Category Archives: Events and jobs

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

October 6, 2017

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Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University Hospital – Posting End Date: Nov 2, 2017, 11:59:00 PM

Assistant Professor in Microbiology – Emporia State University – Deadline- open until filled

Assistant Professor in Virology and Microbiome Research – Auburn University, Alabama – Deadline- open until filled

Faculty Position in Microbial Environmental Metagenomics and Bioinformatics – University of Kansas – Initial review of applications: Nov 14, 2017

 

General microbiome

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

 

Human vaginal microbiome

Microbiome: Detecting diversity – C Humphries – Nature

 

Human gut microbiome

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome. – DA Medina – International Journal of Molecular Sciences

Synthetic biology and the gut microbiome. – J Dou – Biotechnology Journal

The Gut and Its Microbiome as Related to Central Nervous System Functioning and Psychological Well-being: Introduction to the Special Issue of Psychosomatic Medicine. – EA Mayer – Psychosomatic Medicine

Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. – CE Rosen – BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology.

 

Animal experiments 

Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism. – T Florin – Gut Microbes

The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer – JM Noto – PLoS Pathogens

Review: Microbiota, cirrhosis, and the emerging oral-gut-liver axis. – C Acharya – JCI Insight

 

Animal microbiome 

Interactions of pathogenic and commensal strains of Mannheimia haemolytica with differentiated bovine airway epithelial cells grown at an air-liquid interface – D Cozens – bioRxiv

Ixodes scapularis does not harbor a stable midgut microbiome – BD Ross – bioRxiv

 

Plant, root and soil microbiome

Protists are an integral part of the Arabidopsis thaliana microbiome. – M Sapp – Environmental Microbiology

Fusarium verticillioides: Advancements in Understanding the Toxicity, Virulence, and Niche Adaptations of a Model Mycotoxigenic Pathogen of Maize. – AA Blacutt – Phytopathology

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – ER Hester – bioRxiv

Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. – J Almario – Proceedings of the National Academy of Sciences of the United States of America

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration. – CP Ward – Nature Communications

Changes in the abundance and structure of bacterial communities in the greenhouse tomato cultivation system under long-term fertilization treatments – X Zhang – Applied Soil Ecology

 

 

Phages and viruses

Evolution: Zapping viral RNAs – SP Goff – Nature

 

Techniques

Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System. – JF Chignell – Microbial Ecology

Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. – L Bircher – Microbial Biotechnology

On the Reproduction Number of a Gut Microbiota Model. – C Barril – Bulletin of Mathematical Biology

 

Microbes in the news

Woods: The art of aging cheese – Lake Geneva News

Methane-Munching Bacteria Could Poop Out Your Future Clothes – Geek.com

XOMA (XOMA) Announces Multiple New License Agreements for Proprietary Phage Display Libraries – Biospace

Superbug superweapon: Identifying antibiotic-resistant bacteria in 30 minutes – New Atlas

New fundamental insight into the battle against bacteria – Science Daily

Ribaxamase Protects Gut Microbiome, Cuts Opportunistic C. diff Risk – MPR

October 2, 2017

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This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

October 1, 2017

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Events and jobs

Microbiome Center Networking Event – Plant Pathology and Environmental Microbiology, Penn State Agricultural College – October 3, 2017, 4:30 PM – 6:30 PM

General microbiome

Review: Old friends, microbes, and allergic diseases – N Shimojo – Allergology International

 

Human skin microbiome

Study of skin and nail Candida species as a normal flora based on age groups in healthy persons in Tehran-Iran – Z Rafat – Journal de Mycologie Médicale

 

Human gut microbiome

Variability in Eating Frequency is Associated with the Human Gastrointestinal Microbiota –  E Banishay – Journal of the Academy of Nutrition and Dietetics

Animal experiments 

The gut-liver axis: impact of a mouse model of small-bowel bacterial overgrowth –  Q Wang – Journal of Surgical Research

Metagenomic insights into the effects of oligosaccharides on the microbial composition of cecal contents in constipated mice – L Wang – Journal of Functional Foods

Effects of gut microbiota disturbance induced in early life on the expression of extrasynaptic GABA-A receptor α5 and δ subunits in the hippocampus of adult rat  – L Liang – Brain Research Bulletin

A Subset of Polysaccharide Capsules in the Human Symbiont Bacteroides thetaiotaomicron Promote Increased Competitive Fitness in the Mouse Gut – NT Porter – Cell and Host Microbe

