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
Ecological succession in the vaginal microbiota during pregnancy and birth.
Morten Arendt Rasmussen,Jonathan Thorsen,Maria Gloria Dominguez-Bello,Martin J. Blaser,Martin S. Mortensen,Asker Daniel Brejnrod,Shiraz A. Shah,Mathis Hjort Hjelmsø,Jenni Lehtimäki,Urvish Trivedi,Hans Bisgaard,Søren J. Sørensen,Jakob Stokholm +12 more
TL;DR: Late gestation is associated with an increase in maternal vaginal microbiota diversity, and vaginal bacteria at birth only modestly predict the composition of the neonatal microbiota.
Journal ArticleDOI
Synergistic Effects of Probiotics and Phytobiotics on the Intestinal Microbiota in Young Broiler Chicken
Hao Ren,Wilfried Vahjen,Temesgen Hailemariam Dadi,Eva-Maria Saliu,Farshad Goodarzi Boroojeni,Jürgen Zentek +5 more
TL;DR: The beneficial synergistic effects of probiotics and phytobiotics on the intestinal bacterial composition and their metabolic activity in young broilers and the reduced survival of potentially problematic bacteria, such as ESBL-producing E. coli, indicates that combinations of probiotic and phyllobiotics may lead to a more enhanced functionality than their individual supplementation.
Journal ArticleDOI
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
Jordan E. Bisanz,Paola Soto-Perez,Cecilia Noecker,Alexander A. Aksenov,Kathy N. Lam,Grace E. Kenney,Elizabeth N. Bess,Henry J. Haiser,Than S. Kyaw,Feiqiao Brian Yu,Vayu Maini Rekdal,Connie W.Y. Ha,Suzanne Devkota,Emily P. Balskus,Pieter C. Dorrestein,Emma Allen-Vercoe,Peter J. Turnbaugh +16 more
TL;DR: A comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease, is reported and a tool for mapping phenotypes to genes and sequence variants is validated, enabling the identification of genes that predict bacterial fitness.
Journal ArticleDOI
Fungal Biodiversity of the Most Common Types of Polish Soil in a Long-Term Microplot Experiment.
Jarosław Grządziel,Anna Gałązka +1 more
TL;DR: The study confirmed previous reports that pH has a decisive influence on soil fungal diversity, but also indicated the strong impact of soil type itself.
Journal ArticleDOI
RNA-based spatial community analysis revealed intra-reactor variation and expanded collection of direct interspecies electron transfer microorganisms in anaerobic digestion.
TL;DR: RNA-based analysis revealed active enrichments in GAC-biofilm, including bacteria Geobacter, Syntrophus, Desulfovibrio and Blvii28, and archaea Methanosaeta and Methanospirillum, which are potential electro-active syntrophic microorganisms related with DIET, which expand the previously defined list of DIET microorganisms.
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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