September 20, 2017

 

General microbiome

The human bitter taste receptor T2R38 is broadly tuned for bacterial compounds –  C Verbeurgt – PLoS One

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities. – J Juhász – Biology Direct

Applying allometric theory to fungi – CA Aguilar-Trigueros – The ISME Journal

The Editorial on the Research Topic The Impact of Microorganisms on Consumption of Atmospheric Trace Gases – S Kolb – Frontiers in Microbiology

 

Human oral microbiome

Variations in oral microbiota associated with oral cancer. – H Zhao – Scientific Reports

Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. – M Kuboniwa – Nature Microbiology

 

 

Human gut microbiome

Normalization of the microbiota in patients after treatment for colonic lesions – MA Sze – bioRxiv

Review: Modulation of the gut microbiome: a systematic review of the effect of bariatric surgery. – Y Guo – European Journal of Endocrinology

Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. – T Pavlova – Analytica Chimica Acta

Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes. – K Winglee – Microbiome

Continued Alcohol Misuse in Human Cirrhosis is Associated with An Impaired Gut-Liver Axis. – JS Bajaj – Alcoholism, Clinical and Experimental Research

Fructooligosaccharide (FOS) and Galactooligosaccharide (GOS) Increase Bifidobacterium but Reduce Butyrate Producing Bacteria with Adverse Glycemic Metabolism in healthy young population. – F Liu – Scientific Reports

 

Animal experiments 

Experimental colitis delays and reduces the severity of collagen-induced arthritis in mice – J Hablot – PLoS One

Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA – M DiMarzio – PLoS One

The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice – M Elderman – PLoS One

Review:Role of the gastrointestinal microbiota in small animal health and disease. – A Redfern – The Veterinary Record

Gut Microbiota and IL-17A: Physiological and Pathological Responses. – B Douzandeh-Mobarrez – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The microbiota of water buffalo milk during mastitis – C Catozzi – PLoS One

What determines sclerobiont colonization on marine mollusk shells? – VO Agostini – PLoS One

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. – KH Sharp – Microbiome

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen. – HT Do – Asian-Australasian Journal of Animal Sciences

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India. – SS Charan – Medical and Veterinary Entomology

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions. – F Cornejo-Granados – Scientific Reports

 

Plant, root, and soil microbiome

Evolution with a seed bank: the population genetic consequences of microbial dormancy – WR Shoemaker – bioRxiv

Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longispora albida and Longisporafulva. – C Piao – International Journal of Systematic and Evolutionary Microbiology

Actinomycetes benefaction role in soil and plant health. – AA Bhatti – Microbial Pathogenesis

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation – I Alkorta – FEMS Microbiology Letters

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey. – L Zhang – FEMS Microbiology Ecology

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe. – M Delgado-Baquerizo  – Ecology Letters

Paenibacillus arcticus sp. nov., isolated from Arctic soil. – IT Cha – International Journal of Systematic and Evolutionary Microbiology

Mineral phosphorus fertilization modulates interactions between maize, rhizosphere yeasts and arbuscular mycorrhizal fungi – M Sarabia – Rhizosphere

Zinc Solubilizing Bacillus cereus and related species Modulates Growth, Yield and Zinc Biofortification of Soybean and Wheat Seeds Cultivated in Central India – R Khande – Rhizosphere

Utilisation of mucilage C by microbial communities under drought – MA Ahmed – Biology and Fertility of Soils

 

Built environment

Walker occupancy has an impact on changing airborne bacterial communities in an underground pedestrian space, as small-dust particles increased with raising both temperature and humidity – T Okubo – PLoS One

 

Food microbiology

Diversity and dynamics stability of bacterial community in traditional solid-state fermentation of Qishan vinegar – X Gan – Annals of Microbiology

 

Phages and viruses

Isolation and identification of enteroviruses from sewage and sewage-contaminated water samples from Ibadan, Nigeria, 2012-2013. – JA Adeniji – bioRxiv

The virome of Drosophila suzukii, an invasive pest of soft fruit – NC Medd – bioRxiv

Immune Loss as a Driver of Coexistence During Host-Phage Coevolution – JL Weissman – bioRxiv

 

Bioinformatics

Bioinformatics in the Netherlands: the value of a nationwide community  – CWG  van Gelder – Briefings in Bioinformatics

 

Techniques

Longitudinal multiparameter single-cell analysis of macaques immunized with pneumococcal protein-conjugated or unconjugated polysaccharide vaccines reveals distinct antigen specific memory B cell repertoires – B Lia – PLoS One

Methods matter: Influential purification and analysis parameters for intracellular parasite metabolomics – MA Carey – bioRxiv

COREMIC: a web-tool to search for a root-zone associated CORE MICrobiome – RR Rodrigues – bioRxiv

Quorum sensing improves current output with Acidithiobacillus ferrooxidans. – N Chabert – Microbial Biotechnology

