Category Archives: Techniques

October 22, 2017

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A wide range of interesting articles today on the mouth, respiratory and gut microbiomes: Airway microbiota and obstruction in asthma, the tongue microbiome and pneumonia in the elderly, gut microbiome interactions with host G-protein coupled receptors, the effects of prebiotics and milk oligosaccharides on the mouse gut metabolome and stressor induced immune alterations, the impact of social stress on the gut microbiome and the host gut transcriptome, the impact of a Bacteroides integrase in a mouse model of colitis, and evidence that oral bacteria can colonize the gut in genetically and dysbiotic susceptible mice, leading to increased gut inflammation. 

  • Events and jobs

Postdoctoral Researcher in Microbiome Bioinformatics – Karolinska Institutet

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  • Human respiratory microbiome

Different Functional Genes of Upper Airway Microbiome Associated with Natural Course of Childhood Asthma – Bong-Soo Kim – European Journal of Allergy and Clinical Immunology

*Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction – Benjamin A. Turturice – PLOSone

  • Human oral microbiome

*Relationships of variations in the tongue microbiota and pneumonia mortality in nursing home residents – Shinya Kageyama – Journal of Gerontology

  • Human gut microbiome

Review: Host-Microbe Interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

Development of severe bronchopulmonary dysplasia is associated with alterations in fecal volatile organic compounds – Daniel J C Berkhout – Pediatric Research

Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health – Barbara A. Williams – International Journal of Molecular Sciences

Review: Food allergy: The influence of breast-feeding and gut microbiota – S. Hazebrouck – Revue Française d’Allergologie

Review: Whole cereal grains and potential health effects: Involvement of the gut microbiota – Lingxiao Gong – Food Research International

Review: Probiotic strains and mechanistic insights for the treatment of type 2 diabetes – Christiane S. Hampe – Endocrine

Review: Early-Life Gut Dysbiosis: A Driver of Later-Life Fibrosis? – Karen J. Ho – Journal of Investigative Dermatology

Review: Nutritional programming by glucocorticoids in breast milk: targets, mechanisms and possible implications – Jonneke J. Hollanders – Best Practice & Research Clinical Endocrinology & Metabolism

Review: Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBioMedicine

  • Fecal Transplants

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis – P. Kump – Alimentary Pharamacology and Therapeutics

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  • Animal experiments

* Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

*Stressor-induced immunomodulation is attenuated by prebiotics and milk oligosaccharides: Role of the colonic metabolome – M. Bailey – Brain, Behavior, and Immunity

*The colonic epithelial transcriptome and intestinal microbiome are significantly changed by social stressor exposure – A.R. Mackos – Brain, Behavior, and Immunity

*A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis – Roopa Hebbandi Nanjundappa – Cell

Metformin Alters Upper Small Intestinal Microbiota that Impact a Glucose-SGLT1-Sensing Glucoregulatory Pathway – Paige V. Bauer – Cell Metabolism

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota – Andréa de Andrade Rangel de Freitas – Science of The Total Environment

Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice – Takuya Kuno – Molecular Pharmaceutics

Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population – P. Villette – Epidemiology & Infection

High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community – Debora Garzetti – Genome Announcements

  • Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance – Stephan P. Rosshart – Cell

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations – Lhermie Guillaume – Foodborne Pathogens and Disease

  • Forensic Microbiome

Successive bacterial colonisation of pork and its implications for forensic investigations – Jessica Handke – Forensic Science International

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification – Sarah E. Schmedes – Forensic Science International: Genetics

  • Plant, root, and soil microbiome

Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa – P.C. Carmichael – Journal of Applied Microbiology

Mycorrhizae, invasions, and the temporal dynamics of mutualism disruption – Sara Grove – Journal of Ecology

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter – Quan YuanSoil Biology and Biochemistry

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

  • Waste and Pollution 

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community – Evangelia S. Papadopoulou – Environmental Pollution