Animal microbiome 

Hype or Opportunity? Using Microbial Symbionts in Novel Strategies for Insect Pest Control – AK Arora – Journal of Insect Physiology

Nutritional immunology: Diversification and diet-dependent expression of antimicrobial peptides in the black soldier fly Hermetia illucens – H Vogel – Developmental & Comparative Immunology

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – E Ruppé – Clinical Microbiology and Infection

Pathogen invasion changes the intestinal microbiota composition and induces innate immune responses in the zebrafish intestine – HT Yang – Fish & Shellfish Immunology

Plant, root and soil microbiome

Experimental warming reduces the diversity and functional potential of the Sphagnum microbiome – AA Carrell – bioRxiv

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome – S Jacquiod – Journal of Hazardous Materials

Fate of potential indicator antimicrobial resistance genes (ARGs) and bacterial community diversity in simulated manure-soil microcosms – M Wang – Ecotoxicology and Environmental Safety

Built environment 

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – CL Amorim – Ecotoxicology and Environmental Safety

Food microbiology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – JJ Lee –  Food Research International

Review: Novel insights into the microbiology of fermented dairy foods – G Macori – Current Opinion in Biotechnology

Simulated gastrointestinal conditions increase adhesion ability of Lactobacillus paracasei strains isolated from kefir to Caco-2 cells and mucin – AA Bengoa – Food Research International

Chapter: Chapter 6 – Genetically Modified Microorganisms: Harmful or Helpful? – O Csutak – Genetically Engineered Foods

 

Techniques

Enhancement of subsoil denitrification using an electrode as an electron donor – S Qin – Soil Biology and Biochemistry

Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition – G Cesarano – Applied Soil Ecology

Next Generation Sequencing: Problems and opportunities for next generation studies of microbial communities in food and food industry – G Cardinali – Current Opinion in Food Science

An integrated electrolysis – electrospray – ionization antimicrobial platform using Engineered Water Nanostructures (EWNS) for food safety applications – N Vaze – Food Control

Inactivation of microbiota from urban wastewater by single and sequential electrocoagulation and electro-Fenton treatments – E Anfruns-Estrada – Water Research

Microbes in the news

I’ve always wondered: Why don’t hippos get cholera? – The Conversation

Women’s bacteria thwarted attempt at anti-HIV vaginal gel – Ottawa Citizen

How to Use Your Second Brain: Microbiome Expert Laure Ysebrant on Strategic Eating, Building Immunity, and Fake Fibre. – Thrive Global

A New Drug Uses CRISPR to Fight Antibiotic-Resistant Bacteria – Futurism

A TURNING OF PHAGE – Study Break

PEOPLE ARE MORE INTERESTING THAN BACTERIA: THE DR. CYRIL SHERER SAGA – The Jerusalem Post

September 30, 2017

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Events and jobs

Master of Biomedical Science – University of Melbourne – Start Date: February

Visiting Professor (Part Time) Microbiology – Chamberlain College of Nursing, Jacksonville, FL Campus

Assistant Professor of Biology, Microbiology – The Department of Biology at Barnard College, Columbia University – Starting July 2018

 

General microbiome

What will membrane vesicles (MVs) bring to bacterial communication? – M Toyofuku – Microbes and Environments

Direct and context-dependent effects of light, temperature, and phytoplankton shape bacterial community composition – SF Paver – Ecosphere

 

 

Human skin microbiome

The response of human bacteria to static magnetic field and radiofrequency electromagnetic field.  – DPE Crabtree – The Journal of Microbiology

 

 

Human gut microbiome

Gut inflammation and dysbiosis in human motor neuron disease – J Rowin – Physiological Reports

Review: Tart Cherries and health: Current knowledge and need for a better understanding of the fate of phytochemicals in the human gastrointestinal tract. – AC Mayta-Apaza – Critical Reviews in Food Science and Nutrition

Mechanisms of gut microbiota-mediated bone remodeling. – J Yan – Gut Microbes

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – ZA Costliow – mSystems

A gut feeling about multiple sclerosis – FJ Quintana – Proceedings of the National Academy of Sciences of the United Sates of America

 

Animal experiments 

Vancomycin and ceftriaxone can damage intestinal microbiota and affect the development of the intestinal tract and immune system to different degrees in neonatal mice. – RY Cheng – Pathogens and Diseases

