April 21, 2015

I don’t always eat steak, but when I do, I will put some garlic on it.

Conferences

WAO Symposium on Food Allergy and the Microbiome – December 2015 – Miami, FL, USA

Call for papers: Interactions of the Human Microbiome and Immune System in Health Resilience and Disease Pathogenesis – Journal of Immunology Research

Microbiome of pregnancy and birth

Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health – Ted Jost – Nutrition Reviews

Human oral microbiome

Editorial on “The oral microbiome in an ecological perspective: More than just a sum of microbes” – Egija Zaura and Alex Mira – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis – William G. Flight – Journal of Clinical Microbiology

Review behind a thick paywall: The pediatric microbiome and the lung – Michael Tracy – Current Opinion in Pediatrics

Review: Lung Microbiomes: New Frontiers? – Kathryn DeRiemer – American Journal of Respiratory and Critical Care Medicine

Review: A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis – Alexander E. Zajac – International Forum of Allergy & Rhinology

Human gut microbiome

Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome – Rajendra Raghow – World Journal of Diabetes

Gut Microbiome Compositional and Functional Differences between Tumor and Non-tumor Adjacent Tissues from Cohorts from the US and Spain – Gut Microbes

Review: No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens – Martina Sassone-Corsi and Manuela Raffatellu – The Journal of Immunology

Review on chronic kidney disease: Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment – Nosratola D. Vaziri – Nephrology Dialysis Transplantation

Review: The Role of Microbial Amino Acid Metabolism in Host Metabolism – Evelien P. J. G. Neis – Nutrients

Review: Linking Smoking, Coffee, Urate, and Parkinson’s Disease – A Role for Gut Microbiota? – Filip Scheperjans – Journal of Parkinson’s Disease

Animal and other models of microbiome research

Have some garlic with your steak: Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota – Wei-Kai Wu – Journal of Functional Foods

Innate Lymphoid Cells Control Early Colonization Resistance against Intestinal Pathogens through ID2-Dependent Regulation of the Microbiota – Xiaohuan Guo – Immunity

Effect of donor animal species and their feeding on the composition of the microbial community establishing in a rumen simulation – M. Witzig – Journal of Applied Microbiology

Impact of a novel protein meal on the gastrointestinal microbiota and host transcriptome of larval zebrafish Danio rerio – Eugene Rurangwa – Frontiers in Physiology

Animal microbiome

Shit happens: Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies – Sebastian Menke – Methods in Ecology and Evolution

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera) – Karen M. Kapheim – PLOS ONE

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Tieshan Jiang – PLOS ONE

Plant root and soil microbiome

Bacterial diversity amplifies nutrient-based plant–soil feedbacks – Simone Weidner – Functional Ecology

Non-random species loss in bacterial communities reduces antifungal volatile production
W. H. Gera Hol – Ecology

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis – N. Kh. Sergaliev – Eurasian Soil Science

Physiological profiles of microbial communities in mine soils afforested with different tree species – Marcin Chodak – Ecological Engineering

Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland – Chao Liang – Frontiers in Microbiology

Water microbiome

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing – Elianne Sirnæs Egge – Molecular Ecology

Extremophiles

Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria – Chiara Pesciaroli – Annals of Microbiology

Geochemical Characteristics and Microbial Community Composition in Toxic Metal-Rich Sediments Contaminated with Au-Ag Mine Tailings – Man Jae Kwon – Journal of Hazardous Materials

Uranium isotopes fingerprint biotic reduction – Malgorzata Stylo – PNAS

Bioreactor microbiome

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane – Florence Braun – PLOS ONE

Reactor performance and methanogenic archaea species in thermophilic anaerobic co-digestion of waste activated sludge mixed with food wastewater – Hyun Min Jang – Chemical Engineering Journal

Functional food microbiology

A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe – Sylvie Miquel – Microbial Cell Factories

Metagenomics and bioinformatics

CoMeta: Classification of Metagenomes Using k-mers – Jolanta Kawulok, Sebastian Deorowicz – PLOS ONE

Large-scale contamination of microbial isolate genomes by Illumina PhiX control – Supratim Mukherjee – Standards in Genomic Sciences

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL – Ali May – Nucleic Acids Research

Mini review: The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life – Eugene V. Koonin – Journal of Molecular Evolution

Not really metagenomics but of interest: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis – Guillaume Méric – Genome Biology and Evolution

Haven’t we microbiologists already been doing this for years?
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform – Shadi Shokralla – Scientific Reports

Techniques

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction – Conny Mathay – Biopreservation and Biobanking

Microbes in the news

Housing characteristics and microbial communities in homes of asthmatic children – Elisabeth Bik – MicroBEnet

OCHS science experiment finds space a hospitable place for bacteria – Cindy Nevitt – Press of Atlantic City

Uranium isotopes carry the fingerprint of ancient bacterial activity – Phys.org

Immune cells support good gut bacteria in fight against harmful bacteria – University of Chicago

Q&A: What Is Listeria? Bacteria Found in Blue Bell Ice Cream – Mary Clare Jalonick – ABC News

Grant will help University of Minnesota study antibiotic-resistant bacteria – Star Tribune

Science, publishing, and career

Mya Breitbart awarded the 2015 STEM Woman of the Year – University of South Florida

Bik’s Picks

Fast imaging of live organisms with sculpted light sheets – Aleksander K. Chmielewski – Scientific Reports

Cheesy, metallic, sweet: 170-year-old champagne is clue to winemaking’s past – Allie Wilkinson – Nature

New Evidence of Prehistoric Trade With Asia Found at Bering Land Bridge Site – Huffington Post
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