  • Built environment

Human health risks for Legionella and Mycobacterium avium complex (MAC) from potable and non-potable uses of roof-harvested rainwater – Kerry A.Hamilton – Water Research

  • Techniques

Optimization of GC/TOF MS analysis conditions for assessing host-gut microbiota metabolic interactions: Chinese rhubarb alters fecal aromatic Amino acids and phenol metabolism – Shan Yin – Analytica Chimica Acta

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  • Microbes in the news

Stress may harm gut health as much as junk food – Honor Whiteman – Medical News Today

Different Microbial Communities Live Along Female Reproductive Tract – GenomeWeb

Gut Health May Begin in the Mouth – Lydialyle Gibson – Havard

October 21, 2017

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Plant and soil microbiome focus today: Rhizospheric microbial communities of the frankincense producing Boswellia sacra tree, Coffea arabica, and the damask rose, as well as plant species in the Puerto Rico tropical forest, the Mediterranean mountains, and extreme Arctic and Alpine climates. 

Events and jobs

Post-doctoral Fellowship in Microbial Genomics – Brigham & Women’s Hospital – The Massachusetts Host-Microbiome Center

Microbiology Sales Executive – Ireland

Microbiology Lab Technician – Catalent – Brussels, Belgium

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  • General microbiome

Special Meeting Sections for the ASM Conference on Mechanisms of Interbacterial Cooperation and Competition – George A. O’Toole – Journal of Bacteriology

  • Human oral microbiome

Nutrigenomics in periodontics – An overview – Singh Soundanya –
International Journal of Oral Health Dentistry

  • Human gut microbiome

Review: Health and environmental applications of gut microbiome: a review – Soumya Chatterjee – The Journal of Society of Ecological Chemistry and Engineering

The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux—A Prospective Longitudinal Interventional Study – Christoph Castellani – Frontiers in Cellular and Infection Microbiology

Review: Host–Microbiota Mutualism in Metabolic Diseases – Salvatore Fabbiano – Frontiers in Endocrinology

Review: Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts – Verónica Urdaneta – Frontiers in Medicine

Review: Prebiotic–Probiotic Relationship: The Genetic Fundamentals of Polysaccharides Conversion by Bifidobacterium and Lactobacillus Genera – Penka Petrova – Food Bioconversion

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome – Tanja V. Maier – mBio

Review: Can the gastrointestinal microbiota be modulated by dietary fibre to treat obesity? – H. C. Davis – Irish Journal of Medical Science

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

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  • Animal experiments

Study on alterations of physiological functions in aged constipation rats with fluid-deficiency based on metabonomic and microbiology analysis – Deliang Liu – Royal Society of Chemistry

  • Animal microbiome

The Low-Diversity Fecal Microbiota of the Critically Endangered Kākāpō Is Robust to Anthropogenic Dietary and Geographic Influences – Elena K. Perry – Frontiers and Microbiology

Alternative growth promoters modulate broiler gut microbiome and enhance body weight gain – Serajus Salaheen – Frontiers in Microbiology

Microbial Communities in North American Ixodid Ticks of Veterinary and Medical Importance – Andrea S. Varela-Stokes – Frontiers in Veterinary Science

Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate – Camila S. Cunha – Systematic and Applied Microbiology

  • Plant, root, and soil microbiome

Root and rhizosphere bacterial phosphatase activity varies with tree species and soil phosphorus availability in Puerto Rico tropical forest – Kristine Grace Cabugao – Frontiers in Plant Science

Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches – Ines Krohn-Molt – Frontiers in Microbiology

Inoculation with arbuscular mycorrhizal fungi alleviates harmful effects of drought stress on damask rose – EslamAbdel-Salam – Saudi Journal of Biological Sciences

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

Plant growth promoting rhizobacteria in amelioration of salinity stress: a systems biology perspective – Gayathri Ilangumaran – Frontiers in Plant Science

