March 22, 2015

Human oral microbiome

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human vaginal microbiome

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. – Helena Mendes-Soares – Pathogens and Disease

Human gut microbiome

Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis – Ratnakar Shukla – Digestive Diseases and Sciences

Review: Psychobiotics and the gut–brain axis: in the pursuit of happiness – Zhou L – Neuropsychiatric Disease and Treatment

Microbiome of pregnancy and birth

The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Colonisation of the gut by bifidobacteria is much more common in vaginal deliveries than Caesarean sections – Sarka Musilova – Acta Paediatrica

Review: The Birth of the Holobiont: Multi-species Birthing Through Mutual Scaffolding and Niche Construction – Lynn Chiu, Scott F. Gilbert – Biosemiotics

Animal models

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota – Jessica Ann Thompson – Cell Reports

Vagotomy prevents the effect of probiotics on caspase activity in a model of postmyocardial infarction depression – M. Malick – Neurogastroenterology & Motility

Faecalibacterium prausnitzii prevents physiological damage in a chronic low-grade inflammation murine model – Rebeca Martín – BMC Microbiology

Peyer’s patch innate lymphoid cells regulate commensal bacteria expansion – Masaaki Hashiguchi – Immunology Letters

Animal microbiome

Review: A Review of Infectious Agents in Polar Bears (Ursus maritimus) and Their Long-Term Ecological Relevance – Anna C. Fagre – EcoHealth

Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH – Neeti Pandey andRaman Rajagopal – Insect Science

Genetic diversity of cyanophages of the myoviridae family as a constituent of the associated community of the Baikal sponge Lubomirskia baicalensis – T. V. Butina – Russian Journal of Genetics

Soil and plant root microbiome

Effects of Thinning and Induced Drought on Microbiological Soil Properties and Plant Species Diversity at Dry and Semiarid Locations – Javier Hedo de Santiago – Land Degradation & Development

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN-Soil, Air, Water

Water microbiome

Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China – Yongming Wang – Environmental Science and Pollution Research

Spatial distribution of marine airborne bacterial communities – Jasmin S. Seifried – Microbiology Open

Microbiome of the built environment

Interphase microbial community characteristics in the fermentation cellar of Chinese Luzhou-flavor liquor determined by PLFA and DGGE profiles – Xiaofei Ding – Food Research International

Bioreactor microbiology

Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing – Duntao Shu – Bioresource Technology

Cu and Cr enhanced the effect of various carbon nanotubes on microbial communities in an aquatic environment – Fei Wang – Journal of Hazardous Materials

Review: Utilization of microbial community potential for removal of chlorpyrifos: a review – Maya Yadav – Critical Reviews in Biotechnology

Metagenomics and Bioinformatics

A robust approach for identifying differentially abundant features in metagenomic samples – Michael B. Sohn – Bioinformatics

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe – Tianmin Wang – BMC Bioinformatics

The impact of quality filter for RNA-Seq – Pablo H.C.G. de Sáa – Gene

Poster: MetaGenSense: a web application for analysis and visualization of high throughput sequencing metagenomic data – Damien Correia – F1000 posters

SISPA-Seq for rapid whole genome surveys of bacterial isolates – Meredith S. Wright – Infection, Genetics and Evolution


The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Deep metabotyping of the murine gastro-intestinal tract for visualization of digestion and microbial metabolism – Silke S Heinzmann and Philippe Schmitt-Kopplin – Journal of Proteome Research

Application of a new Dynamic Gastrointestinal Simulator (SIMGI) to study the impact of red wine in colonic metabolism – C. Cueva – Food Research International

Isolation of dextran-hydrolyzing intestinal bacteria and characterization of their dextranolytic activities – Jin Kyoung Kim – Biopolymers

Diet-induced obesity causes metabolic impairment independent of alterations in gut barrier integrity – Caroline Kless – Molecular Nutrition & Food Research

Other microbial science papers

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals – Thomas Obadia – PLOS Computational Biology

How bacterial pathogens colonize their hosts and invade deeper tissues – David Ribet, Pascale Cossart – Microbes and Infection

Antimicrobial stewardship: the role of scientists? – Laura Bowater – Journal of Antimicrobial Chemotherapy

Cyanobacteria: the bright and dark sides of a charming group – Katia Sciuto, Isabella Moro – Biodiversity and Conservation

Microbes in the news
The ChuckNorrisMicrobiome will get you, and you, and you … – Jonathan Eisen – The Tree of Life

The Oral Microbiota Affects More Than Just the Mouth – Lily Berrin – PLOS blog

This Week in Microbiology #100: Omnis cellula e cellula – MicrobeWorld

Wisconsin Longitudinal StudyDecades later, benchmark study yields data on human condition – Pamela Herd –

Special microbes make anti-obesity molecule in the gut – American Chemical Society – Eureka Alert

About the baboon microbiome study: Are our gut bacteria swapped when we snuggle up? – Tim Sandle – Digital Journal

Wireless Sensors Help Scientists Map Staph Spread Inside Hospital – Scott Hensley – NPR

Science spreads antibiotic resistance by genetic experimentation – Karen Hardison – Digital Journal
Great #openaccess collection of papers on RNA – Jonathan Eisen – MicroBEnet

Visualizing the deadly threat of meningitis on campuses – Jamie Lampros – Standard Examiner

Epidemic Predicted by Bill Gates Who Pleads: Microbes Not Missiles – Jeanette Smith – Guardian LV

Science, publishing, and career

Forget Harvard and Stanford. It really doesn’t matter where you go to college – Jeffrey J. Selingo

Wolf Prize for Agricultural Science for Linda Saif: Award shines light on Ohio State scientist – Laura Arenschield – The Columbus Dispatch

Michigan judge asks PubPeer to turn over anonymous user information – Kelly Servick – Science Insider

In science, irreproducible research is a quiet crisis – Carolyn Johnson – Boston Globe

Bik’s Picks

Copy Cat: Someone Keeps Photocopying Their Cat at the University of Wisconsin Library – Samantha Grossman –

First fine-scale genetic map of the British Isles – Science Daily

Dude, why is my mushroom glowing? Scientists have the answer – Will Dunham – Reuters

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