February 4, 2015

Animal models of microbiome research

Age-related immune clearance of hepatitis B virus infection requires the establishment of gut microbiota – Han-Hsuan Chou – PNAS

Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model – Sheng-Yong Mao – Environmental Microbiology

Animal microbiome

Effects of the Diet on the Microbiota of the Red Palm Weevil (Coleoptera: Dryophthoridae) – Matteo Montagna – PLOS ONE

Plant microbiome

Editorial: Evolving insights to understanding mycorrhizas – Ian A. Dickie – New Phytologist

Soil and sediment microbiome

Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea – Felix F. Raulf – Environmental Microbiology

Cyanobacteria drive community composition and functionality in rock–soil interface communities – Angel Valverde – Molecular Ecology

Water microbiome

Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary – Erin M. Eggleston – Environmental Microbiology

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity – Matthieu Leray and Nancy Knowlton – PNAS USA


Phylogenomics with paralogs – Marc Hellmuth – PNAS USA

16S Classifier: A Tool for Fast and Accurate Taxonomic Classification of 16S rRNA Hypervariable Regions in Metagenomic Datasets – Nikhil Chaudhary – PLOS ONE

DNA extraction and sequencing techniques

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform – Lucas Sinclair – PLOS ONE

Comparison of Eleven Methods for Genomic DNA Extraction Suitable for Large-Scale Whole-Genome Genotyping and Long-Term DNA Banking Using Blood Samples – Androniki Psifidi – PLOS ONE


Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD – Vicky De Preter – Gut


Review: The effects of consuming probiotic-fermented milk on the immune system: A review of scientific evidence – Lourdes Santiago-López – International Journal of Dairy Technology

Microbes in the News

Aquarium Microbiome Project – Shedd Aquarium

Video: Aquarium Microbiome Project – YouTube

A plea to stop ignoring microbial ecosystem effects of antimicrobial agents – Jonathan Eisen – MicroBEnet

Why you should embrace bacteria – Jody Berger – Deseret News

Infant Microbiota Influenced By Mother’s Birth Delivery, Gestation Period – Chris Weller – Medical Daily

Birth method, gestation duration may alter infants’ gut microbiota and influence later health – ASM

A warm (surprise!) welcome to the microbiome community – Alexandra Carmichael – uBiome

A Bacteria That Hasn’t Had To Evolve In More Than Two Billion Years – George Dvorsky – io9.com

Bik’s Picks

Cigarette Butt Decomposition and Associated Chemical Changes Assessed by 13C CPMAS NMR – Giuliano Bonanomi – PLOS ONE

What’s Up With That: Why Do Cats Love Boxes So Much? – Bryan Gardiner – Wired.com

Satire: Genome Study Finds Gene For Believing Genome Studies – The Allium


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