Review: Mycorrhizosphere Interactions to Improve a Sustainable Production of Legumes – José-Miguel Barea – Microbes for Legume Improvement

Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains – José F. Cobo-Díaz – Forests

Review: Response and interaction of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi in the soybean rhizosphere – Ram Swaroop Meena – Plant Growth Regulation

Review: Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? – Joelle Sasse – Trends in Plant Science

Microbial indicators for soil quality – Michael Schloter – Biology and Fertility of Soils

Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants – Xiao Xiao – Applied Microbiology and Biotechnology

Soil water content during and after plant growth influence nutrient availability and microbial biomass – Ran Xue – Journal of soil science and plant nutrition

Isolation, screening and biochemical characterization of Phosphate-solubilizing rhizobacteria associated with Coffea arabica L – Befekadu Teshome – Advanced Journal of Biodiversity

Temporal variations of soil microbial community under compost addition in black soil of Northeast China – Wei Yang – Applied Soil Ecology

Differential seasonal effects of water addition and nitrogen fertilization on microbial biomass and diversity in a temperate desert – Gang Huang – Catena

Assessment of microbial diversity in the rhizosphere of Pinus roxburghii (Sarg.) and bio-inoculant potential of selected pine bacterial isolates for wheat varieties based on culture independent and culture dependent techniques – I. Naz – Plant Biology

Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree – Abdul Latif Khan – PLOSone

Taxonomic structure and functional association of foxtail millet root microbiome – Tao Jin – GigaScience

  • Biotechnology

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction – Dhaneshwaree Asem – PLOSone

Impact of treated wastewater for irrigation on soil microbial communities – A.M. Ibekwe – Science of the Total Environment

Advancing the design and delivery of CRISPR antimicrobials – Jennie R.Fagen – Current Opinion in Biomedical Engineering

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  • Phages and viruses

Pre-Print: Insights into viral community composition of the cnidarian model metaorganism Aiptasia using RNA-Seq data – Jan D Brüwer – PeerJ

How does parvovirus B19 DNA achieve lifelong persistence in human cells? – Gloria Bua – Future Virology

  • Bioinformatics

Annotation: A Computational Solution for Streamlining Metabolomics Analysis – Xavier Domingo-Almenara – Analytical Chemistry

  • Techniques

Review: Combined imaging and molecular techniques for evaluating microbial function and composition: A review – Christopher G. Weisener – Surface and Interface Analysis

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  • Microbes in the news

Simple Bacteria Offer Clues to the Origins of Photosynthesis – Jordana Cepelewicz – Quanta Magazine

Bacteria Found in Women’s Upper Reproductive Tracts – Diana Kwon – The Scientist

New Research Shows Asymmetry in Bacteria Might Help Us Fight Antibiotic Resistance – Karla Lant – Futurism

Metal-eating bacteria could have left their “fingerprints” on Mars, proving it once hosted life – Matt Williams – Universe Today

How gut bacteria saved ‘dirty mice’ from death – Elizabeth Pennisi – Science

 

October 20, 2017

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A wide variety of studies today from the digestive microbiota of carnivorous pitcher plants, to the skin microbiome of dogs, and the impacts of probiotics on male fertility in a mouse model of obesity. 

Events and jobs

Microbiome World Congress – November 7-8, 2017, Capital Hilton, Washington, DC – registration

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  • General microbiome

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae – Zhaobin Huang – Frontiers in Microbiology

Review: Uncultivated microbes in need of their own taxonomy – Konstantinos T Konstantinidis – The ISME Journal

Review: The growing tree of Archaea: new perspectives on their diversity, evolution and ecology – Panagiotis S Adam – The ISME Journal

  • Human respiratory microbiome

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition – Anton Y. Peleg – Journal of Cystic Fibrosis

  • Human gut microbiome

Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study – Thomas Howe McConville – PLOSone

Review: Antibiotics, gut microbiome, and obesity – Karen S. W. Leong – Clinical Endocrinology

