March 30, 2018

In today’s digest you can read a perspective on the social network of microorganisms by Karsten Zengler, a paper on relationship between HIV-1 infection and chronic periodontitis by Tábata Larissa, a paper on sponges-cyanobacteria associations – a global diversity overview by Despoina Konstantinou and/or for an easier read check the report on bacteria in rubber duckies in our ‘News’ section. Enjoy!

Jobs

PhD position Ecology and Evolution of Microbial Infectious Ecosystems, University of Groningen, Groningen, Netherlands

Research Assistant-Post Doc, Karl Landsteiner University of Health Sciences, Krems, Austria

Post-doctoral opportunity at Weill Cornell in New York City, NY, USA

Post Doc Position for Genetic Engineering to Improve Microbial Soluble Expression, BOKU, Vienna, Austria

General microbiome

Perspective: The social network of microorganisms — how auxotrophies shape complex communities – Karsten Zengler – Nature Reviews Microbiology

Intracellular signaling through the comRS system in Streptococcus mutans genetic competence – Simon A.M. Underhill – bioRxiv

Ecological Insights from the Evolutionary History of Microbial Innovations – Mario E Muscarella – bioRxiv

Probing the metabolism of microorganisms – Stilianos Louca – Science

Human respiratory microbiome

Review: Streptococcus pneumoniae: transmission, colonization and invasion – Jeffrey N. Weiser – Nature Reviews Microbiology

Oral microbiome

Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis – Tábata Larissa – Expert Review of Clinical Immunology

Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status –  Rachel M. Presti – AIDS

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt – Clinical and Translational Immunology

Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease – Elena Barengolts – PLOS One

Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger – Fengping He – Biochemical and Biophysical Research Communications

Single Sampling Versus Multiple Testing Strategy to Assess Gut Microbiota Composition: Does It Matter? – T. G. J. de Meij – Current Microbiology

Scaling Safe Access to Fecal Microbiota Transplantation: Past, Present, and Future – Pratik Panchal – Current Gastroenterology Reports

Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile – Rafael Araos – Digestive Diseases and Sciences

Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis – Robert Šket – Frontiers in  Physiology

Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases – Maria C. Opazo – Frontiers in Microbiology

Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity – Zachariah DeFilipp – Blood Advances

Animal experiments 

Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows – Shoukun Ji – Frontiers in Cellular and Infection Microbiology

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections – Larissa B. Thackray – Cell Reports

Animal microbiome 

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali – Benjamin J. Krajacich – PLOS One

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota – Tao Sun – Scientific Reports

Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis – Alessandro Catenazzi – Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny – Alicia K. Bird – Frontiers in Microbiology

Plant, root, and soil microbiome

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site – José A. Siles – Applied Microbiology and Biotechnology

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants – Katiúscia Kelli Montanari-Coelho – World Journal of Microbiology and Biotechnology

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem – Tatoba R. Waghmode – Frontiers in Microbiology

Bacterial diversity and community structure in the rhizosphere of four Ferula species – Xiuling Wang – Scientific Reports

Water and extremophile microbiome

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean – Despoina Konstantinou – PLOS One

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation – Zheng Xu – Chemosphere

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area – Andrew K. Leight – Frontiers in Microbiology

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin – Min Ren – Frontiers in Microbiology

Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat – Tanita Wein – Frontiers in Microbiology

Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress – Jian Han –  Frontiers in Microbiology

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael W. Henson – The ISME Journal

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation – Babett Wintsche – Frontiers in Microbiology

Phages and viruses

Review: Autophagy during viral infection — a double-edged sword – Younho Choi – Nature Reviews Microbiology

Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa – Veronna Marie – Journal of Water and Health

Kinetic Modeling of Virus Growth in Cells – John Yin – Microbiology and Molecular Biology Reviews

Bioinformatics

EzMap: a simple pipeline for reproducible analysis of the human virome – Patrick Czeczko  – Bioinformatics

Techniques

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan C.Raju – Journal of Microbiological Methods

Mapping bacteria on filter membranes, an innovative SERS approach – SiyueGao – Journal of Microbiological Methods

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile – Zhirong Li  – Journal of Microbiological Methods

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga –  Journal of Microbiological Methods

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm – Guillaume Gautier – Journal of Microbiological Methods

Rapid detection of carbapenemase-producing Acinetobacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method – Vincent van Almsick – Journal of Microbiological Methods

A quest to find good primers for gene expression analysis of Candida albicans from clinical samples – Gabriela C.Alonso – Journal of Microbiological Methods

Microbes in the news 

The inside of rubber duckies are full of bacteria. You don’t seem surprised

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’

Researchers develop model to show how bacteria grow in plumbing systems

Harvard scientists uncover an exploitable Achilles’ heel common to most bacteria

Altering Gut Microbiome May Increase Resistance to C. difficile infection

Our Own Microbiome Might Be Triggering The Autoimmune Disease Lupus

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