Dietary soy, meat, and fish proteins modulate the effects of prebiotic raffinose on composition and fermentation of gut microbiota in rats. – G Bai – International Journal of Food Sciences and Nutrition

 

Animal microbiome 

Effects of obesity, energy restriction and neutering on the faecal microbiota of cats. – MM Fischer – The British Journal of Nutrition

The lipopolysaccharide core oligosaccharide of Burkholderia plays a critical role in maintaining a proper gut symbiosis with the bean bug Riptortus pedestris – JK Kim – Journal of Biological Chemistry

 

Plant, root and soil microbiome

Nectar-inhabiting microorganisms influence nectar volatile composition and attractiveness to a generalist pollinator. – CC Rering – The New Phytologist

Fossil Asterinaceae in the phyllosphere of the eastern Himalayan Neogene Siwalik forest and their palaeoecological significance – A Vishnu (née Mandal) – Botanical Journal of the Linnean Society

African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils – DK Puozaa – PLoS One

 

Microbiome of built environment 

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. – BI Cayford – Biofouling

 

Food microbiology

Yeast community in traditional Portuguese Serpa cheese by culture-dependent and -independent DNA approaches – MTP Gonçalves Dos Santos – International Journal of Food Microbiology

 

 

Techniques

Prediction of the intestinal resistome by a novel 3D-based method – E Ruppe – bioRxiv

PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media – DBH Barton – bioRxiv

Validation of standards suitable for genome size estimation of fungi – P Talhinhas – Journal of Microbiological Methods

Optimization of media components for production of antimicrobial compound by Brevibacillus brevis EGS9 isolated from mangrove ecosystem – T Arumugam – Journal of Microbiological Methods

Development of a set of multiplex PCRs for detection of genes encoding cell wall-associated proteins in Staphylococcus pseudintermedius isolates from dogs, humans and the environment – N Phumthanakorn – Journal of Microbiological Methods

Microbial Forensic Analysis of Human-Associated Bacteria Inhabiting Hand Surface – J Park – Forensic Science International: Genetics Supplement Series

Models of microbiome evolution incorporating host and microbial selection – Q Zeng – Microbiome

Control of Clostridium difficile Infection by Defined Microbial Communities. – J Collins – Microbiology Spectrum

Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells – TP Driscoll – mBio

NMR window of molecular complexity showing homeostasis in superorganisms – J Kikuchi – Analyst

Lipid and protein fingerprinting for Fusarium oxysporum f. sp. cubense strain-level classification – D.F.O. Rocha – Analytical and Bioanalytical Chemistry 

 

Microbes in the news

Drink Up! Volunteers Swallow Bacteria That Causes Typhoid – npr

Gordon receives 2017 Horwitz Prize – Washington University School of Medicine

HyGIeaCare® Receives First Patent from USPTO – EIN News Desk

Why Does My Vagina Smell Like Cheese? An Expert Explains – Romper

Benefits of polyphenols on gut microbiota and implications in human health – Nutra Ingredients

September 24, 2017

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Events and jobs

Microbiology Non Registered Technician – Seattle, Washington – Work Schedule: Sunday – Thursday, 11:00pm – 7:30am

 

General microbiome

The Gram-positive model organism Bacillus subtilis does not form detectable cardiolipin-specific lipid domains – AR Pogmore – bioRxiv

 

 

Multi-site human microbiome

USA300 MRSA lineages persist on multiple body sites following infection – TD Read – bioRxiv

 

Human oral microbiome

Review: The role of wine and food polyphenols in oral health – A Esteban-Fernández – Trends in Food Science & Technology

 

Human skin microbiome

The micro-evolution and epidemiology of Staphylococcus aureus colonization during atopic eczema disease flare – CP Harkins – Journal of Investigative Dermatology

 

 

Human gut microbiome

Chapter: Bifidobacteria: Ecology and Coevolution With the Host – F Turroni – The Bifidobacteria and Related Organisms

Stress Responses of Bifidobacteria: Oxygen and Bile Acid as the Stressors – S Kawasaki – The Bifidobacteria and Related Organisms

Gut microbiota and the liver.  – A Federico – Minerva Gastroenterologica e Dietologica.

