Category Archives: Plant Root Soil microbiome

September 17, 2017

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Sunday dose- lots of techniques and news on microbes!

Events and jobs

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

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

 

General microbiome

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

 

 

Human nearly-sterile sites 

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

 

Human gut microbiome

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

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

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

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

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

 

Animal experiments

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

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

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

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

 

Animal microbiome 

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

 

Plant, root and soil microbiome

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

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

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

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

 

Built environment 

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

 

Food microbiology

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

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

 

 

Techniques

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

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

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

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

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

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

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

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

 

Microbes in the news

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

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

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

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

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

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

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

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

 

September 16, 2017

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Events and jobs

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

 

General microbiome

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

 

Pregnancy and early life

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

 

 

Human gut microbiome

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

 

Animal experiments 

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

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

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

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

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

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

 

Animal microbiome 

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

 

Plant, root, and soil microbiome

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

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

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

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

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

 

Water microbiome and extremophile 

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

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

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

 

 

Techniques

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

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

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

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

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

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

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

 

Microbes in the news 

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

Popular health supplements contaminated with faecal bacteria – Irish Examiner

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

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

 

 

September 15, 2017

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Events and jobs

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

 
General microbiome

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

 

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

 
Pregnancy and early life

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

 

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

 
Human respiratory microbiome

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

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

 

Human nearly-sterile sites 

 

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

 

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

 

Human gut microbiome

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

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

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

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

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

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

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

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

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

 
Animal experiments 

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

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

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

 

Animal microbiome

 

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

 
Plant, root, and soil microbiome

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

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

 

Food microbiology

 

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

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

 

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

 

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

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

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

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

 

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

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

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

September 14, 2017

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Events and jobs

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

MICROBIOLOGY MANAGER – ICDS, County Waterford

 

General microbiome

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

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

 

Pregnancy and early life

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

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

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

 

Human respiratory microbiome

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

 

 

Human nearly-sterile sites 

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

 

Human gut microbiome

C. difficile Microbiome Manipulation – J Wick – Infection Prevention

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

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

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

 

Animal experiments 

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

 

Animal microbiome 

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

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

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

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

 

Plant, root, and soil microbiome

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

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

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

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

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

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

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

 

Built environment 

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

 

 

Bioinformatics

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

 

Techniques

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

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

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

 

Microbes in the news

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

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

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

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

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

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

Why bacteria ‘shapeshift’ in space – CU Boulder Today

Gut Bacteria May Impact Multiple Sclerosis Progression – Genome Web

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

September 12, 2017

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Today’s post is short and sweet. A European Food Safety Authority panel releases a report on deoxynivalenol (DON), a review on the effects of obesity on depression, and fish oil might be good for your gut microbiota.

General microbiology

Viable But Non-Culturable Cells Are Persister Cells – Jun-Seob Kim et al. – bioRxiv

Regulated release of cryptococcal polysaccharide drives virulence and suppresses immune cell infiltration into the central nervous system – Steven T. Denham et al. – bioRxiv

*Scientific Opinion: Risks to human and animal health related to the presence of deoxynivalenol and its acetylated and modified forms in food and feed – EFSA Panel on Contaminants in the Food Chain et al. – EFSA Journal

Strategies for editing virulent staphylococcal phages using CRISPR-Cas10 – S.M. Nayeemul Bari et al. – ACS Synthetic Biology

Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria – Alfonso Santos-Lopez et al. – bioRxiv

Human gut microbiome

The Role of Gut Microbiome in the Pathogenesis of Prostate Cancer: a Prospective, Pilot Study – Golombos DM et al. – Urology

Review: Pathogenesis of Helicobacter pylori infection – Vania Camilo et al. – Helicobacter

Helicobacter Special Issue: XXXth International Workshop on Helicobacter & Microbiota in Inflammation & Cancer

*Biological and clinical implications of herbal medicine and natural products for the treatment of inflammatory bowel disease – Bao-Jian Guo et al. – Annals of The New York Academy of Sciences

Plant non-starch polysaccharides that inhibit key enzymes linked to type 2 diabetes mellitus – Dan Liu et al. – Annals of The New York Academy of Sciences

Mini-Review: Role of microbiota in the pathogenesis of functional disorders of the lower GI tract: Work in progress – Jonna Jalanka and Robin Spiller – Neurogastroenterology and Motility

*Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women – Cristina Menni et al. – Scientific Reports

Press: Omega 3 helps the gut stay healthy, study finds – Medical Xpress

Human gut-microbiome-brain axis

*Review: Effects of obesity on depression: a role for inflammation and the gut microbiota – Schachter J et al. – Brain, Behavior, and Immunity

Preimmunization with a heat-killed preparation of Mycobacterium vaccae enhances fear extinction in the fear-potentiated startle paradigm – Fox JH et al. – Brain, Behavior, and Immunity

Animal experiments

Rapamycin treatment attenuates age-associated periodontitis in mice – An JY et al. – Geroscience

