Category Archives: Microbes in the News

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 7, 2017

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Events and jobs

Director of the Microbiome Research Laboratory – UT Southwestern

DOCTORAL STUDENT OR POSTDOCTORAL RESEARCHER –  Faculty of Veterinary Medicine, University of Helsinki – Application deadline: Nov 5, 2017

 

General microbiome

Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production – Y Boltyanskaya – Antonie van Leeuwenhoek

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. – MA Engevik – Microbiology Spectrum

 

Pregnancy and early life

Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father – LC Kenny – bioRxiv

 

Human respiratory microbiome

Long-term effects of inhaled corticosteroids on sputum bacterial and viral loads in COPD. – M Contoli – The European Respiratory Journal

 

 

Human gut microbiome

Bifidobacteria and the infant gut: an example of co-evolution and natural selection. – F Turroni – Cellular and Molecular Life Sciences

Inflammatory bactericidal lectin RegIIIβ: Friend or Foe for the host? – T Miki – Gut Microbes

Review: Host-microbiota interplay in mediating immune disorders. – KM Felix – Annals of the New York Academy of Sciences

Review: Probiotics for the prevention of Hirschsprung-associated enterocolitis: a systematic review and meta-analysis. – H Nakamura – Pediatric Surgery International

 

Animal experiments 

Can intestinal microbiota be associated with non-intestinal cancers? – C Jacqueline – Scientific Reports

Gnotobiotics: getting a grip on the microbiome boom – S Mallapaty – Lab Animal

Nanoparticle curcumin ameliorates experimental colitis via modulation of gut microbiota and induction of regulatory T cells. – M Ohno – PLoS One

 

Animal microbiome 

Comparative analysis of microbial communities associated with bacteriomes, reproductive organs and eggs of the cicada Subpsaltria yangi. – D Wang – Archives of Microbiology

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. – H Shen – Microbiology Open

Elucidating the microbial community associated with the protein preference of sludge degrading worms – S de Valk – Environmental Technology

 

Plant, root and soil microbiome

Mycorrhizal fungi show regular community compositions in natural ecosystems. – E Verbruggen – The ISME Journal

Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays – J Vacheron – Molecular Plant-Microbe Interactions

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development. – SC Castle – Oecologica

 

Water microbiome and extremophile 

Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. – D Kalenitchenko – The ISME Journal

Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages – BS  Park – Marine and Freshwater Research

Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. – R Rathour – Genome Announcements

 

Built environment 

Managing the excessive proliferation of glycogen accumulating organisms in industrial activated sludge by nitrogen supplementation: A FISH-NanoSIMS approach – CA Onetto – Systematic and Applied Microbiology

 

 

Phages and viruses

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. – G Freer – Current Medicinal Chemistry

 

Techniques

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing – P Schwendner – Microbiome

 

Microbes in the news

Puppies Linked To Bacterial Infection Outbreak Across 12 States – Forbes

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

Episode Review: VICE’s ‘Post-Truth News and Microbiome’ – The Hoya

Second grade handwashing experiment leads to big decrease in bacteria, illness – EurekAlert

Validating microbiome claims:Including the latest DNA techniques-Formulation Summit – Cosmetics Design Europe

Macromolecules: Weapons in the Fight Against Antibiotic Resistance  – American Veterinarian

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

Bacteria can spread antibiotic resistance through soil – Phys.org

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 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 29, 2017

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General microbiome

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria – I. Martínez, Journal of Biotechnology

Biofilms: Survival and defense strategy for pathogens – Ashutosh Kumar, International Journal of Medical Microbiology

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities – Zhao Yang-Guo, Environmental Engineering Science

Comparison of the impacts of zinc ions and zinc nanoparticles on nitrifying microbial community – Qiang Wu, Journal of Hazardous Materials

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

Pregnancy and early life

Impact of delivery mode on the colostrum microbiota composition – Marco Toscano, BMC Microbiology

Multi-site human microbiome

Human Microbiome in Brazil – Luciana Campos Paulino, The Brazilian Microbiome

Forensic genetics and genomics: Much more than just a human affair – Miguel Arenas, PLoS Genetics