 

Animal microbiome 

Chapter: Honeybee-Specific Bifidobacteria and Lactobacilli – T Olofsson – The Bifidobacteria and Related Organisms

Antimicrobial resistant Escherichia coli in the reproductive tract microbiota of cows and sows – AT Luque – Comparative Immunology, Microbiology and Infectious Diseases

Review: Mechanisms of Plasmodium-Enhanced Attraction of Mosquito Vectors – AO Busula – Trends in Parasitology

Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts – BER Rubin – bioRxiv

 

Plant, root, and soil microbiome

Conservation tillage enhances the stability of the rhizosphere bacterial community responding to plant growth – Z Wang – Agronomy for Sustainable Development

Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion – MA Anthony – Ecosphere

Effects of exogenously applied salicylic acid and putrescine alone and in combination with rhizobacteria on the phytoremediation of heavy metals and chickpea growth in sandy soil. – N Khan – International Journal of Phytoremediation

 

Built environment

Medium shapes the microbial community of water filters with implications for effluent quality – M Vignola – Water Research

 

Food microbiology

Effects of the predominant bacteria from meju and doenjang on the production of volatile compounds during soybean fermentation – DW Jeong – International Journal of Food Microbiology

Predominant yeasts in Chinese traditional sourdough and their influence on aroma formation in Chinese steamed bread – T Liu – Food Chemistry

Chapter: Microbial Pigments From Bacteria, Yeasts, Fungi, and Microalgae for the Food and Feed Industries – L Dufossé – Food Dyes

 

Phages and viruses

An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach. – K Parmar – Current Microbiology

 

Techniques

Isolation, Cultivation, and Storage of Bifidobacteria – M Modesto – The Bifidobacteria and Related Organisms

Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics – M Price – bioRxiv

Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method. – A Dilhari – AMB Express

Fecal microbiota transplantation: past, present and future perspectives. – S Bibbò – Minerva Gastroenterologica e Dietologica.

 

Microbes in the news

I Sent Away a Sample of My Poop, and Here’s What I Learned About My Health – Pop Sugar

DESPERATE ACT Mum-of-one who’s spent £37k on surgery now injects herself with BACTERIA in an attempt to look younger – The Sun

What’s Next for Assembly Biosciences Incorporated (NASDAQ:ASMB) After Having Less Shares Shorted?  – The Press Telegraph

Your Towels Are Way Dirtier Than You Think – Time

Cnidarians remotely control bacteria – Phys.org

Mysterious flesh-eating bacteria is raging in Australia – ARS Technica

Lipid vesicles replace blood in new bacteria test – Phys.org

DEATH BY HURRICANE: THERE COULD SOON BE A CURE FOR A FLESH-EATING BACTERIA THAT ALMOST JUST KILLED A MAN IN TEXAS – News Week

Swiss startup says high-tech water filter can remove bacteria, viruses and plastic – Market Watch

Buruli ulcer: How to avoid being infected by gruesome flesh-eating bacteria – Abc.net

 

September 17, 2017

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Sunday dose- lots of techniques and news on microbes!

Events and jobs

Senior Laboratory Technician (Microbiology) – Symbio Laboratories, Perth, Australia

Two Assistant Professor Positions: Microbiology (0709823) or Ecology (0709824) – School of Biological Sciences, Illinois State University in Normal, IL

 

General microbiome

Review: Seeing is understanding: Salmonella’s way to penetrate the intestinal epithelium – K Zhang – International Journal of Medical Microbiology

 

 

Human nearly-sterile sites 

Metabolomic findings in sepsis as a damage of host-microbial metabolism integration – NV Beloborodova – Journal of Critical Care

 

Human gut microbiome

Molecular estimation of alteration in intestinal microbial composition in Hashimoto’s thyroiditis patients – HM Ishaq – Biomedicine & Pharmacotherapy

Immune regulation by histamine and histamine-secreting bacteria – W Barcik – Current Opinion in Immunology

Comparison of gut microbiota in adult patients with type 2 diabetes and healthy individuals – M Sedhigi – Microbial Pathogenesis

Review: Do Bacteria Shape our Development? Crosstalk between Intestinal Microbiota and HPA Axis – C de Weerth – Neuroscience & Biobehavioral Reviews

Corrigendum: Corrigendum to “Bifidobacterium animalis subsp. lactis LKM512 reduces levels of intestinal trimethylamine produced by intestinal microbiota in healthy volunteers: A double-blind, placebo-controlled study” [J. Funct. Food 36 (2017) 94–101] – M Matsumoto – Journal of Functional Foods

