November 15, 2016

Microbial profiling in the classroom, viral abundance in seawater membrane vesicles, two Akkermansia in vitro studies, the phyllospere of Phoenix’ urban forest, the (im)possibility to reconstruct plasmids, high confidence protein annotations.

General microbiome

Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont – Lynn Chiu – PhilSci Archive

Microbial Community-Level Physiological Profiling as an Inquiry Laboratory Exercise – Pamela A. Marshall – The American Biology Teacher

Human oral microbiome

Bacterial communities associated with apical periodontitis and dental implant failure – Simon Dingsdag – Microbial Ecology in Health and Disease

Human respiratory microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff –  Current Opinion in Pulmonary Medicine

Human gut microbiome

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh – Shafiqul Alam Sarker – Environmental Microbiology

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery – Priscila Sala – Journal of International Medical Research

Review: The Human Microbiome and I-Cubed: A Modern Medical Paradigm – David S. Younger – World Journal of Neuroscience

Animal and in vitro models

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent – F. Van Herreweghen – Beneficial Microbes

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism – Renee L. Greer – Nature Communications

Animal microbiome

Black rhinoceros (Diceros bicornis) and domestic horse (Equus caballus) hindgut microflora demonstrate similar fermentation responses to grape seed extract supplementation in vitro – N. F. Huntley – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Zhongmin Dai – Scientific Reports

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University

Diversity of phylloplane microflora in certain tea cultivars of Assam, North-East India – Amarjyoti Tanti – European Journal of Biological Research

Review: Do genetically modified plants affect adversely on soil microbial communities?
– Zheng-jun Guan – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology

Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches – Valerie F. Schwab – Biogeosciences

Trade-off between taxon diversity and functional diversity in European lake ecosystems – Lars Grossmann – Molecular Ecology

Glycerol enhances fungal germination at the water-activity limit for life – Andrew Stevenson – Environmental Microbiology

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India – Amrita Kumari Panda – AMB Express

Phages and viruses

Next-generation sequencing and norovirus – Matthew Cotten & Marion Koopmans – Future Virology

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates – Steven J Biller – ISME Journal

Metagenomics and bioinformatics

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data – Sergio Arredondo-Alonso – bioRxiv

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Optimal prediction of the number of unseen species – Alon Orlitsky – PNAS

Constraint-based stoichiometric modelling from single organisms to microbial communities
– Willi Gottstein – Journal of the Royal Society Interface

Metabolomics, culturomics, proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns – Emma Timmins-Schiffman – The ISME Journal

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols – Max Crüsemann – Journal of Natural Products

Probiotics

Review: Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis – Jennifer McKean – The Journal of Alternative and Complementary Medicine

Microbes in the news

Good News at Fred Hutch: Evolutionary biologists Drs. Harmit Malik and Jesse Bloom win American Society for Microbiology awards – Fred Hutch

NTU don once downed a dish of live bacteria, for science’s sake – Straits Times

MCR-1 resistance gene could make its way into bacteria and superbugs in Australia – NT News
Biofilm battle is key to antibiotic war – University of Queensland

‘Probiotics’ on salad greens could make them safer, healthier – The University of Queensland

Monique Keiran: Laziness and hubris making us sick – Times Colonist

From the American Heart Association annual meeting: Could C-Section Birth Raise Child’s Risk of Obesity? – Dennis Thompson – Pantagraph

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