Animal microbiome

Disparity in the nasopharyngeal microbiota between healthy cattle on feed, at entry processing and with respiratory disease – Zeineldin M et al. – Veterinary Microbiology

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Ober RA et al. – Veterinary Microbiology

Plant, root and soil microbiome

Seasonal and inter-annual variability in litter decomposition and nitrogen availability in a mid-Appalachian watershed – Jeff W. Atkins et al. – Ecosphere

Probiotics, Prebiotics and Synbiotics

Probiotic Supplementation in Chronic Kidney Disease: A Double-blind, Randomized, Placebo-controlled Trial – Borges NA et al. – Journal of Renal Nutrition

Apple pectin-derived oligosaccharides produce carbon dioxide radical anion in Fenton reaction and prevent growth of Escherichia coli and Staphylococcus aureus – Martinov J et al. – Food research international

Microbes in the news

Researchers found omega 3 helps the gut stay healthy – Pharmabiz

Microbes on the market

Tata and OptiBiotix seal deal for India prebiotic expansion – Gary Scattergood+ – Food Navigator Asia

Startups focus on the microbiome – Olivia Tucker – Version Weekly

 

September 11, 2017

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General microbiome

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

Pan-genome analysis of Bacillus for microbiome profiling – Yihwan Kim, Scientific Reports

Using CRISPR-Cas systems as antimicrobials – David Bikard, Current Opinion in Microbiology

Pregnancy and early life

The composition of the vaginal microbiome in first trimester pregnant women influences the level of autophagy and stress in vaginal epithelial cells – Dimitrios Nasioudis, Journal of Reproductive Immunology

Multi-site human microbiome

Veterinary antibiotics in food, drinking water, and the urine of preschool children in Hong Kong – Na Li, Environment International

Acne vulgaris patients have a distinct gut microbiota in comparison with healthy controls – Y. Deng, Journal of Investigative Dermatology

Immune mechanisms of food allergy and its prevention by early intervention – Victor Turcanu, Current Opinion in Immunology

Intestinal microbiome-gut-brain axis and irritable bowel syndrome – Moser G., Wiener Medizinische Wochenschrift

Human skin microbiome

Integrated metabolome-microbiome analyses to evaluate the alleviating effects of short-term green tea supplementation for UVB-induced erythema – E. Jung, Journal of Investigative Dermatology

Isomerization of urocanic acid by ultraviolet radiation and its role in modulation of skin microbiome, antimicrobial peptides, and immune function – V. Patra, Journal of Investigative Dermatology

Universal transcriptomic analysis of host-microbiome interactions in psoriasis – T. Furnholm, Journal of Investigative Dermatology

Skin microbiota alteration link to skin symptoms after a harsh cleanser – A.G. Gueniche, Journal of Investigative Dermatology

Forensic human identification using skin microbiomes – Sarah E. Schmedes, Applied Environmental Microbiology

Human gut microbiome

“Clostridium mediterraneense” a new bacterial species isolated from the human gut – Sokhna Ndongo, New Microbes and New Infections

Definition, Pathogenesis and Management of that cursed Dyspepsia – Pramoda Koduru, Clinical Gastroenterology and Hepatology

Gastrointestinal Conditions in the Female Athlete – Barry Kent Diduch, Clinics in Sports Medicine

Human oral microbiome

Location-Specific Oral Microbiome Possesses Features Associated with Chronic Kidney Disease – Jianzhong Hu, Kidney International Reports

The salivary microbiome is consistent between subjects and resistant to impacts of short-term hospitalization – Damien J. Cabral, Scientific Reports

Animal experiments

Effects of dietary fructooligosaccharide on the growth, antioxidants, immunity and disease resistance of Chinese mitten crab – Erteng Jia, Aquaculture

The microbiota influences cell death and microglial colonization in the perinatal mouse brain – Alexandra Castillo-Ruiz, Brain, Behavior, and Immunity

Differences in amino acid catabolism by gut microbes with/without prebiotics inclusion in GDDY-based diet affect feed utilization in rainbow trout – Omolola C. Betiku, Aquaculture

Effects of organic acids and essential oils blend on growth, gut microbiota, immune response and disease resistance of Pacific white shrimp (Litopenaeus vannamei) against Vibrio parahaemolyticus – Wangquan He, Fish & Shellfish Immunology

Imazalil exposure induces gut microbiota dysbiosis and hepatic metabolism disorder in zebrafish – Cuiyuan Jin, Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Local immune response of two mucosal surfaces of the European seabass, Dicentrarchus labrax, fed tryptophan- or methionine-supplemented diets – R. Azeredo, Fish & Shellfish Immunology

Segment specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs – Kaifan Yu, Physiological Genomics

Animal microbiome

Inside the guts of the city: Urban-induced alterations of the gut microbiota in a wild passerine – Aimeric Teyssier, Science of The Total Environment

