September 17, 2017

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

 

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September 16, 2017

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

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

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

September 5, 2017

Jobs

Postdoctoral fellow in genomics of uncultured microbial parasites (SciLifeLab, Sweden) via Science Careers

Call for Assistant Professors and Professors (IST Austria, including for Life Sciences) via Science Careers

 

Human Microbiome

Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection – Monica Di Paola – Scientific Reports

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy S.W. Wong – Microbiome (BMC)

Influence of Pregnancy History on the Vaginal Microbiome of Pregnant Women in their First Trimester – Dimitrios Nasioudis – Scientific Reports

Gut microbiome in ADHD and its relation to neural reward anticipation – Esther Aarts – PLoS ONE

A cross-sectional comparative study of gut bacterial community of Indian and Finnish children – Shreyas V. Kumbhare – Scientific Reports

Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine – Hailong Cao – Scientific Reports

Review article: the human intestinal virome in health and disease – S. R. Carding – Alimentary Pharmacology and Therapeutics

Review: Organ-specific protection mediated by cooperation between vascular and epithelial barriers – Ilaria Spadoni – Nature Reviews Immunology

Review: Microbiota of chronic diabetic wounds: ecology, impact and potential for innovative healing strategies – Sonia Gonçalves Pereira – Frontiers in Microbiology

Animal Microbiome

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer – Yimeng Li – Frontiers in Microbiology

High-fat diet increases pain behaviors in rats with or without obesity – Zongbin Song – Scientific Reports

Research Highlights: The microbiota maintains oxygen balance in the gut – Irene Vacca – Nature Reviews Microbiology

Studying the Differences of Bacterial Metabolome and Microbiome in the Colon between Landrace and Meihua Piglets – Zhuang Chen – Frontiers in Microbiology

Dietary heme induces gut dysbiosis, worsens colitis and potentiates the development of adenomas in mice – Marco Constante – Frontiers in Microbiology

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease – Myles R. Minter – Scientific Reports

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – Virginie Lemieux-Labonté – Microbiome (BMC)

 

Environmental and Soil Microbiome

Composted Cattle Manure Increases Microbial Activity and Soil Fertility More Than Composted Swine Manure in a Submerged Rice Paddy – Suvendu Das – Frontiers in Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria – Eveline M. van den Berg – Frontiers in Microbiology

Beneficial microbes

Lactobacillus casei BL23 produces microvesicles carrying proteins associated with its probiotic effect – Ana P. Domínguez Rubio – Frontiers in Microbiology

Probiotic mixture Golden Bifido prevents neonatal Escherichia coli K1 translocation via enhancing intestinal defense – Qing Zeng – Frontiers in Microbiology

Protective Effect of Akkermansia muciniphila against Immune-mediated Liver Injury in a Mouse Model – Wenrui Wu – Frontiers in Microbiology

 

Methods

Review: Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa W. Hugerth – Frontiers in Microbiology

Total rRNA-Seq analysis gives insight into bacterial, fungal, protozoal and archaeal communities in the rumen using an optimized RNA isolation method – Chijioke O. Elekwachi – Frontiers in Microbiology

Non-Microbiology picks

The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis – Julien Tripette – PeerJ

September 3, 2017

Events and jobs

PhD position – Jana Seifert, UNIVERSITÄT HOHENHEIM

PhD position – Amélia Camarinha Silva, UNIVERSITÄT HOHENHEIM

Microbiology Instructor – City College, Florida

Assistant/Associate/Full Professor (Clinical Microbiology) – University of Arizona

General microbiome

Targeting the Microbiome for Mental Health: Hype or Hope? – Jane A. Foster, Biological Psychiatry

Multi-site human microbiome

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome – Geoffrey D. Hannigan, bioRxiv

Human gut microbiome

Gut Protozoa: Friends or Foes of the Human Gut Microbiota? – Magali Chabé, Trends in Parasitology

Intestinal Lactobacillus in health and disease, a driver or just along for the ride? – Dustin D. Heeney, Current Opinion in Biotechnology

Human oral microbbiome

Periodontal disease and periodontal bacteria as triggers for rheumatoid arthritis – Zijian Cheng, Best Practice & Research Clinical Rheumatology