Review: Gut microbiota changes in the extreme decades of human life: a focus on centenarians – Aurelia Santoro – Cellular and Molecular Life Sciences

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

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  • Animal Experiments

Lactobacillus rhamnosus PB01 (DSM 14870) supplementation affects markers of sperm kinematic parameters in a diet-induced obesity mice model – Fereshteh Dardmeh – PLOSone

  • Animal microbiome

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization – Beate M Slaby – The ISME Journal

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs – Andrew R. Williams – PLOSone

Individual signatures and environmental factors shape skin microbiota in healthy dogs – Anna Cuscó – Microbiome

Review: Metagenomic investigation of gastrointestinal microbiome in cattle – Minseok Kim – AJAS

  • Plant, root, and soil microbiome

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community – David W Armitage – The ISME Journal

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities – Roland C Wilhelm – The ISME Journal

Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness – David R. Toole – Biological Invasions

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis – Margarida M. Santana – Frontiers in Microbiology

  • Water and extremophile microbiome

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

Mixotrophy drives niche expansion of verrucomicrobial methanotrophs – Carlo R Carere – The ISME Journal

High abundance and expression of transposases in bacteria from the Baltic Sea – Theoden Vigil-Stenman – The ISME Journal

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB contaminated marine sediments – B. Matturro – FEMS Microbiology Ecology

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities – Oliver Röhl – Environmental Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept – Christina Pavloudi – PeerJ

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites – Gerrit Wienhausen – Frontiers in Microbiology

  • Built environment

Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome

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  • Probiotics / prebiotics

Review: Probiotics in the Prevention of Gestational Diabetes Mellitus – Luisa F. Gomez Arango – Nutrition and Diet in Maternal Diabetes

  • Phages and viruses

Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release – Gurinder K. Vinner – PLOSone

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology – Rachel L Marine – The ISME Journal

  • Techniques

A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping – Wan-Xiang Xu – PLOSone

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October 16, 2017

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Events and jobs

Two open pre-doctoral research fellow positions  –  Click here and here for details- Bioinformatics Research Group – Małopolska Centre of Biotechnology in Kraków, Poland

R & D Scientist – Fluid-Screen, Inc. (FSI) – Cambridge, MA

 

Animal microbiome 

An immune-related gene expression atlas of the shrimp digestive system in response to two major pathogens brings insights into the involvement of hemocytes in gut immunity – NK Ahila – Microbial Pathogenesis

Do host-associated gut microbiota mediate the effect of an herbicide on disease risk in frogs? – SA Knutie – Journal of Animal Ecology

 

Plant, root and soil microbiome

Review: Pesticidal prospectives of chitinolytic bacteria in agricultural pest management – ARNS Subbanna – Soil Biology and Biochemistry

Impact of the Fenton-like treatment on the microbial community of a diesel-contaminated soil – F Polli – Chemosphere

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. – LW Mendes – The ISME Journal

 

 

Phages and viruses

Relevance of host cell surface glycan structure for cell specificity of influenza A virus – M Kastner – bioRxiv

 

Techniques

Single-cell transcriptional dynamics of flavivirus infection – F Zanini – bioRxiv

Slow digestible colored rice flour as wall material for microencapsulation: Its impacts on gut bacterial population and metabolic activities – I Wattananapakasem – Food Research International

 

Microbes in the news 

MBL Imaging Technology Reveals Organization of Gut Bacteria – Capecod.com

The secret germ warfare tests conducted off Devonport – The Herald

5 Good reasons to wash your hands as often as possible – South Coast Herald

Frank A. Bures: Hair growth after fecal transplants – Winona Daily News

THE BEAUTY OF BIO: DOES PROBIOTIC SKINCARE WORK? – The Times

Bacteria offer protection against breast cancer? – The Times of India

Viruses discovered a century ago may be our best defense against a threat that could kill 10 million people a year by 2050 – Business Insiders

