February 24, 2015

Human oral microbiome

Review: The Oral Microbiome and Cancer – A. Ross Kerr – Journal of Dental Hygiene

Human esophageal/stomach microbiome

Association between tobacco use and the upper gastrointestinal microbiome among Chinese men – Emily Vogtmann – Cancer Causes & Control

Human gut microbiome

Diversity in gut bacterial community of school-age children in Asia – Jiro Nakayama – Scientific Reports

Characterization of the human gut microbiome during travelers’ diarrhea – Bonnie P. Youmans – Gut Microbes

Review: Interactive roles of gut microbiota and gastrointestinal motility in the
development of inflammatory disorders – Hirofumi Okubo – Macrophage

Review: Microbial endocrinology: the interplay between the microbiota and the endocrine system – Hadar Neuman – Microbiology Reviews

Review: Gut/brain axis and the microbiota – Emeran A. Mayer – The Journal of Clinical Investigation

Animal models of microbiome research

Exercise training modifies gut microbiota in normal and diabetic mice – Jennifer Elizabeth Lambert – Applied Physiology, Nutrition, and Metabolism

Impact of dietary deviation on disease progression and gut microbiome composition in lupus-prone SNF1 mice – Benjamin M. Johnson – Clinical & Experimental Immunology

Host genetic determinants of microbiota-dependent nutrition revealed by genome-wide analysis of Drosophila melanogaster – Adam J. Dobson – Nature Communications

Microbial community structure in the gut of the New Zealand insect Auckland tree weta (Hemideina thoracica) – David W. Waite – Archives of Microbiology

Animal microbiome

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing – Xufeng Han – PLOS ONE

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges – Fan Zhang – PNAS USA

Plant microbiome

Identification of novel Bromus- and Trifolium-associated circular DNA viruses – Simona Kraberger – Archives of Virology

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Review: Microbial Symbionts: A Potential Bio-Boom – Mustafa Morsy – Journal of Investigative Genomics

Water microbiome

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth – Takuro Nunoura – PNAS USA

Resilience and recovery: the effect of triclosan exposure timing during development, on the structure and function of river biofilm communities – J.R. Lawrence – Aquatic Toxicology

Adaption of the microbial community to continuous exposures of multiple residual antibiotics in sediments from a salt-water aquacultural farm – Min Wang – Journal of Hazardous Materials


Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool – Aurélia Caputo – Biology Direct

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage – Nicholas H. Putnam – ArXiv

Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information – Jan Zoll – Journal of Clinical Virology

Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology – Lilian Pukk – Molecular Ecology Resources

AMAS: optimizing the partition and filtration of adaptive seeds to speed up read mapping – Ngoc Hieu Tran, Xin Chen – arXiv

The Genome 10K Project: A Way Forward – Klaus-Peter Koepfli – Annual Reviews of Animal Biosciences

Other papers of interest

Allergy in Children in Hand Versus Machine Dishwashing – Bill Hesselmar – Pediatrics

Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis – Rachel Bleich – PNAS USA

Microbes in the news

Were early seas transformed by sponge microbiome? – Catherine Brahic – New Scientist

Bacteria Thrive in the Ocean Depths of Challenger Deep – NBC News

Scientists discover bacteria in marine sponges harvest phosphorus for the reef community – Phys.org

Infant Gut Microbiome Linked to Allergic Predisposition (interview with Christine Cole Johnson) – Medical Research

Genetic variety in gut critters tied to disease – Max Green – Columbia Chronicle

Exposure to bacteria, good for a strong immune system? – Justin J Reyes – KGNS

After 8 centuries, rats exonerated in spread of Black Death. Gerbils implicated. – Sarah Kaplan – Washington Post

Your Soap Has Bacteria In It, But It Still Gets You Clean – Poncie Rutsch – NPR Shots

Antibiotics cause dangerous bacteria communities to appear, study says – Suzanne Plunkett – Reuters

Antibiotics give rise to new communities of harmful bacteria – Science Daily

Hand-wash your dishes to help protect kids from allergies – Jessica Firger – CBS News

The Problem With Dirty Money – Paul Rodgers – Forbes

Bik’s Picks

Peanut consumption in infancy prevents peanut allergy, study finds – Science Daily

Climate change is really bad news if you like oysters, scallops and clams – Puneet Kollipara – Washington Post

Space is cool, but NASA’s cheeseburgers look gross – Brian Koerber – Mashable


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