July 6, 2015

Oral microbiomes of dogs and their owners, airway mycobiome in CF patients, memory B cells and antibodies to gut microbiota, and yogurt containing seawater (?).

Human oral microbiome

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing – Changin Oh – PLOS ONE

Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw – Shirin Kalyan – Journal of Translational Medicine

Review: Oral malodorous gases and oral microbiota: From halitosis to carcinogenesis – Naoko Tanda – Journal of Oral Biosciences

Human respiratory microbiome

A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements – Rolf Kramer – Journal of Clinical Microbiology

Review: The role of the local microbial ecosystem in respiratory health and disease – Wouter A. A. de Steenhuijsen Piters – Philosophical Transactions B

Review: The mechanism or mechanisms driving atopic asthma initiation: The infant respiratory microbiome moves to center stage – Patrick G. Holt – Journal of Allergy and Clinical Immunology

Human gut microbiome

Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota – Cornelia Lindner – Nature Immunology

Dietary modulation of the gut microbiota – a randomised controlled trial in obese postmenopausal women – Lena K. Brahe – British Journal of Nutrition

Anti-TNF treatment with adalimumab induces changes in the microbiota of Crohn’s disease – Busquets David – Journal of Crohn’s and Colitis

Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract – Mina Bashir – European Journal of Nutrition

Review: Suppression of inflammation by helminths: a role for the gut microbiota? – Paul Giacomin – Philosophical Transactions B

Review: Immune-microbiota interactions in health and disease – Noah W. Palm – Clinical Immunology

Animal models

Lentinula edodes-derived polysaccharide rejuvenates mice in terms of immune responses and gut microbiota – Xiaofei Xu – Food and Function

Effect of Lactobacillus plantarum FH185 on the Reduction of Adipocyte Size and Gut Microbial Changes in Mice with Diet-induced Obesity – Sun-Young Park – Korean Journal for Food Science of Animal Resources

In vitro probiotic characteristics of Lactobacillus plantarum ZDY 2013 and its modulatory effect on gut microbiota of mice – Renhui Huang – Journal of Dairy Science

Reduced airway microbiota diversity is associated with elevated allergic respiratory inflammation – Wenkai Yu – Annals of Allergy, Asthma & Immunology

The prebiotics 3’Sialyllactose and 6’Sialyllactose diminish stressor-induced anxiety-like behavior and colonic microbiota alterations: evidence for effects on the gut-brain axis – Andrew J. Tarr – Brain, Behavior, and Immunity

Effect of yogurt containing deep sea water on health-related serum parameters and intestinal microbiota in mice – Sun Moon Kang – Journal of Dairy Science

Animal microbiome

In situ identification and quantification of starch-hydrolyzing bacteria attached to barley and corn grain in the rumen of cows fed barley-based diets – Yun Xia – FEMS Microbiology Ecology

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing – Lim S. – Journal of Molecular Microbiology and Biotechnology

Wolbachia influences the production of octopamine and affects Drosophila male aggression – Chelsie E. Rohscheib – Applied and Environmental Microbiology

Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages – Alison S. Jacob – Journal of Eukaryotic Microbiology

Interactions between multiple helminths and the gut microbiota in wild rodents – Jakub Kreisinger – Philosophical Transactions B

Plant, root, and soil microbiome

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time – Britt Koskella – Philosophical Transactions B

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States – Ederson da C. Jesus – GCB Bioenergy

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota
Eduard Vico Oton – The ISME Journal

Composition of soil microbial communities in the rhizosphere of cucumber cultivars with differing nitrogen acquisition efficiency – Xingang Zhou – Applied Soil Ecology

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms – Qian Zhang – Environmental Science & Technology

New traceability strategies based on a biological Bar Code by PCR-DGGE using bacterial and yeast communities for determining farming type of peach – Ahmed El Shobaky – Egyptian Journal of Basic and Applied Sciences

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing – Bakthavachallam Subha – Marine Pollution Bulletin

Water microbiome

Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea – Nicolás Rascovan – ISME Journal

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis – Benjamin Bolduc – The ISME Journal

Built Environment Microbiome

Bacteriological assessment of the hospital environment in two referral hospitals in Yaoundé-Cameroon – Kamga Hortense Gonsu – Pan African Medical Journal

Green spaces and cognitive development in primary schoolchildren – Payam Dadvand – PNAS

Food microbiology

Source Tracking and Succession of Kimchi Lactic Acid Bacteria during Fermentation
Se Hee Lee – Journal of Food Science

House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs – Fabio Minervini – Food Microbiology


Estimating the computational limits of detection of microbial non-model organisms – Mathias Kuhring – Proteomics

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation – Bernhard Tschitschko – The ISME Journal

Microbial Ecology

Paleobiological Perspectives on Early Microbial Evolution – Andrew H. Knoll – Cold Spring Harbor Perspectives in Biology

Review: Building the microbiome in health and disease: niche construction and social conflict in bacteria – Luke McNally – Philosophical Transactions B

Hypothesis: Restriction modification systems as engines of diversity – Kim Sneppen – Frontiers in Microbiology

Review: A Replisome’s journey through the bacterial chromosome – Thomas R. Beattie – Frontiers in Microbiology

Bioinformatics and metagenomics

Horizontal gene transfer in an acid mine drainage microbial community – Jiangtao Guo – BMC Genomics

ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data – Abhishek Biswas – Bioinformatics

Comparing K-mer based methods for improved classification of 16S sequences – Hilde Vinje – BMC Bioinformatics

Databases for Microbiologists – Igor B. Zhulin – Journal of Bacteriology


Here, there, and everywhere: From PCRs to next‐generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places – Karl Gruber – EMBO Reports

Microbes in the news

Bacteria ‘Fight Club’ could help find new cures for diseases – Alexandra Ossola – Popular Science
Sold on Symbiosis: A love of the ocean lured Nicole Dubilier into science; gutless sea worms and their nurturing bacterial symbionts keep her at the leading edge of marine microbiology – Anna Azvolinsky – The Scientist

Terroir: how fungi, yeasts and bacteria affect the taste of your wine – Max Allen – The Australian

Brookline’s Maya Sekhar wins grand prize at state science fair (work on phages)

Almost half of Americans don’t understand threat of antibiotic resistance – Ginger Skinner – Consumer Reports

The Human Microbiome: do not underestimate microbes! – John Dalton – David Game College

Faecal transplants, diet on trend as society embraces gut health – Hamish Fitzsimmons – ABC.au

Aquarium Microbiome Project – Shedd Aquarium – YouTube

The Microbiology Weekly – Cesar Sanchez

This Bacteria-Slaying Light Fixture Is Perfectly Safe For Humans – Andrew Liszewski – Gizmodo

Researcher finds bacteria in pistachio trees – Angela Simental – Las Cruces Sun

Bacteria-Eating Viruses Could Be New Ally Against Superbugs In A ‘Post-Antibiotic Era’ – Ben Hirschler – Reuters / Huffington Post

Linking the microbiome and colorectal cancer: an author Q+A – Sophie Marchant – BioMedCentral blogs

Bik’s Picks

US Fish & Wildlife struggles to save remaining polar bears – Sam Catherman – News Quench

Professor: Nothing Fishy About Portuguese Man o’ War at Jersey Shore – NBC

Japan And The U.S. Are Going To Have An Actual Giant Robot Battle – Damon Beres – The Huffington Post



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