 

Animal experiments

Sulfate-reducing bacteria stimulate gut immune responses and contribute to inflammation in experimental colitis – VR Figliuolo – Life Sciences

Dietary pomegranate extract and inulin affect gut microbiome differentially in mice fed an obesogenic diet – S Zhang – Anaerobe

Gut Microbe–Mediated Suppression of Inflammation-Associated Colon Carcinogenesis by Luminal Histamine Production – C Gao – The American Journal of Pathology

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – M Masarwi – The Journal of Nutritional Biochemistry

 

Animal microbiome 

Metarhizium brunneum – an enzootic wireworm disease and evidence for its suppression by bacterial symbionts – T Kabaluk – Journal of Invertebrate Pathology

 

Plant, root and soil microbiome

Biodiversity of soil bacteria exposed to sub-lethal concentrations of phosphonium-based ionic liquids: Effects of toxicity and biodegradation – M Sydow – Ecotoxicology and Environmental Safety

A metagenomic-based, cross-seasonal picture of fungal consortia associated with Italian soils subjected to different agricultural managements – S Panelli – Fungal Ecology

The importance of plants to development and maintenance of soil structure, microbial communities and ecosystem functions – FM Vezzani – Soil and Tillage Research

Distribution of apple and blackcurrant microbiota in Lithuania and the Czech Republic – I Vepštaitė-Monstavičė – Microbiological Research

 

Built environment 

Ecotoxicological and microbiological assessment of sewage sludge associated with sugarcane bagasse – LRD Sommaggio – Ecotoxicology and Environmental Safety

 

Food microbiology

Review: Seafood Pathogens and Information on Antimicrobial Resistance: A Review – S Elbashir – Food Microbiology

Microbial diversity on commercial eggs as affected by the production system. A first approach using PGM – C Neira – International Journal of Food Microbiology

 

 

Techniques

To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes – J Walter – Current Opinion in Biotechnology

Review: Worms, Bugs and Drugs: C. elegans as a Model for Host-Microbe-Drug Interactions – AP García-González – Current Opinion in Systems Biology

Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients – AE Frankel – Neoplasia

A comparative study to evaluate natural attenuation, mycoaugmentation, phytoremediation, and microbial-assisted phytoremediation strategies for the bioremediation of an aged PAH-polluted soil – M García-Sánchez – Ecotoxicology and Environmental Safety

Aronia (Aronia melanocarpa) phenolics bioavailability in a combined in vitro digestion/Caco-2 cell model is structure and colon region dependent – J Wu – Journal of Functional Foods

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota – G Li – Cell Metabolism

High-throughput sequencing analysis reveals different Lactobacillus populations that dominate during “Chorizo de León” cured meat making – NM Quijada – Food Microbiology

Whole-genome Comparison of Urinary Pathogenic Escherichia coli and Faecal Isolates of UTI Patients and Healthy Controls – KL Nielsen – International Journal of Medical Microbiology

 

Microbes in the news

Swapping Spit: You Likely Share Your Roommate’s Microbiome, Even Without Kissing – Seeker

Microbiome in Ear May Play Role in Ear Infections – Contagion Live

Human Microbiome Market Size, Status and Forecast To 2025 – Med Gadget

Science spotlight: in-cosmetics Formulation Summit approaching – Cosmetics Design-Europe

JooMo launches new body-wash with skin bacteria tech – Cosmetics Design-Europe

Data from: Microbiome symbionts and diet diversity incur costs on the immune system of insect larvae – DRYAD

Legionella bacteria found in water at Ludlow Community Hospital – BBC News

Researchers take first steps towards development of biosensor for detection of bacteria – News Medical

 

September 16, 2017

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Events and jobs

Interim Microbiology Manager – Central Belt – North Lanarkshire, Scotland, UK

 

General microbiome

Haloarchaea: worth exploring for their biotechnological potential – A Singh – Biotechnology Letters

 

Pregnancy and early life

Rotavirus Vaccine Response Correlates with the Infant Gut Microbiota Composition in Pakistan – V Harris – Gut Microbes

 

 

Human gut microbiome

Infections by human gastrointestinal helminths are associated with changes in faecal microbiota diversity and composition – TP Jenkins – PLoS One

 

Animal experiments 

Review: Gut Microbial Influences on the Mammalian Intestinal Stem Cell Niche. – BCE Peck – Stem Cells International

