overturn when methane from the bottom water is transferred to the surface layer in lake Rotsee.
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Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units
Lisa Joos,Stien Beirinckx,Annelies Haegeman,Jane Debode,Bart Vandecasteele,Steve Baeyen,Sofie Goormachtig,Lieven Clement,Caroline De Tender +8 more
TL;DR: The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity.
Journal ArticleDOI
Multiple impacts of microplastics can threaten marine habitat-forming species
Cinzia Corinaldesi,Sara Canensi,Antonio Dell'Anno,Michael Tangherlini,Iole Di Capua,Stefano Varrella,Trevor J. Willis,Carlo Cerrano,Roberto Danovaro +8 more
TL;DR: The authors investigated the effects of microplastics on the red coral, a long-lived habitat-forming organism belonging to the Corallium genus, which is present at almost all latitudes from shallow-water to deep-sea habitats.
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Insect herbivory reshapes a native leaf microbiome
Parris T. Humphrey,Parris T. Humphrey,Parris T. Humphrey,Noah K. Whiteman,Noah K. Whiteman,Noah K. Whiteman +5 more
TL;DR: It is found that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves impacted by insect herbivory, which predicts tight co-clustering with putative phytopathogens across hosts.
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Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions.
Ty J. Samo,Jeffrey A. Kimbrel,Daniel Nilson,Jennifer Pett-Ridge,Peter K. Weber,Xavier Mayali +5 more
TL;DR: In this article, the effects of phycosphere-associated bacteria for two bio-relevant microalgal species (Phaeodactylum tricornutum and Nannochloropsis salina) were examined using stable isotope tracing and high spatial resolution mass spectrometry imaging (NanoSIMS) to quantify elemental exchanges at the single-cell level.
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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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