April 14, 2016

Events

Translational Microbiome Conference, April 20-21, Boston MA

Guggenheim Securities Microbiome Day, April 21, New York. I cannot find a website for the conference, but got several links to press releases from companies that will participate, such as Enterome and Evelo Biosciences

General microbiome

Intricacies of assessing the human microbiome in epidemiological studies – Courtney K. Robinson – Annals of Epidemiology

Pregnancy and birth

Secretory IgA in the Coordination of Establishment and Maintenance of the Microbiota – Oliver Pabst – Trends in Immunology

Human skin microbiome

The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin – Vanessa R Salgado – Memórias do Instituto Oswaldo Cruz

Human respiratory microbiome

Conference abstract: Analysis of the Sputum Microbiome in the Severe Asthma – Rihuang Qiu – Chest Journal

Human gut microbiome

(also contains animal experiments): Helminth infection promotes colonization resistance via type 2 immunity – Deepshika Ramanan – Science

Assessing the Colonic Microbiota in Children: Effects of Sample Site and Bowel Preparation – Shaw, Alexander G. – Journal of Pediatric Gastroenterology & Nutrition

Editorial: further evidence that proton pump inhibitors may impact on the gut microbiota – A. W. Walker – Alimentary Pharmacology & Therapeutics

Couple of papers from the Didier Raoult lab in New Microbes and New Infections (half of the next issue of that journal is by people from his group)
Isolation of a new species Peptoniphilus phoceensis from the human gut – Gaël Mourembou
Romboutsia timonensis, a new Species isolated from human Gut – Davide Ricaboni
« Bariatricus massiliensis », as a new bacterial species from the human gut microbiota – Simon Bessis

Review: Adaptation of Candida albicans to commensalism in the gut – Daniel Prieto – Future Microbiology

Review: Potential Role of the Microbiome in Barrett’s Esophagus and Esophageal Adenocarcinoma – Erik J. Snider – Digestive Diseases and Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Gut microbiota, inflammation and colorectal cancer – Jun Sun – Genes & Diseases

Review: Age-mediated changes in the gastrointestinal tract – Hamid A. Merchant – International Journal of Pharmaceutics

Review: Current Understanding of Dysbiosis in Disease in Human and Animal Models – DeGruttola, Arianna K. – Inflammatory Bowel Diseases

Animal models

Resilience of the intestinal microbiota following pathogenic bacterial infection is independent of innate immunity mediated by NOD1 or NOD2 – Susan J. Robertson – Microbes and Infection

Changes of Mouse Gut Microbiota Diversity and Composition by Modulating Dietary Protein and Carbohydrate Contents: A Pilot Study – Eunjung Kim – Preventive Nutrition and Food Science

Chemopreventive Metabolites Are Correlated with a Change in Intestinal Microbiota Measured in A-T Mice and Decreased Carcinogenesis – Amrita K. Cheema – PLOS ONE

Animal microbiome

Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau – Dan Xue – Livestock Science

Evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40 days after arrival at a feedlot – Edouard Timsit – Veterinary Microbiology

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels – Han Liu – Scientific Reports

Plant, root, and soil microbiome

Multiple effects of a commercial Roundup® formulation on the soil filamentous fungus Aspergillus nidulans at low doses: evidence of an unexpected impact on energetic metabolism – Valérie Nicolas – Environmental Science and Pollution Research

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils – Peng Cao – Microbial Ecology

Rhizosphere of Avicennia marina (Forsk.) Vierh. as a landmark for polythene degrading bacteria – Mohd. Shahnawaz – Environmental Science and Pollution Research

Wastewater microbiology

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Characterization of microbial communities in wetland mesocosms receiving caffeine-enriched wastewater – Dongqing Zhang – Environmental Science and Pollution Research

Food microbiology

Bacterial community analysis of Tatsoi cultivated by hydroponics – Ok K. Koo – Journal of Environmental Science and Health, Part B

Heterofermentative lactic acid bacteria dominate in Korean commercial kimchi – Hee-Young Kim – Food Science and Biotechnology

Spatial Distribution of the Metabolically Active Microbiota within Italian PDO Ewes’ Milk Cheeses – Ilaria De Pasquale – PLOS ONE

Effect of postharvest practices on the culturable filamentous fungi and yeast microbiota associated with the pear carpoplane – Quinton Volschenk – Postharvest Biology and Technology

Review: Control of ochratoxin A-producing fungi in grape berry by microbial antagonists: A review – Hongyin Zhang – Trends in Food Science & Technology

More microbiology

Implementing an Antibiotic Stewardship Program: Guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America – Tamar F. Barlam – Clinical Infectious Diseases

Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis – R. Fang – Epidemiology and Infection
http://journals.cambridge.org/action/displayAbstract?

Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems – Jan Ribbe – Biophysical Journal

Opinion: Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control – Suzanne A. Ford – PLOS Pathogens

Review: Directed evolution and synthetic biology applications to microbial systems – Marcelo C Bassalo – Current Opinion in Biotechnology

Microbes in the news

Gut bacteria could help prevent cancer – Science Daily

AmpliPhi Bio’s bacteriophage cocktail shows encouraging infection-fighting prowess in cystic fibrosis isolates; shares up 13% – Seeking Alpha

What do you want to know about your microbiome? uBiome opens poll on which of 6 top projects should win $100K in research help – Beth Mole – Ars Technica

Worm Infection Counters Inflammatory Bowel Disease by Drastically Changing Gut Microbiome – PR Newswire

The Microbiome: What Is It and How Does It Affect You? – Marsha Nunley – PR web

Science, publishing, and career

Why our peer review system is a toothless watchdog – Ivan Oransky and Adam Marcus – STAT News

Don’t dismiss science fairs. Make them better – Patrick Skerrett – STAT News

Dutch push for a quantum leap in open access – Martin Enserink – Science

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