South Asian Health: Inflammation, Infection, Exposure, and the Human Microbiome – Jennifer Leng, Journal of Immigrant and Minority Health

Natural Products as Platforms To Overcome Antibiotic Resistance – Sean E. Rossiter, Chemical Reviews

Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis – Gabriel Horta-Baas, Journal of Immunology Research

Human respiratory microbiome

Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period – Juan de Dios Caballero, mBio

Sputum microbiota in severe asthma patients: Relationship to eosinophilic inflammation – Naijian Li, Respiratory Medicine

Human skin microbiome

Culture characterization of the skin microbiome in type 2 diabetes mellitus: a focus on the role of innate immunity – Akshay Thimmappaiah Jagadeesh, Diabetes Research and Clinical Practice

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt, Epidemiology

Human gut microbiome

Bacterial chat: intestinal metabolites and signals in host -microbiota -pathogen interactions – Bruna C. Lustri, Infection and Immunity

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

Molecular basis of gut microbiome-associated colorectal cancer: A synthetic perspective – Alan R. Healy, Journal of American Chemical Society

Metagenomic Paleomicrobiology Characterizes Fecal Microbiomes and Viromes of Pre-Columbian Cultures from Vieques, Puerto Rico – Jessica I. Rivera-Perez, ProQuest

A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota – Henry Watson, BMJ Journals

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer – Scott G. Daniel, mSystems

The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species – Aaron W. Miller, mSystems

Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron – Zachary A. Costliow, mSystems

Human oral microbiome

Host Genetic and Environemental Associations and the Human Salivary Microbiome – Brittany Ann Demmitt, ProQuest

Animal microbiome

Pathogenesis of oral FIV infection – Craig Miller, PLoS ONE

Photosynthetic epibionts and endobionts of Pacific oyster shells from oyster reefs in rocky versus mudflat shores – Laurent Barillé, PLoS ONE

Free-living and captive turtles and tortoises as carriers of new Chlamydia spp. – Agata Mitura, PLoS ONE

Microbiomes Associated with Animals: Implications for Livestock and Animal Production – Hilario Cuquetto Mantovani, The Brazilian Microbiome

Maintenance of distal intestinal structure in the face of prolonged fasting: A comparative examination of species from five vertebrate classes – Marshall D. McCue, The Anatomical Record

Plant, root, and soil microbiome

Assessment of derelict soil quality: Abiotic, biotic and functional approaches – Quentin Vincent, Science of The Total Environment

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza, PLoS ONE

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira, PLoS ONE

Temporal dynamics in microbial soil communities at anthrax carcass sites – Karoline Valseth, BMC Microbiology

Pyrosequencing reveals soil enzyme activities and bacterial communities impacted by graphene and its oxides – Yan Rong, Journal of Agriculture and Food Chemistry

Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome – Chao Xue, Biology and Fertility of Soils

The Brazilian Soil Microbiome – Fernando Dini Andreote, The Brazilian Microbiome

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria – Junwei Zhao, International Journal of Systematic and Evolutionary Microbiology

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem – Yi Hao, Environmental Pollution

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime, ISME

Jaminaea pallidilutea sp. nov. (Microstromatales), a basidiomycetous yeast isolated from plant material of mangrove forests in Iran – Shaghayegh Nasr, International Journal of Systematic and Evolutionary Microbiology

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa) – Swapnil Sapre, Microbiological Research

Bacterial traits and quality contribute to the diet choice and survival of bacterial-feeding nematodes – Ting Liu, Soil Biology and Biochemistry

A novel Burkholderia ambifaria strain able to degrade the mycotoxin fusaric acid and to inhibit Fusarium spp. growth – Ester Simonetti, Microbiological Research

Impact of herbicide application on Beneficial soil microbial community, Nodulation and Yield parameters of chickpea (Cicer arietinum L.) – Raghavendra, K. S, Bulletin of Environment, Pharmacology and Life Sciences

