Category Archives: Animal microbiome

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 13,2017

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Our midweek digest is a treat for wine drinkers- two studies looking at vineyard microbiomes and news of how Nestlé is moving into microbiome research. Lastly, read about an exciting workflow that makes it easier to map the resistome.

General Microbiome

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles.

Parnell LA .Scientific Reports

Human gut microbiome

Host-microbe interaction in the gastrointestinal tract.

Parker A.Environmental Microbiology Report

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients.

Ticinesi A.Scientific Reports

Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters.

Obermajer T.Scientific Reports

Animal experiments and microbiome

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models.

Cekanaviciute E, PNAS

The microbiota influences cell death and microglial colonization in the perinatal mouse brain.

Castillo-Ruiz A. Brain, Behaviour, and Immunity

Microbial colonization is required for normal neurobehavioral development in zebrafish.

Phelps D,.Scientific Reports

Biotechnology 

Ozone-cathode microbial desalination cell; An innovative option to bioelectricity generation and water desalination.

Gholizadeh A. Chemosphere.

Plant and soil microbiome

Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.

Mezzasalma V. PLoS One.

Is microbial terroir related to geographic distance between vineyards?

Miura T. Environmental Microbiology Reports

Bacteria utilising plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Uksa M. Environmental Microbiology Reports

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

Bailly A. Frontiers in Microbiology

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis.

Michas A. Microbiome

Lung Microbiome

Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.

Miranda-CasoLuengo AA.BMC Genomics

Mechanistic insight into the function of the microbiome in lung diseases.

Ubags NDJ. European Respiratory Journal

Antibiotics

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE.Nature Communications

Resistome

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Earls MR. PLoS One

Rapid resistome mapping using nanopore sequencing.

van der Helm E.Nucleic Acids Research  

Network of microbial and antibiotic interactions drive colonization and infection with multidrug-resistant organisms

Wang J. PNAS

News

Nestlé moves into gut microbiome tests.

News- Nature Biotechnology

Protocol

Shotgun metagenomics, from sampling to analysis.

Quince C,Nature Biotechnology

Erratum 

Erratum to: Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species.

Hale VL. Microbial Ecology

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 6, 2017

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Our midweek digest is short and sweet, but contains interesting reads- Chabé’s critical review of role of gut protozoa is worth a read

Human gut microbiome

REVIEW: Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Chabé M. Trends in Parasitology

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

Ocean, river, and stream microbiome

Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia). Zouch H. Frontiers in Microbiology

Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities.

Butaitė E. Nature Communication

Animal  microbiome

Succession and Fermentation Products of Grass Carp (<i>Ctenopharyngodon idellus</i>) Hindgut Microbiota in Response to an Extreme Dietary Shift. Hao YT. Frontiers in Microbiology

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome.

Lemieux-Labonté V. Microbiome

Biotechnology 

Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors.

Szabó E. AMB Express

Antibiotic, probiotics, and prebiotics

Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs.

Jiang P. Journal of Proteome Research

Probiotics and gastrointestinal conditions: An overview of evidence from the Cochrane Collaboration.

Parker EA. Nutrition

Faecal microbiome 

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants.

Wong WSW. Microbiome

Communication

Interspecies quorum sensing in co-infections can manipulate trypanosome transmission potential.

Silvester E. Nature Microbiology

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 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

 

September 1, 2017

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A rich Digest to start your September. A special issue of Immunological Reviews on the host-microbiome interaction, water can be dangerous – both in Texas and your washing machines, and how about some music inspired by the microbiome?

Jobs

Microbiology jobs in Kansas – New Scientist Jobs

Post Doctoral Researcher – The Ohio State University

Laboratory Assistant III – Microbiology – Contingent – Allegiance Health – Jackson, MI

Microbiology Lab Technician (Up to $2500, Global MNC, No experience required)

General microbiology

Towards a universal molecular microbiological test – Richard J. N. Allcock et al. – Journal of Clinical Microbiology

Human microbiome inspired antibiotics with improved β-lactam synergy against MDR Staphylococcus aureus -Chu J et al. – ACS Infectious Diseases

Pregnancy and early life

Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months – Floor Hugenholtz et al. – International Journal of Microbiology

Human skin microbiome

Application of sebomics for the analysis of residual skin surface components to detect potential biomarkers of type-1 diabetes mellitus – Satyajit S. Shetage et al. – Scientific Reports

Human near-sterile sites

Bone Remodeling and the Microbiome – Pacifici R – Cold Spring Harbor Perspectives in Medicine

Human lung microbiome

Comparing microbiota profiles in induced and spontaneous sputum samples in COPD patients – Solveig Tangedal et al. – Respiratory Research

Human gut microbiome

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease – Kyohei Nishino et al. – Journal of Gastroenterology
https://link.springer.com/article/10.1007%2Fs00535-017-1384-4

*Review: Host-microbiota interactions and adaptive immunity – Kathy D. McCoy et al. – Immunological Reviews (Special Issue: Microbiome-Immune System Interplay)

Animal experiments

Mouse: Commensal bacteria make GPCR ligands that mimic human signalling molecules – Louis J. Cohen et al. – Nature

Review: Exposure of livestock to GM feeds: Detectability and measurement – Anna Nadal et al. – Food and Chemical Toxicology

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery -Eric R. Burrough et al. – Frontiers in Veterinary Science

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Emily V. Lamoureux et al. – mSystems

Animal microbiome

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont – Lin Cai et al. – Scientific Reports

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles – David Kamanda Ngugi et al. – PNAS

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin – Daniel Medina et al. – Frontiers in Microbiology

Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load – R. Olsen et al. – Poultry Science

Plant, root and soil microbiome

Antioxidant and Antibacterial Activity of Organic Extracts of Roots of Glycyrrhiza Glabra Linn – Zafar Iqbal et al. – American Journal of Applied and Industrial Chemistry

Effect of red clover on the microbial transformation of phenanthrene and octadecane in the soil – A. V. Nazarov et al. – Eurasian Soil Science

Biogeography of plant-associated fungal symbionts in mountain ecosystems: A meta-analysis – Stephanie N. Kivlin et al. – Diversity and Distribution

Water and extremophile microbiome

Biodiversity analysis of the unique geothermal microbial ecosystem of the Blue Lagoon (Iceland) using next-generation sequencing (NGS) – Katarzyna A. Palinska et al. – Hydrobiologia

Impacts of tropospheric ozone exposure on peatland microbial consumers – Richard J. Payne et al. – Soil Biology and Biochemistry

Progress and perspectives in aquatic microbial ecology: highlights of the SAME 14, Uppsala, Sweden, 2015 – Eva S. Lindström & Paul A. del Giorgio – Aquatic Microbial Ecology

*Prevalence of β-lactamase genes in domestic washing machines and dishwashers and the impact of laundering processes on antibiotic resistant bacteria – Laura Rehberg et al. – Journal of Applied Microbiology

Built environment microbiome

A high-flow-rate impinger for the study of concentration, viability, metabolic activity, and ice nucleation activity of airborne bacteria – Tina Šantl-Temkiv et al. – Environmental Science & Technology

Phages and viruses

Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome – Matthew C. Johnson et al. – Journal of Structural Biology

Microbes in the news

Welcome Mat: Franklin art fair returns on Labor Day – Maureen Feighan – The Detroit News

Methane emissions tackled with gas-guzzling bacteria – Monash University – Science Daily

Altered Gut Bacteria Could Indicate Parkinson’s – Sylvia Booth Hubbard – News Max

*Health officials are warning Texans to stay out of Harvey floodwaters for a disturbing reason – Erin Brodwin – Business Insider

*Study shows nurses’ scrubs become contaminated with bacteria in hospitals – Medical Express

Cheaters take advantage – Irene Vacca – Nature Reviews Microbiology

Bacteria – Dot Wordsworth – The Spectator

New Oral Microbiome Study Could Provide Better Estimate of Time since Death – University of Tennessee

*Scientists Made Music From the Human Microbiome, and It’s Seriously Cool – Gears of Biz

How A Mother’s Letter Inspired A Scientist To Revolutionize Consumer Microbiome Testing – Afif Ghannoum – Forbes

Non-microbiology pick

Advocating for Diversity and Inclusion in Faculty Hiring – Darryl Yong and Sumun Pendakur – Notices of the AMS

August 31, 2017

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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