April 2, 2015

Animal models of microbiome research

Dietary fat intake and age influence gut microbiota and colonic inflammation in C57BL/6J mice – Su Jeong Kim – The FASEB Journal

Maternal obesity alters gut microbial ecology in offspring of NOD mice – Meijun Zhu – The FASEB Journal

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Animal microbiome

Cheetah (not microbiome but could not resist): Dietary Factors Associated with Faecal Consistency and Other Indicators of Gastrointestinal Health in the Captive Cheetah (Acinonyx jubatus) – Katherine M. Whitehouse-Tedd – PLOS ONE

Ants: Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini – Laura E. Williams, Jennifer J. Wernegreen – PeerJ

Sponges: Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea – Valliappan Karuppiah – Applied Microbiology and Biotechnology

Editorial: Sponge symbionts and the marine P cycle – Albert S Colman – PNAS USA

Soil and plant root communities

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert – Klára Řeháková – Frontiers in Microbiology

Soil microbial functional diversity and biomass as affected by different thinning intensities in a Chinese fir plantation – Xin-Li Chen – Applied Soil Ecology

Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients – Ramesh R. Pokharel, Rick Zimmerman – Organic Agriculture

Impact of preferential methane flow through soil on microbial community composition
Julia Gebert, Mirjam Perner – European Journal of Soil Biology

Characterization of bacterial strains and their impact on plant growth promotion and yield of wheat and microbial populations of soil – Ashok Kumar – African Journal of Agricultural


Gut Commensal Immunomodulatory Factors: Identification and Structure-Function Studies – Sungwhan Oh – The FASEB Journal

Review: Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems – Stephen A Jackson – Current Opinion in Biotechnology


Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents – E. Tournier

Other articles of interest

Dengue: Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference – Sam H. Shen – PNAS USA

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes – David Roy Smith and Patrick J. Keeling – PNAS USA


A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments – Nicholas A. Bokulich – PeerJ Preprint

Microbes in the news

I enjoyed reading this: Microbiome Blues in E – Michael Tanner – Clinical Correlations
“You haven’t been squeaky clean since you were bunking with a placenta. “

Drinking water microbiology — from measurement to management – David Coil – MicroBEnet

Movie Night at Bozeman Public Library, April 7th: Bugs with Benefits, an Intro to the Human Microbiome – Bozeman Daily

Do Antibiotics Raise Diabetes Risk via Gut Microbiota? – Liam Davenport – Medscape

About Genome Biology study: Longer DNA fragments reveal rare species diversity – Phys.org

Editorial about mBio study: Soil source for vine bacteria – Nature

Treating the Root Cause of IBS: Small Intestine Bacterial Overgrowth – Maura Henninger – Huffington Post

Origin Sciences Ltd: Newly-Published Data Shows the Effectiveness of OriCol™ for Sampling the Gut Microbiome – BusinessWire

Smart phone diagnosis? Biosensing platform quickly and accurately diagnoses disease and monitors treatment remotely – Science Daily

Science, publishing, and career

Peer review with Elizabeth Marincola (CEO of PLOS) – Royal Society

Fighting Plagiarism In Scientific Papers – Tommaso Dorigo – Science 2.0

Editor’s point of viewScience’s Big Scandal: Even legitimate publishers are faking peer review – Charles Seife – Slate

Stanford Graduate student charged with poisoning labmates’ drinks – Kylie Jue – Stanford Daily

Four simple tools to promote gender balance at conferences – Julie Pfeiffer – The Tree of Life

Bik’s Picks

The human sex ratio from conception to birth – Steven Hecht Orzack – PNAS USA

Failed synchronization of the womb’s clock with mother’s body clock critical in miscarriages – Science Daily

Watch the century’s fastest lunar eclipse Saturday – CBS News


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