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 11, 2017

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Events and jobs

Microbiology Laboratory Analyst – Cork (Ringaskiddy Road, Monkstown, Co. Cork)

 

Pregnancy and early life

Effect of probiotics on perinatal outcome in patients at high risk of preterm birth. – N Kirihara – The Journal of Obstetrics and Gynaecology Research

 

 

Human oral microbiome

Quantification of carious pathogens in the interdental microbiota of young caries-free adults. – D Bourgeois – PLoS One

 

Human gut microbiome

The gut microbiome in atherosclerotic cardiovascular disease – Z Jie – Nature Communications

Review: The microbiome as a novel paradigm in studying stress and mental health. – RT Liu – The American Psychologist

Review: The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – CL Hager – Digestive and Liver Disease

Review: Selected aspects of the human gut microbiota – M Ventura – Cellular and Molecular Life Sciences

 

Animal experiments 

Modulation of the gut microbiota by the mixture of fish oil and krill oil in high-fat diet-induced obesity mice. – C Ciu – PLoS One

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – X Qu – PLoS One

 

Animal microbiome 

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites – C Richards – PLoS One

 

Plant, root, and soil microbiome

The impact of the omics era on the knowledge and use of Lysobacter spp. to control phytopathogenic microorganisms. – G Puopolo – Journal of Applied Microbiology

The effect of pH, electrolytes and temperature on the rhizosphere geochemistry of phytosiderophores. – M Walter – Plant and Soil

Pathogenic potential of environmental resident fungi from ornithogenic soils of Antarctica – JRP Sousa – Fungal Biology

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh – DR Chaudhary – Microbial Ecology

 

Built environment 

Unravelling the core microbiome of biofilms in cooling tower systems. – L Di Gregorio – Biofouling

 

 

Phages and viruses

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics – S Roux – Nature Communications

Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – A Harms – bioRxiv

 

Techniques

Modified RNA-seq method for microbial community and diversity analysis using rRNA in different types of environmental samples. – YW Yan – PLoS One

A GLM-based latent variable ordination method for microbiome samples. – MB Sohn – Biometrics

Rapid enteric testing to permit targeted antimicrobial therapy, with and without Lactobacillus reuteri probiotics, for paediatric acute diarrhoeal disease in Botswana: A pilot, randomized, factorial, controlled trial – JM Pernica – PLoS One

A Tomato Spotted Wilt Virus S RNA-based Replicon System in Yeast –  K Ishibashi – Scientific Reports

Analyses Approaches for Bacteria – E Ribeiro – Exposure to Microbiological Agents in Indoor and Occupational Environments

 

Microbes in the news

Bacteria self-organize to build working sensors – EurekAlert

Effects of nutritional factors on the intestinal microbiota – Freie Universität

October 10, 2017

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Effects of amino acid supplements on metabolic health, a discussion of the broader risks and benefits of microbiome research, a book chapter evaluating microbiome statistical analysis tools.

Events and jobs

Assistant Professor in Microbiology, Tenure Track – Department of Microbiology & Immunology, University of British Columbia

General microbiome

Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research – Daria Shamarina – Microbiome

Pregnancy and early life

Review: Early microbiota, antibiotics and health – Alicja M Nogacka – Cellular and Molecular Life Sciences

Human gut microbiome

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control – Francesco Bifari – Genes & Nutrition

Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? – Dario Sorrentino – World Journal of Gastroenterology

Phages and viruses

Pre-print: Nasty Prophages and the Dynamics of Antibiotic-Tolerant Persister Cells – Alexander Harms – bioRxiv

Bioinformatics

Book Chapter: Processing and Analyzing Human Microbiome Data – Xuan Zhu – Statistical Human Genetics

Interpretation of microbiota-based diagnostics by explaining individual classifier decisions – A Eck – BMC Bioinformatics

Techniques

Pre-print: Umbilical cord blood diagnostics for early onset sepsis in premature infants: detection of bacterial DNA and systemic inflammatory response – Leena B Mithal – bioRxiv

Pre-print: Accuracy of microbial community diversity estimated by closed- and open-reference OTUs – Robert C Edgar – PeerJ

Microbes in the news

Bacteria with synthetic gene circuit self-assemble to build working device with gold nanoparticles – Phys Org

New test identifies antibiotic-resistant bacteria in 30 minutes – The Statesman

Microbes on the market

Summit Highlights Microbiome Preservation During Ridinilazole Treatment in Exploratory Phase 2 Clinical Trial at ID Week 2017 – Globe Newswire

October 8, 2017

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General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

October 7, 2017

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Events and jobs

Director of the Microbiome Research Laboratory – UT Southwestern

DOCTORAL STUDENT OR POSTDOCTORAL RESEARCHER –  Faculty of Veterinary Medicine, University of Helsinki – Application deadline: Nov 5, 2017

 

General microbiome

Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production – Y Boltyanskaya – Antonie van Leeuwenhoek

Biochemical Features of Beneficial Microbes: Foundations for Therapeutic Microbiology. – MA Engevik – Microbiology Spectrum

 

Pregnancy and early life

Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father – LC Kenny – bioRxiv

 

Human respiratory microbiome

Long-term effects of inhaled corticosteroids on sputum bacterial and viral loads in COPD. – M Contoli – The European Respiratory Journal

 

 

Human gut microbiome

Bifidobacteria and the infant gut: an example of co-evolution and natural selection. – F Turroni – Cellular and Molecular Life Sciences

Inflammatory bactericidal lectin RegIIIβ: Friend or Foe for the host? – T Miki – Gut Microbes

Review: Host-microbiota interplay in mediating immune disorders. – KM Felix – Annals of the New York Academy of Sciences

Review: Probiotics for the prevention of Hirschsprung-associated enterocolitis: a systematic review and meta-analysis. – H Nakamura – Pediatric Surgery International

 

Animal experiments 

Can intestinal microbiota be associated with non-intestinal cancers? – C Jacqueline – Scientific Reports

Gnotobiotics: getting a grip on the microbiome boom – S Mallapaty – Lab Animal

Nanoparticle curcumin ameliorates experimental colitis via modulation of gut microbiota and induction of regulatory T cells. – M Ohno – PLoS One

 

Animal microbiome 

Comparative analysis of microbial communities associated with bacteriomes, reproductive organs and eggs of the cicada Subpsaltria yangi. – D Wang – Archives of Microbiology

Antibiotic pretreatment minimizes dietary effects on reconstructure of rumen fluid and mucosal microbiota in goats. – H Shen – Microbiology Open

Elucidating the microbial community associated with the protein preference of sludge degrading worms – S de Valk – Environmental Technology

 

Plant, root and soil microbiome

Mycorrhizal fungi show regular community compositions in natural ecosystems. – E Verbruggen – The ISME Journal

Differential contribution of plant-beneficial functions from Pseudomonas kilonensis F113 to root system architecture alterations in Arabidopsis thaliana and Zea mays – J Vacheron – Molecular Plant-Microbe Interactions

Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development. – SC Castle – Oecologica

 

Water microbiome and extremophile 

Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. – D Kalenitchenko – The ISME Journal

Importance of free-living and particle-associated bacteria for the growth of the harmful dinoflagellate Prorocentrum minimum: evidence in culture stages – BS  Park – Marine and Freshwater Research

Metagenomic Sequencing of Microbial Communities from Brackish Water of Pangong Lake of the Northwest Indian Himalayas. – R Rathour – Genome Announcements

 

Built environment 

Managing the excessive proliferation of glycogen accumulating organisms in industrial activated sludge by nitrogen supplementation: A FISH-NanoSIMS approach – CA Onetto – Systematic and Applied Microbiology

 

 

Phages and viruses

Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. – G Freer – Current Medicinal Chemistry