Transcriptome analysis of Pseudostellaria heterophylla in response to the infection of pathogenic Fusarium oxysporum. – X Qin – BMC Plant Biology

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. – Y Daquerre – BMC Genomics

 

Microbes in the news

Rocks, not bacteria, triggered Earth’s oxidation – Cosmos

The Table At Your Favorite Restaurant May Be Way Grosser Than You ThoughtThe Table At Your Favorite Restaurant May Be Way Grosser Than You Thought – Men’s Health

Researchers unlock potential pathway to treat flesh-eating bacteria – Phys.org

Revealed: The nasty infections you can pick up at the gym – and how to avoid deadly bacteria lingering on your workout gear  – Daily Mail Online

Flagship seeks $500M for sixth fund; unveils another microbiome firm – Fierce Biotech

CAN SPRAYING BACTERIA IN YOUR FACE ACTUALLY HAVE HEALTH BENEFITS? – CDA Press

Space-Grown Bacteria Could Pose Major Problems for Astronauts – Health Line

See jerkface bacteria hiding in tumors and gobbling chemotherapy drugs – Ars Technica

How BIOHM’s At Home Candida Test Is Giving Consumers Peace of Mind – Forbes

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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

 

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 9, 2017

 

Pregnancy and early life

Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants – MA Stanislawski – Microbiome

 

Human oral microbiome

The tongue microbiome in healthy subjects and patients with intra-oral halitosis – SK Seerangaiyan – Journal of Breath Research

Effects of lactoferrin and lactoperoxidase-containing food on the oral microbiota in the elderly – M Nakano – Microbiology & Immunology

Unraveling the human salivary microbiome diversity in Indian populations – A Sarkar – PLoS One

 

 

Human gut microbiome

Review: Influence of gut microbiota on the development and progression of nonalcoholic steatohepatitis – F de Faria Ghetti – European Journal of Nutrition

Markers of intestinal permeability are already altered in early stages of non-alcoholic fatty liver disease: Studies in children – A Nier – PLoS One

Review: the human intestinal virome in health and disease – SR Carding – AP &T

Meds Modify Microbiome, Mediating Their Effects – NM Koropatkin – Cell Metabolism

 

Animal experiments

Maternal treatment with short-chain fatty acids modulates the intestinal microbiota and immunity and ameliorates type 1 diabetes in the offspring – JC Needell – PLoS One

The intestinal microbiota determines the colitis-inducing potential of T-bet-deficient Th cells in mice – J Zimmermann – European Journal of Immunology

A study of the prebiotic-like effects of tomato juice consumption in rats with diet-induced non-alcoholic fatty liver disease (NAFLD). – FJ García-Alonso – Food & Function

Patterns of host gene expression associated with harboring a foregut microbial community. – KD Kohl – BMC Genomics

 

Animal microbiome 

Bacterial community composition and distribution in different segments of the gastrointestinal tract of wild-caught adult Penaeus monodon – P Mongkol – Aquaculture Research

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome – V Lemieux-Labonté – Microbiome

 

Plant, root, and soil microbiome

Soil microbiomes associated with Verticillium wilt suppressive broccoli and chitin amendments are enriched with potential biocontrol agents.  – P Inderbitzin – Phytopathology

Olive mill waste and glyphosate-based herbicide addition to olive grove soils: effects on microbial activities and their responses to drying–rewetting cycles – N Boukhdoud – Soil Use and Management

Changes in soil microbial communities after 10 years of winter wheat cultivation versus fallow in an organic-poor soil in the Loess Plateau of China – H Tian – PLoS One

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata. – M Gllart – Microbial Ecology

Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.). – ZF Yan – Int. J. Syst. Evol. Microbiol.

 

Water microbiome and extremophile 

Microbial ecological associations in the surface sediments of Bohai strait –  B Wang – Chinese Journal of Oceanology and Limnology

Contrasting seasonal drivers of virus abundance and production in the North Pacific Ocean. – PJ Gainer – PLoS One

 

Built environment 

Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: key process parameters and microbial indicators of process instability – J Lee – Bioresource Technology

 

 

Phages and viruses

Temperate phages as frequency-dependent weapons in bacterial competition – XY Li – bioRxiv

 

Techniques

A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network. – S Zou – PLoS One

Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome – SF Rahman – bioRxiv

Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. – C Agrimonti – Critical Reviews in Food Science and Nutrition

Identification of regulatory targets for the bacterial Nus factor complex – G Baniulyte – bioRxiv

Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study – S Langevin – The Journal of General Virology

Infection via mosquito bite alters Zika virus replication kinetics in rhesus macaques – D Dudley – bioRxiv

Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1 – F Mauffrey – bioRxiv

 

