Microbiome digest, November 11, 2014

Human oral microbiome

Physiological Adaptations of Key Oral Bacteria – C. W. Ian Douglas – Advances in Microbial Physiology

Human gut microbiome

Development and Survival of Th17 Cells within the Intestines: The Influence of Microbiome- and Diet-Derived Signals – Joseph H. Chewning – The Journal of Immunology

Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? – Alfredo Focà – Mediators of Inflammation

Animal microbiome

Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change – Karlette A. Fernandes – PLOS ONE

The Effect of Phytochemical Tannins-Containing Diet on Rumen Fermentation Characteristics and Microbial Diversity Dynamics in Goats Using 16S rDNA Amplicon Pyrosequencing – B. R. Min – Agriculture, Food & Analytical Bacteriology

Microbial diversity in forestomach and caecum contents of the greater long-tailed hamster Tscherskia triton (Rodentia: Cricetidae) – Akio Shinohara – Mammalian Biology – Zeitschrift für Säugetierkunde

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection – Andrea J. Jani – PNAS USA

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk – Roberta M. O’Connor – PNAS USA

Arbuscular mycorrhizal fungi communities in a coral cay system (Morrocoy, Venezuela) and their relationships with environmental variables – M.M. Alguacil – Science of the Total Environment

Soil microbiome

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities – Jun-Min Li – Scientific Reports

Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples – Franziska B. Brandt – Systematic and Applied Microbiology

Seasonal influence of climate manipulation on microbial community structure and function in mountain soils – Jérémy Puissant – Soil Biology and Biochemistry

Effect of organic and conventional practices on carbon-substrate utilisation by the soil microbial community in a ‘Cripps Pink’/M7 apple orchard – Andre H Meyer – South African Journal of Plant and Soil

* The Soil Biota Composition along a Progressive Succession of Secondary Vegetation in a Karst Area – Jie Zhao – PLOS ONE

Effects of salinization and crude oil contamination on soil bacterial community structure in the Yellow River Delta region, China – Yong-chao Gao – Applied Soil Ecology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula – Camila N. Signori – Frontiers in Microbiology

Metagenomics

Assessment of quality control approaches for metagenomic data analysis – Qian Zhou – Scientific Reports

PaperClip: rapid multi-part DNA assembly from existing libraries – Maryia Trubitsyna – Nucleic Acids Research

Microbial phylogeny

* Assessing the global phylum level diversity within the bacterial domain: A review – Noha H. Youssef – Journal of Advanced Research

Science, publishing, career

Crosspost: Using Google Scholar in Scholarly Workflows – Jonathan Eisen – microBEnet

Hilarious: Overly honest references: “Should we cite the crappy Gabor paper here?” – RetractionWatch – (Note: paper has been removed – see a screenshot here)

Microbes in the news

* Bacteria Hysteria? Deadly bacteria normally found in toilets was discovered in the microwave of these students – The Journal.ie

Bik’s Picks

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication – Michael J. Montague – PNAS USA

UCSF develops site to make sense out of sugar science – Erin Allday – SFGate

Found: The Ideal Fatness for Elephant Seals – Elizabeth Preston – Discover

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