 

Techniques

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing – P Schwendner – Microbiome

 

Microbes in the news

Puppies Linked To Bacterial Infection Outbreak Across 12 States – Forbes

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN

Episode Review: VICE’s ‘Post-Truth News and Microbiome’ – The Hoya

Second grade handwashing experiment leads to big decrease in bacteria, illness – EurekAlert

Validating microbiome claims:Including the latest DNA techniques-Formulation Summit – Cosmetics Design Europe

Macromolecules: Weapons in the Fight Against Antibiotic Resistance  – American Veterinarian

Scientists are trying to figure out how to keep bacteria from running rampant on space missions – Popular Science

Bacteria can spread antibiotic resistance through soil – Phys.org

October 6, 2017

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Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University Hospital – Posting End Date: Nov 2, 2017, 11:59:00 PM

Assistant Professor in Microbiology – Emporia State University – Deadline- open until filled

Assistant Professor in Virology and Microbiome Research – Auburn University, Alabama – Deadline- open until filled

Faculty Position in Microbial Environmental Metagenomics and Bioinformatics – University of Kansas – Initial review of applications: Nov 14, 2017

 

General microbiome

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

 

Human vaginal microbiome

Microbiome: Detecting diversity – C Humphries – Nature

 

Human gut microbiome

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome. – DA Medina – International Journal of Molecular Sciences

Synthetic biology and the gut microbiome. – J Dou – Biotechnology Journal

The Gut and Its Microbiome as Related to Central Nervous System Functioning and Psychological Well-being: Introduction to the Special Issue of Psychosomatic Medicine. – EA Mayer – Psychosomatic Medicine

Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. – CE Rosen – BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology.

 

Animal experiments 

Colonic thioguanine pro-drug: investigation of microbiome and novel host metabolism. – T Florin – Gut Microbes

The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer – JM Noto – PLoS Pathogens

Review: Microbiota, cirrhosis, and the emerging oral-gut-liver axis. – C Acharya – JCI Insight

 

Animal microbiome 

Interactions of pathogenic and commensal strains of Mannheimia haemolytica with differentiated bovine airway epithelial cells grown at an air-liquid interface – D Cozens – bioRxiv

Ixodes scapularis does not harbor a stable midgut microbiome – BD Ross – bioRxiv

 

Plant, root and soil microbiome

Protists are an integral part of the Arabidopsis thaliana microbiome. – M Sapp – Environmental Microbiology

Fusarium verticillioides: Advancements in Understanding the Toxicity, Virulence, and Niche Adaptations of a Model Mycotoxigenic Pathogen of Maize. – AA Blacutt – Phytopathology

Linking nitrogen load to the structure and function of wetland soil and rhizosphere microbial communities – ER Hester – bioRxiv

Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition. – J Almario – Proceedings of the National Academy of Sciences of the United States of America

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration. – CP Ward – Nature Communications

Changes in the abundance and structure of bacterial communities in the greenhouse tomato cultivation system under long-term fertilization treatments – X Zhang – Applied Soil Ecology

 

 

Phages and viruses

Evolution: Zapping viral RNAs – SP Goff – Nature

 

Techniques

Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System. – JF Chignell – Microbial Ecology

Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology. – L Bircher – Microbial Biotechnology

On the Reproduction Number of a Gut Microbiota Model. – C Barril – Bulletin of Mathematical Biology

 

Microbes in the news

Woods: The art of aging cheese – Lake Geneva News

Methane-Munching Bacteria Could Poop Out Your Future Clothes – Geek.com

XOMA (XOMA) Announces Multiple New License Agreements for Proprietary Phage Display Libraries – Biospace

Superbug superweapon: Identifying antibiotic-resistant bacteria in 30 minutes – New Atlas

New fundamental insight into the battle against bacteria – Science Daily

Ribaxamase Protects Gut Microbiome, Cuts Opportunistic C. diff Risk – MPR