Isolation And Characterization of Phosphate Solubilizing Microorganisms From Maize Rhizosperic Soils – S. Vinod Babu, Bulletin of Environment, Pharmacology and Life Sciences

Aerobic deterioration of corn stalk silage and its effect on methane production and microbial community dynamics in anaerobic digestion – Huan Zhang, Bioresource Technology

Plant Microbiome: Composition and Functions in Plant Compartments – Maike Rossmann, The Brazilian Microbiome

Changing soil legacies to direct restoration of plant communities – E Pernilla Brinkman, AoB Plants

Water and extremophile microbiome

Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment – Andrea Highfield, Viruses

Shifts in diversity and function of lake bacterial communities upon glacier retreat – Hannes Peter, ISME

Expression and characterization of a new heat-stable endo-type alginate lyase from deep-sea bacterium Flammeovirga sp. NJ-04 – Benwei Zhu, Extremophiles

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams – Jacob R. Price, Science of The Total Environment

Insight into the microbial community and its succession of a coupling anaerobic-aerobic biofilm on semi-suspended bio-carriers – Bing Tang, Bioresource Technology

Acclimation to extremely high ammonia levels in continuous biomethanation process and the associated microbial community dynamics – Hailin Tian, Bioresource Technology

Effect of hydraulic retention time on microbial community in biochemical passive reactors during treatment of acid mine drainage – Yaneth Vasquez, Bioresource Technology

Microbial megacities fueled by methane oxidation in a mineral spring cave – Clemens Karwautz, ISME

Built environment

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces – Rachel I. Adams, Microbiome

Food microbiology

Traditional Norwegian Kveik Yeasts: Underexplored Domesticated Saccharomyces cerevisiae Yeasts – Richard Preiss, bioRxiv

Probiotics / prebiotics

Prebiotic Oligosaccharides: Special Focus on Fructooligosaccharides, Its Biosynthesis and Bioactivity – Sudhir P. Singh, Applied Biochemistry and Biotechnology

Single-strain vs multi-strain probiotic supplementation strategy against rheumatoid arthritis – Giancarlo Ceccarelli, Arthritis and Rheumatology

The Genomic Basis of Lactobacilli as Health-Promoting Organisms –  Elisa Salvetti, Microbiology Spectrum

Phages and viruses

Phage mobility is a core determinant of phage-bacteria coexistence in biofilms – Matthew Simmons, bioRxiv

Bioinformatics

Bioinformatics for Microbiome Research: Concepts, Strategies, and Advances – Leandro Nascimento Lemos, The Brazilian Microbiome

Techniques

A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes – Michelle Spoto, bioRxiv

Direct PCR offers a fast and reliable alternative to conventional DNA isolation methods for animal gut microbiomes – Elin Videvall, bioRxiv

Microbes in the news

Artwork brings ‘echoes of DNA’ to UB’s new medical school building – ELLEN GOLDBAUM, UBNow

JooMo launches new body wash with skin bacteria tech – Lucy Whitehouse, Cosmetics Design Europe

September 27, 2017

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Human oral microbiome

Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions – Baek K – Journal of Dental Research

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt – Sexually Transmitted Infections

Human gut microbiome

[Review] Modulation of Type 1 Diabetes Risk by the Intestinal Microbiome – Knip M – Current Diabetes Reports

[Review] The Relationship Between the Human Genome and Microbiome Comes into View – Julia K. Goodrich – Annual Review of Genetics

Animal microbiome

[pre-print] The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C. Medd – bioRxiv

Characterisation of North American Brucella isolates from marine mammals – Adrian M. Whatmore – PLOS ONE

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach – Ann Arfken – PLOS ONE

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology – Sarah E. Macdonald – PLOS ONE

Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps – Gianluigi Mauriello – PLOS ONE

Plant, root, and soil microbiome

Multiscale Investigation on Biofilm Distribution and its Impact on Macroscopic Biogeochemical Reaction Rates – Zhifeng Yan – Water Resources Research

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia – Tarek A. A. Moussa – PLOS ONE

