November 5, 2015

Context and the human microbiome, review about respiratory tract, gut microbiome in UC patients, arsenic effects on mouse microbiome, and microbiome of a river-to-ocean transition.


3 PhD fellowship in Evolutionary and Ecological Metagenomics – Natural History Museum of Denmark

General microbiome

Review: Context and the human microbiome – Daniel McDonald, Amanda Birmingham and Rob Knight – Microbiome

Pregnancy and birth

Breastfeeding and the risk of dental caries: a systematic review and meta-analysis – R Tham – Acta Paediatrica

Breastfeeding and asthma and allergies: a systematic review and meta-analysis – CJ Lodge – Acta Paediatrica

Human respiratory microbiome

Review: The Microbiome and the Respiratory Tract – Robert P. Dickson – Annual Review of Physiology

Human gut microbiome

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis – David Kevan – Journal of Crohn’s and Colitis

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition – Christopher Quince – American Journal of Gastroenterology

Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung’s associated enterocolitis – Holger Till – Frontiers in Microbiology

eBook chapter: Human GI Tract Microbiota in Health and Disease: A Focus on Inflammatory Bowel Diseases – Clarissa Santos Rocha – Innovative Immunology

Review: Factors determining colorectal cancer: the role of the intestinal microbiota – Esther Nistal – Frontiers in Oncology

Animal models

In cattle: Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function – Shengyong Mao – Scientific Reports

In cattle: Manipulating rumen microbiome and fermentation through interventions during early life: a review – David R. Yáñez-Ruiz – Frontiers in Microbiology


In mice: Administration of defined microbiota is protective in a murine Salmonella infection model – Sarah-Lynn E. Martz – Scientific Reports

In mice: Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism – Rishu Dheer – Toxicology and Applied Pharmacology

Drosophila: Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – BioRxiv

In rats: The microbiota-gut-brain axis as a potential therapeutic approach for HIV-1+ cocaine abuse – Steven B. Harrod – Drug and Alcohol Dependence

In mice: Alteration of the intestinal microbiota by short-time antibiosis protects mice from CNS-specific autoimmunity – C. Gödel – Journal of the Neurological Sciences


Plant, root, and soil microbiome

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of the Total Environment

Caffeine fostering of mycoparasitic fungi against phytopathogens – Akifumi Sugiyama – Plant Signaling & Behavior

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes – Kathryn M. Docherty – PLOS ONE

Fungal association and utilization of phosphate by plants: success, limitations, and future prospects – Atul K. Johri – Frontiers in Microbiology

Thesis: Manipulating the soil microbiome to increase plant health and productivity – Chaparro, Jacqueline Michelle – Colorado State University

Water and extremophile microbiome

Bacterial responses to environmental change on the Tibetan Plateau over the past half century – Yongqin Liu – Environmental Microbiology

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient – Caroline S. Fortunato – PLOS ONE

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea
André Antunes – Genomics, Proteomics & Bioinformatics

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment – Salvador Mirete – Frontiers in Microbiology

Research topic and call for papers: Microbiology of the rapidly changing polar environments – Frontiers in Microbiology

Food microbiology

The diversity and evolution of microbiota in traditional Turkish Divle Cave cheese during ripening – Sebnem Ozturkoglu Budak – International Dairy Journal

More microbes

Ion channels enable electrical communication in bacterial communities – Arthur Prindle – Nature


De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L Westcott, Patrick Schloss – PeerJ Preprint

Unpublished manuscript: Improving De Novo Metatranscriptome Assembly via Machine Learning Algorithms – Hussein Mohsen – not published

Microbes in the news

eBookWelcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You – Rob DeSalle, Susan L. Perkins – eBook

Fighting Cancer With Microbes, Flagship Bets on a $35M Startup– Luke Timmerman – Forbes

Toxin Taints Crabs and Kills Sea Mammals, Scientists Warn – Jonah Bromwich – The New York Times


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