June 6, 2015

A new paper on the microbiome of the human nose, several gut microbiome reviews,  microbiomes of soils and extreme environments, microbiome models and a cool poster about defining OTU. Happy Saturday!

Human oral microbiome

Antimicrobial Effect of a Single Dose of Amoxicillin on the Oral Microbiota – Cecilia Larsson Wexell – Clinical Implant Dentistry and Related Research

Human respiratory microbiome

Staphylococcus aureus and the ecology of the nasal microbiome – Cindy M. Liu – Science Advances

Human gut microbiome

Review: Interactions between Diet, Bile Acid Metabolism, Gut Microbiota, and Inflammatory Bowel Diseases – Devkota S – Digestive Diseases

Review: Gut Microbiota, Cirrhosis, and Alcohol Regulate Bile Acid Metabolism in the Gut – Ridlon J.M – Digestive Diseases

Review: Relationship between Obesity, Gut Microbiome and Hepatocellular Carcinoma Development – Hara E. – Digestive Diseases

Animal models of microbiome research

Absence of the intestinal microbiota exacerbates hepatobiliary disease in a murine model of primary sclerosing cholangitis – James H. Tabibian – Hepatology

Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice – Yan Y. Lam – Obesity

Animal microbiome

Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production – Letian Xu – Microbial Ecology

Feeding of β-1,3/1,6-glucan increases the diversity of the intestinal microflora of carp (Cyprinus carpio) – V. Jung-Schroers – Aquaculture Nutrition

Changes in coral reef communities across a natural gradient in seawater pH – Hannah C. Barkley – Science Advances

Plant root, soil and sediment microbiome

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential – Alessandra Salvioli – ISME Journal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes – Margarita Lopez-Fernandez – Microbial Ecology

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity – Eric Capo – Microbial Ecology

Water microbiome

Phytoplankton community structure in relation to vertical stratification along a north-south gradient in the Northeast Atlantic Ocean – Kristina D. A. Mojica – Limnology and Oceanography

Extremophile microbiome

Supratidal Extremophiles—Cyanobacterial Diversity in the Rock Pools of the Croatian Adria – Maria Brandes – Microbial Ecology

Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment – Elena González-Toril – Microbial Ecology

Metagenomics and bioinformatics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities – Markus Majaneva

Microbiome models, on computers and in lab dishes, see progress – Jop de Vrieze – Nature Medicine

Don’t miss this cool poster: OTU robustness, reproducibility and ecological consistency in the demarcation of operational taxonomic units – Thomas SB Schmidt

Microbes in the news

Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities – Genome Web

The fastest-growing biome on Earth is in our homes. Forget your kids and pets. Your house’s biodiversity hotspots shelter tons of microorganisms – Mary Jo DiLonardo

Socialising Baboons and Gut Microbes – deSciphered: summarising research with simple graphics

Exploring the Link Between Gut Microbes and Diabetes – Betul Hatipoglu

Kaiser Permanente Fresno uses ‘zapper’ to get rid of deadly bacteria – ABC30

This Man Believes Mushrooms Can Solve Virtually All of Humanity’s Problems: next probiotic? – Munchies

Bik’s Picks

Eating placenta ‘does not benefit health’: There is no scientific evidence that eating the placenta after childbirth can protect women against depression and boost energy, US research suggests –  – BBC News

Ancient Shark Fossil Found in Texas – Deborah Grace – Pioneer News

VideoRobots Falling Down at DARPA Robotics Challenge – IEEE Spectrum – Youtube

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