Caloric restriction promotes rapid expansion and long-lasting increase of Lactobacillus in the rat fecal microbiota – C Fraumene – Gut Microbes

SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract – KB Uldahl – Journal of Applied Microbiology

Fungal derived 15-keto-prostaglandin E₂ activates host peroxisome proliferator-activated receptor gamma (PPAR-γ) to promote C. neoformans growth during infection. – RJ Evans – bioRxiv

The effect of regular or reduced-fat distillers grains with solubles on rumen methanogenesis and the rumen bacterial community – E Castillo-Lopez – Journal of Applied Microbiology

Role of Microbiota in Strengthening Ocular Mucosal Barrier Function Through Secretory IgA – A Kugadas – IOVS

 

Animal microbiome 

Virome analysis for identification of novel mammalian viruses in bats from Southeast China. – D Hu – Scientific Reports

 

Plant, root, and soil microbiome

Long-term no-till: A major driver of fungal communities in dryland wheat cropping systems – D Sharma-Poudyal – PLoS One

Nitrile-Degrading Bacteria Isolated from Compost – R Egelkamp – Frontiers in Environmental Science

Application of compost and clay under water-stressed conditions influences functional diversity of rhizosphere bacteria – BS Mickan – Biology and Fertility of Soils

High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits – P Nutaratat – 3 Biotech

Structural and functional variability in root-associated bacterial microbiomes of Cd/Zn hyperaccumulator Sedum alfredii – J Luo – Applied Microbiology and Biotechnology

 

Water microbiome and extremophile 

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – A Pontefract – Frontiers in Microbiology

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia) – A Brouchkov – Gene

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage – V Mesa – Frontiers in Microbiology

 

 

Techniques

Review: Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics – E Stylianou – Molecular Diagnosis & Therapy 

Formation of functional, non-amyloidogenic fibres by recombinant Bacillus subtilis TasA – E Erskine – bioRxiv

IN VITRO AND IN VIVO CHARACTERISATION OF ISOLATES OF CRYPTOCOCCUS NEOFORMANS CAUSING MENINGITIS IN HIV-INFECTED AND UNINFECTED PATIENTS IN VIETNAM – TT Lam – bioRxiv

Morphological and Transcriptomic analysis reveals the osmoadaptive response of endophytic fungus Aspergillus montevidensis ZYD4 to high salt stress – KH Liu – Frontiers in Microbiology

Multilocus and SSU rRNA gene phylogenetic analyses of available cyanobacterial genomes, and their relation to the current taxonomic system – J Mareš – Hydrobiologia

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing – X Li – Frontiers in Microbiology

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition – JA Lee – Environmental Microbiology

 

Microbes in the news 

WITH DESIGNER BACTERIA, CROPS COULD ONE DAY FERTILIZE THEMSELVES – Wired

Popular health supplements contaminated with faecal bacteria – Irish Examiner

Omega 3 intake linked to greater gut microbial diversity – Nutra Ingredients

Scientists Just Discovered Organisms That Are Distinct From Any Life Forms Known to Science – Futurism

 

 

September 15, 2017

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Events and jobs

 
Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

 
General microbiome

 
Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou  – Critical Reviews in Food Science and Nutrition

 

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

 
Pregnancy and early life

 
The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

 

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

 
Human respiratory microbiome

 
Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

 
Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

 

Human nearly-sterile sites 

 

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

 

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

 

Human gut microbiome

 
Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

 
The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

 
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

 
Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

 
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck –  mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

 
Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

 
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

 
Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

 
Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

 
Animal experiments 

 
Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

 
Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

 
Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

 

Animal microbiome

 

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu  – Proceedings of the Royal Society of London B

 
Plant, root, and soil microbiome

 
Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

 
Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia –  Keith Christian – Ecology & Evolution

 

Food microbiology

 

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

 
Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

 

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

 

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

 
Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

 
Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

 
Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

 

Microbes in the news 
NIPGR scientists identify bacteria that can devour fungi

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

 
The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine

September 14, 2017

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Events and jobs

Post-Doctoral Fellowship in Microbiology  – University of California, Irvine – Last date: December 8th, 2017

MICROBIOLOGY MANAGER – ICDS, County Waterford

 

General microbiome

Thesis: Anti-Staphylococcal Activity of Variovorax paradoxus EPS – P Holt-Torres – CSUSB Scholar Works