Animal experiments

Dietary broccoli impacts microbial community structure and attenuates chemically induced colitis in mice in an Ah receptor dependent manner – Troy D. Hubbard, Journal of Functional Foods

Gut health benefits of brown seaweed Ecklonia radiata and its polysaccharides demonstrated in vivo in a rat model – Suvimol Charoensiddhi, Journal of Functional Foods

Yacon flour (Smallanthus sonchifolius) attenuates intestinal morbidity in rats with colon cancer – Mariana Grancieri, Journal of Functional Foods

Plant, root, and soil microbiome

Acclimatization of micropropagated plants of Etlingera elatior(Jack) R. M. Sm. inoculated with arbuscular mycorrhizal fungi – A.R. da Silva, South African Journal of Botany

Effective rhizoinoculation and biofilm formation by arsenic immobilizing halophilic plant growth promoting bacteria (PGPB) isolated from mangrove rhizosphere: A step towards arsenic rhizoremediation – Ivy Mallick, Science of The Total Environment

Food microbiology

Acetic acid bacteria in fermented foods and beverages – Jonas De Roos, Current Opinion in Biotechnology

Microbial ecology of cereal vinegar fermentation: insights for driving the ecosystem function – Zhen-Ming Lu, Current Opinion in Biotechnology

Probiotics / prebiotics

Bugging allergy; role of pre-, pro- and synbiotics in allergy prevention – Christina E. West, Allergology International

The effect of probiotics and zinc supplementation on the immune response to oral rotavirus vaccine: A randomized, factorial design, placebo-controlled study among Indian infants – Robin P. Lazarus, Vaccine

Microbes in the News

Study finds high levels of multidrug-resistant bacteria on Indian poultry farms – Stephanie Soucheray, CIDRAP News

Topical antibiotics and antiseptics disrupt the skin microbiome – Cheryl Guttman Krader, Dermatology Times

August 31, 2017

Today we have a lot of interesting job offers, a lot of news, many papers from Nature’s Scientific Reports and several reviews from Immunological Reviews and to mention each time more and more papers dealing with wastewater treatments. Enjoy your (still) summer microbiome reading.

Events and jobs

Laboratory Manager (Microbiology), Sydney, Australia

Algae Technician, MBD Energy Limited, Townsville 

PhD position: Synthetic Microbiology/Biotechnology, Germany

PhD position (m/f) in the field of microbiota-host interaction in laying hens, Germany

PhD position in the field of microbial ecology of the fowl gastrointestinal tract,  Germany

Post-Doctoral Research Associate, King’s College London , UK

Synthetic Biologist / Geneticist: Ginkgo Bioworks, Boston, MA

General microbiome

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA – Mark Kowarsky – PNAS

Maintenance of microbial cooperation mediated by public goods in single and multiple traits scenarios – Özhan Özkaya – Journal of Bacteriology

Pregnancy and early life

The oral microbiome and adverse pregnancy outcomes – Charles M Cobb – International Journal of Women’s Health

Human respiratory microbiome

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci – Sanjay K. Shukla –  PLOS One

Sphenoid sinus microbiota in pituitary apoplexy: a preliminary study – Gavin J. Humphreys – Pituitary

Oral microbiology

Review: Studying the human oral microbiome: challenges and the evolution of solutions – Angela ML Benn – Australian Dental Journal

Human vaginal microbiome

The human vaginal microbial community – Mario Vaneechoutte – Research in Microbiology

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women – Benjamin J. Callahan – PNAS

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab – Anita Mitra – Scientific Reports

Human nearly-sterile sites 

Dominance of ST131 Escherichia coli carrying blaCTX-M in patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial –  Patrick Harris – bioRxiv

Temporal Stability and Composition of the Ocular Surface Microbiome – Jerome Ozkan – Scientific Reports

Human gut microbiome

Review:Interactions between bile salts, gut microbiota, and hepatic innate immunity – Kristin Schubert – Immunological Reviews

Review:Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – Thomas Clavel – Immunological Reviews

Review: Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease – Joseph M. Pickard – Immunological Reviews

Gut microbiota and chronic kidney disease: implications for novel mechanistic insights and therapeutic strategies – Wei Pan –  International Urology and Nephrology

Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota – Christopher Andrew Gaulke -bioRxiv

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses – Leonardo Mancabelli –  Scientific Reports

Influence of gut microbiota on neuropsychiatric disorders – María Carmen Cenit – World Journal of Gastroenterology

Fecal microbiota transplantation for Clostridium difficile infection in patients with ileal pouches – Nan Lan – Gastroenterology Report

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field – Vanessa C Harris – Open Forum Infectious Diseases

A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota – Ashok K. Sharma – Scientific Reports

Animal experiments

Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs – Zhen Tan – Frontiers in Microbiology

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract – Janina A. Krumbeck – Environmental Microbiology

Animal microbiome

High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion – Zhimin Zhang – Frontiers in Microbiology

Unraveling the gut microbiome of the long-lived naked mole-rat – Tewodros Debebe – Scientific Reports

Plant, root, and soil microbiome

Effects of cationic surfactant on the bioaccumulation of polycyclic aromatic hydrocarbons in rice and the soil microbial community structure – Ni Ni – RSC Advances

The impact of adsorption on the exposure assessment of Bacillus thuringiensis in the water-sediment system: a mathematical model approach – Stefano Cervelli – Biology and Fertility of Soils

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of a bean from Iran for controlling Rhizoctonia solani – Vahid Keshavarz-Tohid – Research in Microbiology

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities – Bachir Iffis – Frontiers in Microbiology

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching – Jiří Bárta – Scientific Reports

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China – Wei Z – PLOS One

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Water and extremophile microbiome 

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping – Katherine R. M. Mackey – Frontiers in Microbiology

Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland – Wenkai Yan – Frontiers in Microbiology

Microbial community structure and diversity within hypersaline Keke Salt Lake environments – Rui Han – Canadian Journal of Microbiology

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities – Bennett S. Lambert –  Nature Microbiology

Anaerobic methanotrophic communities thrive in deep submarine permafrost – Matthias Winkel – bioRxiv

Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China – Xue Zhou – Scientific Reports

Microbial communities in marine sediments modify success of an invasive macrophyte – Paul E. Gribben – Scientific Reports

Built environment 

Novosphingobium clariflavum sp. nov., isolated from a household product plant –  Xin Zhang – International Journal of Systematic and Evolutionary Microbiology

Probiotics / prebiotics

Bifidobacterium longum W11: an antibiotic-resistant probiotic – Francesco Di Pierro – Nutrafoods

Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice – Hongqi Chen – Molecular Medicine Reports

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Probiotics administration following sleeve gastrectomy surgery: A randomized double-blind trial – S Sherf-Dagan – International Journal of Obesity

Phages and viruses

Infection with purified Piscine orthoreovirus demonstrates a causal relationship with heart and skeletal muscle inflammation in Atlantic salmon – Øystein Wessel  – PLOS One

HPeV-3 predominated among Parechovirus A positive infants in the summer of 2013-2014 in Queensland, Australia – Donna M. McNeale – bioRxiv

Review: A bacteriophages journey through the human body – Jeremy J. Barr – Immunological Reviews

Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity – James Brett Case – bioRxiv

Bioinformatics

microPop: Modelling microbial populations and communities in R – Helen Kettle – Methods in Ecology and Evolution

Biotechnology

Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins – Diogo A.M. Alexandrino – New Biotechnology

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community – Man Zhou – Biotechnology for Biofuels

Wastewater microbiology

Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment – Hebin Liang – RSC Advances

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment – Yaohui Bai – Applied Microbiology and Biotechnology

Techniques

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups – Alexandra Jeuck – Protist

Fast and Simple Tool for the Quantification of Biofilm-Embedded Cells Sub-Populations From Fluorescent Microscopic Images – Mikhail Bogachev – bioRxiv

Microbes in the news 

Gut bacteria that “talk” to human cells may lead to new treatments

Gut Microbiome Differences in REM Sleep Behavior Disorder, Parkinson’s, and Healthy Controls

Scientists Made Music From the Human Microbiome, and It’s Seriously Cool

Over 50% of Bacteria and Viruses inside Human Body are Unknown to Science