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing – Ou Li – PLOS ONE

A secreted antibacterial neuropeptide shapes the microbiome of Hydra – René Augustin – Nature Communications

Probiotics / prebiotics

Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy – Minseok Seo – PLOS ONE

Bioinformatics

Predicting metabolic adaptation from networks of mutational paths – Christos Josephides & Peter S. Swain – Nature Communications

Microbes in the news 

Florida Seawater Bacteria Death Toll Rises – Patch

Researchers Find New Microbial Communities in Human Body

Microbes on the market

Paris-based Eligo Bioscience secures $20 million to bring Precision Medicine to the Microbiome – EU-Startups

Science, publishing, and career

New open-access journal Metabarcoding & Metagenomics joins the lines of publisher Pensoft – EurekAlert!

Ed’s non-microbiology picks

Infants make more attempts to achieve a goal when they see adults persist – Julia A. Leonard – Science

University of Tokyo pair invent loop-based quantum computing technique

Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen–specific CTLs – Michael C. Brown – Science Translational Medicine

Stereodivergent synthesis with a programmable molecular machine – Salma Kassem, – Nature

Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques – Ling Xu – Science

September 26, 2017

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Today’s digest is a delight for dog lovers – an interesting look at the nasal microbiome of dogs and two interesting studies on freshwater phages. Lastly, researchers in South Korea establish a human stool bank.

Human Gut Microbiome

REVIEW: A review of the relationship between the gut microbiota and amino acid metabolism

Lin R.Amino Acids

Advanced glycation end products dietary restriction effects on bacterial gut microbiota in peritoneal dialysis patients; a randomized open label controlled trial

Yacoub R. PloS one

Oral Microbiome

Exploring the salivary microbiome of children stratified by the oral hygiene index

Mashima I. PLoS ONE

Animal experiments and microbiome

Ground Juniperus pinchotii and urea in supplements fed to Rambouillet ewe lambs Part 2: Ewe lamb rumen microbial communities

Ishaq SL. Journal of Animal Science

Characterization of the nasal and oral microbiota of detection dogs

Isaiah A. PLoS one

Marine and Inland Water microbiome 

Biodiversity and species competition regulate the resilience of microbial biofilm community

Feng K. Molecular Ecology

Plant and soil microbiome

The Fructan Syndrome: Evolutionary Aspects and Common Themes Among Plants and Microbes

Versluys M. Plant, Cell & Environment

Agricultural land use determines functional genetic diversity of soil microbial communities

Manoharan L. Soil Biology and Biochemistry

Synergetic suppression of soybean cyst nematodes by chitosan and Hirsutella minnesotensis via the assembly of the soybean rhizosphere microbial communities

Mwaheb MAMA .Biological Control

Patterns and mechanisms of responses by soil microbial communities to nitrogen addition

Zhou Z. Soil Biology and Biochemistry

Links between plant and fungal diversity in habitat fragments of coastal shrubland.

Maltz MR. PloS one

The response of soil bacterial communities to mining subsidence in the west China aeolian sand area

Shi P. Applied Soil Ecology

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

Moussa TAA. PLoS one

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

David AS. Molecular Ecology

Virome

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the deep chlorophyll maximum of the South China Sea

Xie ZX. Environmental Microbiology

Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group

Moon K. Environmental Microbiology

Protocol

Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA …

Han P. Applied Microbiology and Biotechnology

Use of RNALater® Preservation for Virome Sequencing in Outbreak settings

Kohl C.Frontiers in Microbiology

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince C. Genome Biology

Microbiome News

Korea’s first stool bank gets down to business

-Korean Biomedical Review

September 25, 2017

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General microbiome

Comprehensive analysis of central carbon metabolism reveals multiple connections between nutrients, biosynthetic capacity, and cell morphology in Escherichia coli – CS Westfall – bioRxiv

 

 

Human oral microbiome

Periodontal Pathogen Colonization in Young Children by PCR Quantification – A Longitudinal Survey. – K Takahashi – The Journal of Clinical Pediatric Dentistry

 

 