Bacterial microbiota associated with Rhipicephalus sanguineus(s.l.) ticks from France, Senegal and Arizona – Magalie René-Martellet, Parasites & Vectors

Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages – James S. Evans, Scientific Reports

The interactions between gut microbiota and entomopathogenic fungi: a potential approach for biological control of Blattella germanica (L.) – Fan Zhang, Pest Management Science

Plant, root, and soil microbiome

Volatiles of roots of wild-growing and cultivated Armoracia macrocarpa and their antimicrobial activity, in comparison to horseradish, A. rusticana – Silvana Petrović, Industrial Crops and Products

Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans – Sayak Ganguli, Genomics Data

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace – Weimin Sun, Science of The Total Environment

Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape – Konstantia Gkarmiri, Applied Environmental Microbiology

Effect of Extracellular Electron Shuttles on Arsenic-Mobilizing Activities in Soil Microbial Communities – Shigeki Yamamura, Journal of Hazardous Materials

Water and extremophile microbiome

Microbiological studies of hot springs in India: a review – Poddar A., Archives of Microbiology

Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms – Qifang Ding, Chemosphere

Food microbiology

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India – Shankar Prasad Sha, Scientific Reports

Probiotics / prebiotics

Passion fruit by-product and fructooligosaccharides stimulate the growth and folate production by starter and probiotic cultures in fermented soymilk – Marcela Albuquerque Cavalcanti Albuquerque, International Journal of Food Microbiology

Gut microbiota alterations from different Lactobacillus probiotic-fermented yoghurt treatments in slow-transit constipation – Chen-Jian Liu, Journal of Functional Foods

Microbes in the news

Scientists to Study Health of Plant-Bacteria Symbiosis in California –  Iqbal Pittalwala, UCR Today

Sugars in breast milk may fight harmful bacteria directly – Laura Sanders, Science News

Atopic dermatitis associated with different bacteria depending on disease severity – Andrew Bowser, Dermatology Times

Park Service using lasers to remove Jefferson Memorial’s grimy coating – Jack Moore, WTOP

Startups focus on the microbiome as an organic solution to increase crop yields – Jonathan Shieber, Tech Crunch

September 9, 2017

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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

 

September 5, 2017

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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

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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

September 2, 2017

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General microbiome

Nutrient stoichiometry shapes microbial coevolution – ML Larsen – bioRxiv

Review: Interplay of innate lymphoid cells and the microbiota – L Britanova – Immunological Reviews

 

 

Human gut microbiome

The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens – S Kim – Immunological Reviews

 

Animal experiments

Effect of Propionibacterium acidipropionici P169 on the rumen and faecal microbiota of beef cattle fed a maize-based finishing diet – E Azad – Beneficial Microbes

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – L Chi – Toxicological Sciences

 

Animal microbiome 

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients – MC Hughey – PeerJ

Effects of probiotic on microfloral structure of live feed used in larval breeding of turbot Scophthalmus maximus – Y Jiang – Chinese Journal of Oceanology and Limnology

 

Plant, root, and soil microbiome

Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action – MD Asemoloye – PLoS One

Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil – AK Borsodi – International Journal of Systematic and Evolutionary Microbiology

 

Water microbiome and extremophiles 

Natronoarchaeum persicum sp. nov., a haloarchaeon isolated from a hypersaline lake – A Naghoni – International Journal of Systematic and Evolutionary Microbiology

Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum – S Woo – PLoS One

Biogeochemical conversion of sulfur species in saline lakes of Steppe Altai – SV Borzenko – Chinese Journal of Oceanology and Limnology

Role of heavy metals in structuring the microbial community associated with particulate matter in a tropical estuary – VA Sheeba – Environmental Pollution

 

Probiotics / prebiotics

Review: To add or not to add probiotics to infant formulae? An updated systematic review – A Skórka – Beneficial Microbes

 

Phages and viruses

Biogeography & Environmental Conditions Shape Phage & Bacteria Interaction Networks Across The Human Microbiome – GD Hannigan – bioRxiv

Review: Impact of transmission cycles and vector competence on global expansion and emergence of arboviruses – A Agarwal – Reviews in Medical Virology

 

Techniques

Validation of RT-qPCR approaches to monitor Pseudomonas syringae gene expression during infection and exposure to pattern-triggered immunity – A Smith – bioRxiv

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

 

Microbes in the news 

Could an altered microbiome predict Parkinson’s disease – Nutra Ingredients

Could faecal microbiota transplantation be used to tackle asthma – Nutra Ingredients

Probiotics effective in preventing sepsis in infants – Healio

Start made on revealing scale of gut bugs’ hijacking our signalling – Chemistry World

Dietary Indoles May Help Extend Lifespan – Emax Health

Baby Bottle Soap Recalled Due to ‘Harmful Bacteria’ – Fortune

Multi-drug resistant bacteria proliferating through poultry waste – TOI