The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals – L Shaw – MBio

 

Pregnancy and early life

Mum’s bacteria linked to baby’s behaviour – CM Powell – Nature

Prenatal stress enhances susceptibility to allergic diseases of offspring – M Moustaki – Endocrine, Metabolic & Immune Disorders Drug Targets

Dietary intake of fat and fibre according to reference values relates to higher gut microbiota richness in overweight pregnant women – H Röytiö – The British Journal of Nutrition

 

Human respiratory microbiome

Dynamic oropharyngeal and faecal microbiota during treatment in infants hospitalized for bronchiolitis compared with age-matched healthy subjects – Q Hu – Scientific Reports

 

 

Human nearly-sterile sites 

The evolutionary logic of sepsis – L Rózsa – Infection, Genetics and Evolution

 

Human gut microbiome

C. difficile Microbiome Manipulation – J Wick – Infection Prevention

Review: Copy-catting host signalling molecules – A York – Nature Reviews Microbiology

Irritable bowel syndrome in Asia: pathogenesis, natural history, epidemiology and management – KA Gwee – Journal of Gastroenterology and Hepatology

Microbial Disruption Indices to Detect Colonization With Multidrug-Resistant Organisms – R Araos – Infection Control and Hospital Epidemiology

 

Animal experiments 

High Fat, High Fructose, High Cholesterol Feeding Causes Severe NASH and Cecal Microbiota Dysbiosis in Juvenile Ossabaw Swine – MR Panasevich – American Journal of Physiology

 

Animal microbiome 

Estimating Herd Immunity to Amphibian Chytridiomycosis in Madagascar Based on the Defensive Function of Amphibian Skin Bacteria – MC Bletz – Frontiers in Microbiology

Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing – X Wu – Scientific Reports

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars –  S Chaturvedi – Scientific Reports

Brevibacillus laterosporus isolated from the digestive tract of honeybees has high antimicrobial activity and promotes growth and productivity of honeybee’s colonies – JM Khaled – Environmental Science and Pollution Research

 

Plant, root, and soil microbiome

Review: The role of soil microorganisms in plant mineral nutrition – current knowledge and future directions – R Jacoby – Frontiers in Plant Science

Redox-mediated quorum sensing in plants – AW Fuller – PLoS One

Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L. – X Zhou – Journal of Basic Microbiology

Chapter: Analytical Interpretation of the Beneficial Interaction Between Microorganisms and Grasses – RG Machado – Intechopen

Effect of simultaneous and sequential inoculations of Meloidogyne incognita, Ralstonia solanacearum and Phomopsis vexans on eggplant in sand mix and fly ash mix soil – M Khan – Phytoparasitica

Effect of Soil Amendments on Microbial Resilience Capacity of Acid Soil Under Copper Stress – VC Mounissamy – The Bulletin of Environmental Contamination and Toxicology

Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems – C Potter – Scientific Reports

 

Built environment 

Response of anaerobic membrane bioreactor to the presence of nano-Bi2WO6: reactor performance, supernatant characteristics, and microbial community – L Chen – Environmental Science and Pollution Research

 

 

Bioinformatics

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome – SM Hücker – PLoS One

 

Techniques

Template Preparation Affects 16S rRNA High-throughput Sequencing Analysis of Phyllosphere Microbial – X Tian – Frontiers in Plant Science

Dissertation: Campylobacter concisus & Inflammatory Bowel Disease: – Insights through cultivation and whole-genome sequencing – KF Kirk – Aalborg Universitetsforlag

Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization – JE Hernández-Salmerón – Journal of Genomics

 

Microbes in the news

Researchers discover new, abundant enzyme that helps bacteria infect animals – Science Daily

Weight Loss Success Determined by Two Gut Microbiota Species – Gen Eng News

Dozens of people got diarrhea from puppy poop bacteria – The Verge

Children infected with rare bacteria during surgery at New Orleans hospital – UPI

‘Microbiomes’ may hold key to kids’ ear infections – UPI

CONDUCTING PLASTIC USED IN TOUCHSCREENS COULD HELP FIGHT — OR GROW — BACTERIA – Digital Trends

Why bacteria ‘shapeshift’ in space – CU Boulder Today

Gut Bacteria May Impact Multiple Sclerosis Progression – Genome Web

ARE BACTERIA THE ANSWERS TO ALL OUR SWEATY PROBLEMS? – Electric Runway