Another unexpected international trip because of sad family circumstances, so blogging from SJC. Bifidobacteria in babies and adults, the human nasal passage, dysbiosis in PSC, giant pandas, and Fairy Circles.And celebrating Microbiome Digest’s 2nd birthday!

Pregnancy and birth

A comparative study of bifidobacteria in human babies and adults – Azra Pachenari  – Bioscience of Microbiota, Food and Health

Human respiratory microbiome

Exploring the bacterial assemblages along the human nasal passage – Melissa L. Wos-Oxley – Environmental Microbiology

Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients – Robert Krause – PLOS ONE

Human gut microbiome

Fermented milk containing Lactobacillus casei strain Shirota preserves the diversity of the gut microbiota and relieves abdominal dysfunction in healthy medical students exposed to academic stress – Akito Kato-Kataoka – Applied and Environmental Microbiology

Bile Acids and Dysbiosis in Non-Alcoholic Fatty Liver Disease – Marialena Mouzaki – PLOS ONE

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD – João Sabino – Gut

Review: Paneth cell α-defensins and enteric microbiota in health and disease
Kiminori Nakamura – Bioscience of Microbiota, Food and Health

Animal experiments

Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves – Sarah J. Meale – Frontiers in Microbiology

Gender-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions – Bei Gao – Environmental Health Perspectives

Animal microbiome

Dietary Shifts May Trigger Dysbiosis and Mucous Stools in Giant Pandas (Ailuropoda melanoleuca) – Candace L. Williams – Frontiers in Microbiology

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome – A. R. Mohamed – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

Unique microbial phylotypes in Namib Desert dune and gravel plain Fairy Circle soils – Andries J. Van der Walt – Applied and Environmental Microbiology

Effects Due to Rhizospheric Soil Application of an Antagonistic Bacterial Endophyte on Native Bacterial Community and Its Survival in Soil: A Case Study with Pseudomonas aeruginosa from Banana – Pious Thomas – Frontiers in Microbiology

Commentary: Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America – Anna Maria Pirttilä – Frontiers in Microbiology

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System – Collin M. Timm – Frontiers in Plant Science

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning – Kai Xue – Frontiers in Microbiology

Water microbiome

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria – Vincent J. Denef – Frontiers in Microbiology

Waste and pollution microbiology

Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators? – Simon Poirier – Water Research

Food microbiology

Review: The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir – Benjamin C. T. Bourrie – Frontiers in Microbiology

Bioinformatics

RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics – Frédéric Jauffrit – Molecular Biology and Evolution

Microbes in the news

The Microbiomes of Indigenous Peoples Are Different–Does It Matter? – By Kevin Bonham – Scientific American

The laser that can spot dangerous bacteria in food – Scientists in South Korea develop early warning system that could be used in homes, restaurants and grocery shops – Shane Hickey – The Guardian

The viral and bacterial links to the brain’s decline – Ed Cara – Newsweek

Antimicrobial resistance in soil: Potential impact on the food chain: New research at the University of Southampton is to investigate if large amounts of antibiotic resistant bacteria are present in agricultural soil which may spread into the food chain. – Science Daily

New study suggests digging in the dirt could reduce stress, inflammation – Mycobacterium vaccae is a common bacterium present in soil – CBC News Manitoba