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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Journal ArticleDOI
A Bioinformatics Guide to Plant Microbiome Analysis
Rares C. Lucaciu,Claus Pelikan,Samuel M. Gerner,Christos Zioutis,Stephan Köstlbacher,Harald Marx,Craig W. Herbold,Hannes Schmidt,Thomas Rattei +8 more
TL;DR: This work discusses sequencing and “omics” techniques with a focus on the requirements needed to adapt these methods to individual research approaches and highlights data integration and complementarity which should help to widen the understanding of the interactions among individual players of the plant holobiont in the future.
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Best practices in metabarcoding of fungi: From experimental design to results
Leho Tedersoo,Mohammad Bahram,Lucie Zinger,R. Henrik Nilsson,Peter G. E. Kennedy,Teng Yang,Sten Anslan,Vladimir S. Mikryukov +7 more
TL;DR: It is demonstrated that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity and specific methods for compositional data analyses provide more reliable estimates of shifts in community structure.
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A Pilot-Scale Field Study: In Situ Treatment of PCB-Impacted Sediments with Bioamended Activated Carbon.
TL;DR: In situ treatment of PCBs using an AC agglomerate as a delivery system for bioamendments is particularly well-suited for environmentally sensitive sites where there is a need to reduce exposure of the aquatic food web to sediment-bound PCBs with minimal disruption to the environment.
Journal ArticleDOI
CFTR dysregulation drives active selection of the gut microbiome
Stacey M Meeker,Kevin S Mears,Naseer Sangwan,Mitchell J. Brittnacher,Eli J. Weiss,Piper M. Treuting,Nicholas Tolley,Christopher E. Pope,Kyle R. Hager,Anh T. Vo,Jisun Paik,Charles W. Frevert,Hillary S. Hayden,Lucas R. Hoffman,Samuel I. Miller,Adeline M. Hajjar,Adeline M. Hajjar +16 more
TL;DR: It is demonstrated that CFTR mutations modulate both the host adaptive immune response and the intestinal microbiome, and these mutations alter adaptive immune responses in patients with cystic fibrosis.
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Biological As(III) oxidation in biofilters by using native groundwater microorganisms.
Simona Crognale,Barbara Casentini,Stefano Amalfitano,Stefano Fazi,Maurizio Petruccioli,Simona Rossetti +5 more
TL;DR: The contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system, is highlighted and several OTUs affiliated with families known to oxidize As( III) are revealed.
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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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