Human nearly-sterile sites 

The Gut Microbial Metabolite Trimethylamine-N-Oxide Is Present in Human Cerebrospinal Fluid. – D Del Rio – Nutrients

 

Human gut microbiome

Obesity increases the risk of small intestinal bacterial overgrowth (SIBO). – BC Roland – Neurogastroenterology & Motility

Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients With Metabolic Dysfunction. –  C Haro – Molecular nutrition & Food Research

The Gut Microbiota and Pediatric Multiple Sclerosis: Recent Findings. – H Tremlett – Neurotherapeutics

Review: Role of the intestinal microbiota in the immunomodulation of influenza virus infection. – CJ Chen – Microbes and Infection

Effect of vitamin A supplementation on gut microbiota in children with autism spectrum disorders – a pilot study. – J Liu – BMC Microbiology

Modulation of the gut microbiota: a focus on treatments for irritable bowel syndrome. – LA Harris – Postgraduate Medicine

Gut Microbiome-based Therapeutics in Liver Cirrhosis: Basic Consideration for the Next Step. – H Fukui – Journal of Clinical and Translational Hepatology

 

Animal experiments 

Effects of dietary threonine supplementation on intestinal barrier function and gut microbiota of laying hens. – XY Dong – Poultry Science

Lack of NLRP3-inflammasome leads to gut-liver axis derangement, gut dysbiosis and a worsened phenotype in a mouse model of NAFLD. – P Irene – Scientific Reports

RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice. – ZD Fu – Drug Metabolism and Disposition

Differential effects of rice bran cultivars to limit Salmonella Typhimurium in chicken cecal in vitro incubations and impact on the cecal microbiome and metabolome. – PM Rubinelli – PLoS One

Houttuynia cordata Facilitates Metformin on Ameliorating Insulin Resistance Associated with Gut Microbiota Alteration in OLETF Rats. – JH Wang – Genes (Basel)

Lack of Effect of Murine Astrovirus Infection on Dextran Sulfate-induced Colitis in NLRP3-deficient Mice. – SR Compton – Comparative Medicine

 

Animal microbiome 

A distinctive and host-restricted gut microbiota in populations of a cactophilic Drosophila species. – VG Martinson – Applied and Environmental Microbiology

Gastrointestinal microbial population of turkey (Meleagris gallopavo) affected by hemorrhagic enteritis virus. – S D’Andreano – Poultry Science

 

Plant, root, and soil microbiome

Colonization of Paracoccus sp. QCT6 and Enhancement of Metribuzin Degradation in Maize Rhizosphere Soil. – X Huang – Current Microbiology

Verrucosispora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. – QY Xie – Antonie van Leeuwenhoek

Oomycete Communities Associated with Reed Die-Back Syndrome. – M Cerri – Frontiers in Plant Science

 

Water and extremophile microbiome 

Depth distribution and assembly of sulfate-reducing microbial communities in marine sediments of Aarhus Bay. – LM Jochum – Applied and Environmental Microbiology

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters. – CC Lesaulnier – Microbiome

 

Built environment 

Metagenomic characterization of ambulances across the USA. – NB O’ Hara – Microbiome

 

Food microbiology

Comparative analysis of the microbial communities in raw milk produced in different regions of Korea. – IS Kim – Asian-Australasian Journal of Animal Sciences

 

 

Techniques

DNA microarray assay and real-time PCR as useful tools for studying the respiratory tract Mycoplasma populations in young dairy calves. – M Bottinelli – Journal of Medical Microbiology

 

Microbes in the news

London Underground covered in vomit and diarrhoea-inducing bacteria found in human POO – Daily Star

BioArt and Bacteria Exhibition is Coming to Oxford – Labiotech.eu

Drug-resistant bacteria emerge from drug companies’ untreated effluents – The Hindu

Vivid green bacteria bloom in the river running through Toledo – Michigan Radio

Kingwood woman dies from flesh-eating bacteria after cutting elbow in flooded home, officials say  – Click2Houston

Microbiome-Derived Immune Modulators (Pediatric) – Puretech Health

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