Microbes in the news 

Mimicry: by gut bacteria metabolites – Nutra Ingredients

Bacterial ‘aphrodisiac’ sends single-celled organism into mating frenzy – Nature News

Bacteria Use Brainlike Bursts of Electricity to Communicate – Quanta Magazine

Bacteria in Children’s Throats Found Strongly Associated with Bone and Joint Infections – Geneng News

How Farmers Can Help Ensure That We Don’t All Die From Super-Powered Bacteria – Fast Company

Harvey’s Floodwaters Contaminated With Nasty, Dangerous Bacteria – Houston Press

FOR THE FIRST TIME, GUT BACTERIA HAS BEEN SPOTTED EATING CHEMICALS IN THE BRAIN – Collective Evolution

University of Idaho research may slow antibiotic resistance to drugs – The Spokesman

 

August 26, 2017

Jobs and Events

PhD Scholarship in Metagenomics, Infectious Diseases, and Antibiotic Resistance – Technical University of Denmark – Closing date: September 22, 2017.

 

General microbiome

The role of hospital toilets in microbial dissemination and the effectiveness of ultraviolet C irradiation – J Cooper – Open Library UBC

 

 

Human skin microbiome

Review: The skin microbiome: impact of modern environments on skin ecology, barrier integrity, and systemic immune programming – SL Prescott – World Allergy Organization Journal

 

Human vaginal microbiome

Review: Women and Their Microbes: The Unexpected Friendship – JA Younes – Cell

 

Human gut microbiome

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania – SA Smits – Science

Normalization of the microbiota in patients after treatment for colonic lesions – MA Sze – bioRxiv

C4B gene influences intestinal microbiota through complement activation in patients with Pediatric-Onset Inflammatory Bowel Disease – E Nissilä- Clin Exp Immunol.

The Microbiome in Crohn’s Disease: Role in Pathogenesis and Role of Microbiome Replacement Therapies – S Khanna – Gastroenterol Clin North Am.

 

Animal experiments 

Effects of polysaccharide from Physalis alkekengi var. francheti on liver injury and intestinal microflora in type-2 diabetic mice – X Zhao – Pharm Biol.

 

Animal microbiome 

Two Gut-Associated Yeasts in a Tephritid Fruit Fly have Contrasting Effects on Adult Attraction and Larval Survival – AM Piper – J Chem Ecol.

Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome – CG Becker – Proc Biol Sci.

Beneficial microbial signals from alternative feed ingredients: a way to improve sustainability of broiler production? – F Van Immerseel – Microb Biotechnol.

 

Plant, root, and soil microbiome

Tiny Microbes, Big Yields: enhancing food crop production with biological solutions – P Trivedi – Microb Biotechnol.

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimeter-scale depth gradients – A Bourceret – Can J Microbiol.

 

Water microbiome and extremophile 

Review: Strategies and ecological roles of algicidal bacteria – N Meyer – FEMS Microbiology Reviews

Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films – E Syranidou – PLoS One

The Response of Heterotrophic Prokaryote and Viral Communities to Labile Organic Carbon Inputs Is Controlled by the Predator Food Chain Structure – RA Sandaa – Viruses

 

Built environment 

The impact of immigration on microbial community composition in full-scale anaerobic digesters – RH Kirkegaard – Scientific Reporters

Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters – L Wu – ISME Journal

 

Food microbiology

Bacterial DNA Detected in Japanese Rice Wines and the Fermentation Starters – M Terasaki – Current Microbiology

Emergence of Leuconostoc mesenteroides as a causative agent of oozing in carrots stored under non-ventilated conditions – Y Lampert – Microb Biotechnol.

 

 

Techniques

A PCR-based assay targeting the major capsid protein gene of a dinorna-like ssRNA virus that infects coral photosymbionts – JL Montalvo-Proaño – Aquatic Microbiology

Microbiome balance in sputum determined by PCR stratifies COPD exacerbations and shows potential for selective use of antibiotics – K Halder – PLoS One

Antibiotic exposure and risk of weight gain and obesity: protocol for a systematic review – H Dutton – Systematic Reviews

High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared to low dairy intake in overweight individuals in a Randomized Controlled Trial – LQ Bendtsen – Appl Physiol Nutr Metab.

Proteomic Analysis of Vibrio parahaemolyticus Under Cold Stress – J Tang – Current Microbiology

 

Microbes in the news

Gut Microbiome and Anxiety Linked to MicroRNA – Geneng News

Got A Computer? Your Help Is Wanted On A Groundbreaking Study – Miami CBS Local

Chronic Stress Discombobulates Gut Microbiome Communities – Psychology Today

 

August 18, 2017

Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

 

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

 

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

 

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

 

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang –  Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia –  Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

 

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal –  Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

 

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

 

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

 

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa  – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

 

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

 

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari –  BMC Bioinformatics

 

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer ​- PeerJ preprints

 

August 10, 2017

Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform