16 April, 2018

Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling

Gut Microbiome

Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine

Fecal Microbiome

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe

Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics

 

Plant, Soil, and Water Microbiome

Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology

Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology

Animal Experiments and Microbiome

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports

Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology

Preprint

Mercury methylating microbial communities of boreal forest soils

Jingying Xu. bioRxiv

Techniques

Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling

Correction

Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine

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April 13, 2018

Today’s digest is short and sweet, but includes exciting science that explores how a vegan diet modulates the gut microbiome and new techniques for detection of DNA SNIPs.

General Microbiome

Effect of nisin on microbiome-brain-gut axis neurochemicals by Escherichia coli-induced diarrhea in mice.Jia Z. Microbial Pathogenesis

Food for Gut: Microbiota Fuels Immune Reconstitution after BMT.Simms-Waldrip TR. Cell Host and Microbe

 

Oral/Gut Microbiome

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids.Martinez-Guryn K. Cell Host and Microbe

Impact of a vegan diet on the human salivary microbiota. Hansen TH. Scientific Reports

 

Plant, Soils, and Water Microbiome

Bacterial communities of four adjacent fresh lakes at different trophic status. Ji B. Ecotoxicology and Environmental Safety

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.Wille L. Plant, Cell and Environment

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.Daleo P. Ecology

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.Ye F. Microbial Ecology

d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere.Hener C, Hummel S. International Journal of Molecular Sciences

 

Animal Microbiome and Experiments

Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.Salami SA. FEMS Microbiology Ecology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.Thies S. Scientific Reports

Pasture Feeding Changes the Bovine Rumen and Milk Metabolome.O’Callaghan TF. Metabolites

Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice.Kim M. European Journal of Immunology

Molecular diversity of the faecal microbiota of Toy Poodles in Japan.Omatsu T. Journal of Veterinary Medicine

Techniques

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.Youngblut ND. Frontiers in Microbiology

April 5, 2018

Of note today: An evaluation of multi-site human microbiome temporal stability over six months; The impacts of 1,000 non-antibiotic drugs on the in vitro gut microbiome; Caspase-1 might modulate the relationship between stress, the gut microbiome, inflammation and depressive-like behaviour in mice; And the impact of warming on the Antarctic soil microbiome

Events and jobs

Community Sequencing Scientists, Indigo, Boston MA

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General microbiome

Review: No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases – Douglas B. Kell – Biological Review

Review: Environmental microbiology to the rescue of planet Earth – Víctor de Lorenzo – Environmental Microbiology

Multi-site human microbiome

*Quantification of Human Microbiome Stability over Six Months: Implications for Epidemiologic Studies – Rashmi Sinha – American Journal of Epidemiology

Review: Of genes and microbes: solving the intricacies in host genomes – Jun Wang – Protein & Cell

Human gut microbiome

Review: Serotonin as a Link Between the Gut-Brain-Microbiome Axis in Autism Spectrum Disorders – Narek Israelyan – Pharmacological Research

The Intestinal Microbiome Influences the Response of Cancers to PD-1–Based Immunotherapy: Might Fecal Transplantation Become Part of Cancer Therapy? – Paolo Biancheri – Gastroenterology

*Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi – Thomas A. Auchtung – mSphere

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

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Animal experiments

*The inflammasome and the microbiota-gut-brain axis – Ma-Li Wong – Neurology, Psychiatry and Brain Research

Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome – Junhui Guo – Genes

Effect of prenatal administration of low dose antibiotics on gut microbiota and body fat composition of newborn mice – Ayumi Yoshimoto – Journal of Clinical Biochemistry and Nutrition

The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts – Savannah L. Logan – PNAS

Microbes vs. chemistry in the origin of the anaerobic gut lumen – Elliot S. Friedman – PNAS

Animal microbiome

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil – Andrea Bagi – BMC Microbiology

Review: Host-microbe interactions in octocoral holobionts – recent advances and perspectives – Jeroen A. J. M. van de Water – BMC Microbiome

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure – Inês Barros – AIMS Microbiology

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary – Zana Brigitta –  Acta Veterinaria Hungarica

Plant, root, and soil microbiome

Microbial community responses to modern environmental and past climatic conditions in Omongwa pan, western Kalahari: A paired 16S rRNA gene profiling and lipid biomarker approach – S. Genderjahn – Biogeosciences

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

*Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region – Dockyu Kim – Journal of Basic Microbiology

Effect of temperature on bacterial community in petroleum hydrocarbon-contaminated and uncontaminated Antarctic soil – C. W. Chong – Polar Biology

Variations of bacterial community diversity within the rhizosphere of three phylogenetically related perennial shrub plant species across environmental gradients – Xiaofan Na – Frontiers in Microbiology

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove – Moriyuki Hamada – Archives of Microbiology

Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam – C.N. Le – Biological Control

Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests – Alessia Bani – Microbial Ecology

Investigation of the core microbiome in main soil types from the East European plain – Elizaveta V. Pershina – Science of The Total Environment

Water and extremophile microbiome

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia) – Andrea Y. Calvo – Canadian Journal of Microbiology

Review: Extremophilic yeasts: the toughest yeasts around? – Pietro Buzzini – Yeast

Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea – Yan-Jiao Zhang – International Journal of Systematic and Evolutionary Microbiology

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K. Nuy – Science of The Total Environment

*Evidence for selective bacterial community structuring on microplastics – Martin Ogonowski – Environmental Microbiology

Microbial Ecology

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis – Promi Das – PLOSone

Review: What will it take to understand the ecology of symbiotic microorganisms? – Angela E Douglas – Environmental Microbiology

Built environment

Fungi-induced paint deterioration and air contamination in the Assiut University hospital, Egypt – Ismail R. Abdel-Rahim – Indoor and Buility Environment

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Probiotics / prebiotics

Lactobacilli and lactoferrin: Biotherapeutic effects for vaginal health – Lucia Bertuccini – Journal of Functional Foods

The viability of probiotics in water, breast milk, and infant formula – Claire Watkins – European Journal of Pediatrics

Bioinformatics

Constructing Lightweight And Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA) – Trevor Cickovski – Bioinformatics

Numerical analyses of intestinal microbiota by data mining – Toshio Kobayashi – Journal of Clinical Biochemistry and Nutrition

Waste and Pollution

Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community – S. W. How – Water Science and Technology

Techniques

Visualization of Microbiota in Tick Guts by Whole-Mount In Situ Hybridization – Caitlin E. Moss – Jove

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Microbes in the news

Phage-host interactions are more complicated than most laboratory studies suggest – Phys.org

 

March 30, 2018

In today’s digest you can read a perspective on the social network of microorganisms by Karsten Zengler, a paper on relationship between HIV-1 infection and chronic periodontitis by Tábata Larissa, a paper on sponges-cyanobacteria associations – a global diversity overview by Despoina Konstantinou and/or for an easier read check the report on bacteria in rubber duckies in our ‘News’ section. Enjoy!

Jobs

PhD position Ecology and Evolution of Microbial Infectious Ecosystems, University of Groningen, Groningen, Netherlands

Research Assistant-Post Doc, Karl Landsteiner University of Health Sciences, Krems, Austria

Post-doctoral opportunity at Weill Cornell in New York City, NY, USA

Post Doc Position for Genetic Engineering to Improve Microbial Soluble Expression, BOKU, Vienna, Austria

General microbiome

Perspective: The social network of microorganisms — how auxotrophies shape complex communities – Karsten Zengler – Nature Reviews Microbiology

Intracellular signaling through the comRS system in Streptococcus mutans genetic competence – Simon A.M. Underhill – bioRxiv

Ecological Insights from the Evolutionary History of Microbial Innovations – Mario E Muscarella – bioRxiv

Probing the metabolism of microorganisms – Stilianos Louca – Science

Human respiratory microbiome

Review: Streptococcus pneumoniae: transmission, colonization and invasion – Jeffrey N. Weiser – Nature Reviews Microbiology

Oral microbiome

Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis – Tábata Larissa – Expert Review of Clinical Immunology

Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status –  Rachel M. Presti – AIDS

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt – Clinical and Translational Immunology

Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease – Elena Barengolts – PLOS One

Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger – Fengping He – Biochemical and Biophysical Research Communications

Single Sampling Versus Multiple Testing Strategy to Assess Gut Microbiota Composition: Does It Matter? – T. G. J. de Meij – Current Microbiology

Scaling Safe Access to Fecal Microbiota Transplantation: Past, Present, and Future – Pratik Panchal – Current Gastroenterology Reports

Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile – Rafael Araos – Digestive Diseases and Sciences

Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis – Robert Šket – Frontiers in  Physiology

Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases – Maria C. Opazo – Frontiers in Microbiology

Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity – Zachariah DeFilipp – Blood Advances

Animal experiments 

Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows – Shoukun Ji – Frontiers in Cellular and Infection Microbiology

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections – Larissa B. Thackray – Cell Reports

Animal microbiome 

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali – Benjamin J. Krajacich – PLOS One

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota – Tao Sun – Scientific Reports

Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis – Alessandro Catenazzi – Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny – Alicia K. Bird – Frontiers in Microbiology

Plant, root, and soil microbiome

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site – José A. Siles – Applied Microbiology and Biotechnology

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants – Katiúscia Kelli Montanari-Coelho – World Journal of Microbiology and Biotechnology

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem – Tatoba R. Waghmode – Frontiers in Microbiology

Bacterial diversity and community structure in the rhizosphere of four Ferula species – Xiuling Wang – Scientific Reports

Water and extremophile microbiome

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean – Despoina Konstantinou – PLOS One

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation – Zheng Xu – Chemosphere

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area – Andrew K. Leight – Frontiers in Microbiology

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin – Min Ren – Frontiers in Microbiology

Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat – Tanita Wein – Frontiers in Microbiology

Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress – Jian Han –  Frontiers in Microbiology

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael W. Henson – The ISME Journal

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation – Babett Wintsche – Frontiers in Microbiology

Phages and viruses

Review: Autophagy during viral infection — a double-edged sword – Younho Choi – Nature Reviews Microbiology

Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa – Veronna Marie – Journal of Water and Health

Kinetic Modeling of Virus Growth in Cells – John Yin – Microbiology and Molecular Biology Reviews

Bioinformatics

EzMap: a simple pipeline for reproducible analysis of the human virome – Patrick Czeczko  – Bioinformatics

Techniques

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan C.Raju – Journal of Microbiological Methods

Mapping bacteria on filter membranes, an innovative SERS approach – SiyueGao – Journal of Microbiological Methods

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile – Zhirong Li  – Journal of Microbiological Methods

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga –  Journal of Microbiological Methods

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm – Guillaume Gautier – Journal of Microbiological Methods

Rapid detection of carbapenemase-producing Acinetobacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method – Vincent van Almsick – Journal of Microbiological Methods

A quest to find good primers for gene expression analysis of Candida albicans from clinical samples – Gabriela C.Alonso – Journal of Microbiological Methods

Microbes in the news 

The inside of rubber duckies are full of bacteria. You don’t seem surprised

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’

Researchers develop model to show how bacteria grow in plumbing systems

Harvard scientists uncover an exploitable Achilles’ heel common to most bacteria

Altering Gut Microbiome May Increase Resistance to C. difficile infection

Our Own Microbiome Might Be Triggering The Autoimmune Disease Lupus

March 26, 2018

Suggestions to read in today’s digest are: a review about microbiological methods applied in studies following the deepwater horizon oil spill by S.Zhang, a paper by W. Pootakham on dynamics of coral‐associated microbiomes during a thermal bleaching event and a paper by X. Jiang on a novel auxotrophic interaction among soil microbes. Enjoy!

Oral microbiome

Reduced salivary secretion contributes more to changes in the oral microbiome of patients with primary Sjögren’s syndrome than underlying disease – Taco A van der Meulen – Annals of the Rheumatic Diseases

Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Human gut microbiome

Plant sterols and human gut microbiota relationship: An in vitro colonic fermentation study – María Cuevas-Tena – Journal of Functional Foods

Fecal microbiome composition and stability in 4- to 8-year old children is associated with dietary patterns and nutrient intake  – Kirsten Berding – The Journal of Nutritional Biochemistry

Gut Microbiota Profiles in Treatment-naïve Children with Attention Deficit Hyperactivity Disorder – Hai-yin Jiang – Behavioural Brain Research

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

Review: The Impact of Klebsiella pneumoniae in Lower Gastrointestinal Tract Diseases – Christina Parvinder Kaur – Journal of Digestive Diseases

Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms – Destanie R. Rose – Brain, Behavior, and Immunity

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies – Marina Panek – Scientific Reports

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Animal experiments 

Chitosan oligosaccharides improve the disturbance in glucose metabolism and reverse the dysbiosis of gut microbiota in diabetic mice – Junping Zheng – Carbohydrate Polymers

Comparative study of effects of assemblages AII and BIV of Giardia duodenalis on mucosa and microbiota of the small intestine in mice – Mariana Felgueira Pavanelli – Biomedicine & Pharmacotherapy

Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice – Dieuwertje E.G. Kok – The Journal of Nutritional Biochemistry

Effects of oxidative stress induced by high dosage of dietary iron ingested on intestinal damage and caecal microbiota in Chinese Yellow broilers – Z. Y. Gou – Journal of Animal Physiology and Animal Nutrition

Animal microbiome 

Effects of short term lead exposure on gut microbiota and hepatic metabolism in adult zebrafish – Jizhou Xia – Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Effects of commercial dietary prebiotic and probiotic supplements on growth, innate immune responses, and intestinal microbiota and histology of Totoaba macdonaldi – Mayra L. González-Félix – Aquaculture

Plant, root, and soil microbiome

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil – Olatz Larrañaga – Environment International

The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology – Samir Droby – Postharvest Biology and Technology

Earthworms differentially modify the microbiome of arable soils varying in residue management – Xin Gong – Soil Biology and Biochemistry

Subterranean infestation by Holotrichia parallela larvae is associated with changes in the peanut (Arachis hypogaea L.) rhizosphere microbiome – Li-Li Geng – Microbiological Research

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

Mycobiota of maize seeds revealed by rDNA‐ITS sequence analysis of samples with varying storage times – Hui – Qin Xing – Microbiology Open

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root‐associated soil of a wild perennial herb – Pil U. Rasmussen – New Phytologist

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – The ISME Journal

Water and extremophile microbiome 

Nutrient enrichment during shrimp cultivation alters bacterioplankton assemblies and destroys community stability – Wen Yang – Ecotoxicology and Environmental Safety

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support – Guillaume Pillot – Bioresource Technology

Changes in microbial communities during volatile fatty acid production from cyanobacterial biomass harvested from a cyanobacterial bloom in a river – Hyun Uk Cho – Chemosphere

Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities – Jèssica Subirats – Water Research

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints – Gang Liu – Water Research

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free‐living bacteria in the water column – Limei Shi – Microbiology Open

Dynamics of coral‐associated microbiomes during a thermal bleaching event – Wirulda Pootakham – Microbiology Open

Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan) – FEMS Microbiology Ecology

Review: A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill – Shuangfei Zhang – Frontiers in Microbiology

Built environment

Sulfate-reducing mixed communities with the ability to generate bioelectricity and degrade textile diazo dye in microbial fuel cells – Waheed Miran – Journal of Hazardous Materials

Work scheme to isolate the different microorganisms found in hydrogen-producing reactors: A study of effectiveness by pyrosequencing analysis – Laura Fuentes  – Journal of Applied Microbiology

Effect of hydraulic retention time on microbial community structure in wastewater treatment electro-bioreactors – Nancy A. ElNaker – Microbiology Open

Food microbiology

Presence of Clostridium difficile in poultry and poultry meat in Egypt – Mostafa Y. Abdel-Glil – Anaerobe

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments – Francesco Fancello – International Journal of Food Microbiology

Post-harvest processing decreases the richness of bacterial taxa in the phyllosphere of broccoli – Min-Soo Kim  – Journal of Applied Microbiology

Probiotics / prebiotics

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium – Dong-Hyun Jung – Journal of Biotechnology

Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9 – Evgeny Vinogradov – Carbohydrate Research

Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge – Laureen Crouzet – Scientific Reports

Microbes in the news

 

 

This Hungry Bacteria Could Help Clean Up Heavy Metals And Greenhouse Gases

March 24, 2018

Events and jobs
Senior Phage Display Scientist: Antibodies – Cambridgeshire, England – Paramount Recruitment

General microbiome
Metagenomic mining of regulatory elements enables programmable species-selective gene expression – Nathan I Johns – Nature Methods

Pregnancy and early life
Seeding of the Fetal Gut Microbiome: Insights Into Origins and Significance – LF Stinson – Journal of Paediatrics and Child Health

Evidence of dysbiosis in the intestinal microbial ecosystem of children and adolescents with primary hyperlipidemia and the potential role of regular hazelnut intake. – Giorgio Gargari – Fems Microbiology Ecology

Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century – Bethany M Henrick – Msphere

Multi-site human microbiome
Microbiome-host systems interactions: protective effects of propionate upon the blood-brain barrier. – Lesley Hoyles – Microbiome

Human vaginal microbiome
Cervical microbiome is altered in cervical intraepithelial neoplasia after loop electrosurgical excision procedure in China – Hongwei Zhang – Scientific Reports

Human nearly-sterile sites (blood, organs, brain)

Human gut microbiome
The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting – Steven Arcidiacono – Standards in Genomic Sciences

Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders. – Joby Pulikkan – Microbial Ecology

An Aberrant Microbiota is not Strongly Associated with Incidental Colonic Diverticulosis. – Roshonda B Jones – Scientific Reports

Untargeted metabolomics identifies trimethyllysine, a TMAO-producing nutrient precursor, as a predictor of incident cardiovascular disease risk. – Xinmin S Li – Jci Insight

Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis – Xinyue Huang – IOVS

Microbial interactions
Cell death as a trigger for morphogenesis. – Boris Aguilar – Plos One

Horizontal Gene Transfer Building Prokaryote Genomes: Genes Related to Exchange Between Cell and Environment are Frequently Transferred – Apuã C. M. Paquola – Journal of Molecular Evolution

Animal experiments
Preprint: Social communication between microbes colonizing the social honey bee Apis mellifera – Irene Newton – bioRxiv

Dietary butyrate glycerides modulate intestinal microbiota composition and serum metabolites in broilers – Xiaojian Yang – Scientific Reports

Bacterial lactase genes diversity in intestinal mucosa of mice with dysbacterial diarrhea induced by antibiotics – Chengxing Long – 3 Biotech

Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata. – Euan R O Allan – The Journal Of Heredity

Tall oil fatty acid inclusion in the diet improves performance and increases ileal density of Lactobacilli spp. in broiler chickens. – K Vienola – British Poultry Science

Effects of dietary Bacillus amyloliquefaciens supplementation on growth performance, intestinal morphology, inflammatory response, and microbiota of intra-uterine growth retarded weanling piglets – Yue Li – Journal Of Animal Science And Biotechnology

Temperature-Dependent Effects of Cutaneous Bacteria on a Frog’s Tolerance of Fungal Infection. – Matthew J Robak – Frontiers In Microbiology

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice. – Fengwei Pan – Microbiome

Animal microbiome
Review: The mosquito holobiont: fresh insight into mosquito-microbiota interactions – Morgane Guégan – Microbiome

Plant, root, and soil microbiome
Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields – Kunkun Fan – Soil Biology and Biochemistry

Seasonal Effects on Microbial Community Structure and Nitrogen Dynamics in Temperate Forest Soil – Tomohiro Yokobe – forests

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. – Yu-Jie Wei – Plos One

Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. – Annelein Meisner – Frontiers In Microbiology

Vanillic acid changed cucumber (Cucumis sativus L.) seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities. – Xingang Zhou – Scientific Reports

Review: Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences. – Mohammadhossein Ravanbakhsh – Microbiome

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination. – E Gonzalez – Microbiome

Rhizosphere Microbiome Modulators: Contributions of Nitrogen Fixing Bacteria towards Sustainable Agriculture – Nicholas Ozede Igiehon – Int. J. Environ. Res. Public Health

Vascular plant-mediated controls on atmospheric carbon assimilation and peat carbon decomposition under climate change – Konstantin Gavazov – Global Change Biology

Water and extremophile microbiome
Preprint: Dynamics and interactions of highly resolved marine plankton via automated high frequency sampling – David M. Needham – bioRxiv

Bioremediation of PCB-contaminated shallow river sediments: The efficacy of biodegradation using individual bacterial strains and their consortia. – Hana Horváthová – Chemosphere

Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community – Xavier Mayali – FEMS Microbiology Ecology

Built environment
Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters – Luanfeng Hou – Current Microbiology

Food microbiology
Review: The influence of diet on anti-cancer immune responsiveness – Laura Soldati – Journal of Translational Medicine

The Efficacy of a Chewing Gum Containing Phyllanthus emblica Fruit Extract in Improving Oral Health. – Ya-Ting Chuang – Current Microbiology

ReviewThe Microbial Diversity of Sherry Wines – Gustavo Cordero-Bueso – Fermentation

Probiotics / prebiotics / antibiotics
The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster – Khachik E. Labachyan – Gut Pathogens

Bacillus clausii inhibits bone loss by skewing Treg-Th17 cell equilibrium in postmenopausal osteoporotic mice – Hamid Y. Dar – Nutrition

Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease. – Christine Tara Peterson – Journal Of Alternative And Complementary Medicine (New York, N.Y.)

Phages and viruses
Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks – Rafal Tokarz – Msphere

Microbes in the news
Skin spray heals US woman’s flesh-eating bacteria wounds – Alice Klein – New Scientist

March 18, 2018

An interesting book and multiple animal microbiome papers for today’s digest!

General microbiome
Book: Clinical Immunology (Fifth Edition): Principles and Practice – Robert R. Rich, Thomas A. Fleisher, William T. Shearer, Harry W. Schroeder, Anthony J. Frew, Cornelia M. Weyand
Multiple chapters may be of interest, including:

Human skin microbiome
Review: Cutaneous Barriers and Skin Immunity: Differentiating A Connected Network – Stefanie Eyerich – Trends in Immunology

Human gut microbiome
TonB-dependent transport by the gut microbiota: novel aspects of an old problem – David N Bolam – Current Opinion on Structural Biology

ReviewFrailty and the gut – Antonio Di Sabatino – Digestive and Liver Disease

Animal experiments
Chronic exposure to low concentrations of lead induces metabolic disorder and dysbiosis of the gut microbiota in mice – Jizhou Xia – Science of the Total Environment

Polystyrene microplastics induce gut microbiota dysbiosis and hepatic lipid metabolism disorder in mice – Liang Lu – Science of the Total Environment

Expression of recombinant human lysozyme in bacterial artificial chromosome transgenic mice promotes the growth of Bifidobacterium and inhibits the growth of Salmonella in the intestine – Lu Dan – Journal of Biotechnology

Comparative analysis of gut microbial community in healthy and tibial dyschondroplasia affected chickens by high throughput sequencing – Xiaole Tong – Microbial Pathogenesis

Polysaccharide of Hericium erinaceus Attenuates Colitis in C57BL/6 Mice via Regulation of Oxidative Stress, Inflammation-related Signaling Pathways and Modulating the Composition of the Gut Microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation – Tamsin Lyons – Journal of Dairy Science

Animal microbiome
Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata – Euan R O Allan – Journal of Heredity

Microbiomes associated with bovine periodontitis and oral health – Ana C. Borsanelli – Veterinary Microbiology

ReviewCurrent perspectives of the chicken gastrointestinal tract and its microbiome – D. Borda-Molina – Computational and Structural Biotechnology Journal

Built environment
Review: Bioremediation of a pentacyclic PAH, Dibenz(a,h)Anthracene- A long road to trip with bacteria, fungi, autotrophic eukaryotes and surprises – Vidya Vasudevan – Chemosphere

Food microbiology
Microbial community dynamics of a blue-veined raw milk cheese from the United Kingdom – Dewi Yunita – Journal of Dairy Science

Probiotics / prebiotics / antibiotics
A mathematical model of multiple delayed feedback control system of the gut microbiota—Antibiotics injection controlled by measured metagenomic data – Yueping Dong – Nonlinear Analysis: Real World Applications

Review: Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics – Zachary JS Mays – Current Opinion in Biotechnology

ReviewThe role of the gut microbiota in the pathology and prevention of liver disease – Alejandra Altamirano-Barrera – The Journal of Nutritional Biochemistry

Phages and viruses
Preprint: Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem – Divya Venkatesh – bioRxiv

New Genomes
Sanguibacter massiliensis sp. nov., Actinomyces minihominissp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov., and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples. – Melhem Bilen – New Microbes and New Infections

Microbes in the news
Weighty challenge: Untangling obesity’s hidden picture – Jamie Morton – NZ Herald

Microbes on the market
Seres Therapeutics (NASDAQ:MCRB) Upgraded at Zacks Investment Research – Amber Thompson – Register Journal