November 15, 2017

Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

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November 10, 2017

Events and jobs
Postdoctoral Fellow – Institute of Genome Sciences (IGS) with Hotopp Lab – Baltimore, Maryland

Pregnancy and early life
Influence of vitamin D on key bacterial taxa in infant microbiota in the KOALA Birth Cohort Study – Chris E. Talsness – PLoS One

Review: Role of the Human Breast Milk-Associated Microbiota on the Newborns’ Immune System: A Mini Review – Marco Toscano – Frontiers in Microbiology

Review: The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota – Christian Milani – Microbiology and Molecular Biology Reviews

Multi-site human microbiome
Segmented Filamentous Bacteria Provoke Lung Autoimmunity by Inducing Gut-Lung Axis Th17 Cells Expressing Dual TCRs – C. Pierce Bradley – Cell Host and Microbe

Human vaginal microbiome
Genitourinary Syndrome of the Menopause: Vaginal Health and Microbiota – Maria Jesús Cancelo-Hidalgo – Menopause

Human gut microbiome
Review: Microbial biotransformations in the human distal gut – Elisabeth M Bik – British Journal of Pharmacology

Review: The Human Microbiome and Obesity: Moving beyond Associations – Padma Maruvada – Cell Host and Microbe

A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation – Hassan Brim – Genes

Multiple articles from Frontiers in Immunology:
LC3-Associated Phagocytosis Is Required for Dendritic Cell Inflammatory Cytokine Response to Gut Commensal Yeast Saccharomyces cerevisiae – Dimitra Lamprinaki – Frontiers in Immunology

Immunological and Clinical Effect of Diet Modulation of the Gut Microbiome in Multiple Sclerosis Patients: A Pilot Study – Marina Saresella – Frontiers in Immunology

Review: TH17 Cell and Epithelial Cell Crosstalk during Inflammatory Bowel Disease and Carcinogenesis – Jan Kempski – Frontiers in Immunology

Animal experiments
Difference in the gut microbiome between ovariectomy-induced obesity and diet-induced obesity – S. Choi – Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

The effects of starter microbiota and the early life feeding of medium chain triglycerides on the gastric transcriptome profile of 2- or 3-week-old cesarean delivered piglets – Paolo Trevisi – Journal of Animal Science and Biotechnology

Animal microbiome
Prodigiosin, Violacein, and Volatile Organic Compounds Produced by Widespread Cutaneous Bacteria of Amphibians Can Inhibit Two Batrachochytrium Fungal Pathogens – Douglas C. Woodhams – Microbial Ecology

Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota – Alina S. Grigorescu – Microbial Ecology

Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis – Na Zhang – PLoS One

Diets Alter the Gut Microbiome of Crocodile Lizards – Hai-Ying Jiang – Frontiers in Microbiology

Plant, root, and soil microbiome
Opinion: Nitrogen limitation of decomposition and decay: how can it occur? – Colin Averill – Global Change Biology

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth – Dalia Molina-Romero – PLoS One

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil – Da-Wei Jing – PLoS One

Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil – Junhui Chen – Biology and Fertility of Soils

Book of interest: Endophytes: Biology and Biotechnology – Dinesh K. Maheshwari

Biosynthetic potential of actinomycetes in brown forest soil on the eastern coast of the aegean sea – I. G. Shirokikh – Eurasian Soil Science

Water and extremophile microbiome
Editorial: Deep Carbon in Earth: Early Career Scientist Contributions to the Deep Carbon Observatory – Donato Giovannelli – Frontiers in Earth Science

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum – Mireia Mestre – Molecular Ecology

Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities – Marc W. Van Goethem – Frontiers in Microbiology

Influences of anthropogenic land use on microbial community structure and functional potentials of stream benthic biofilms – Xiaodong Qu – Scientific Reports

Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea – Bernd Wemheuer – Microorganisms

Biohydrogen production at pH below 3.0: Is it possible? – V.T. Mota – Water Research

Groundwater Microbial Communities Along a Generalized Flowpath in Nomhon Area, Qaidam Basin, China – Y Sheng – Ground Water
No link available yet, linked to PubMed.

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity – Bruno L. Mello – Biotechnology for Biofuels

Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China – Wenting Guo – Applied Microbiology and Biotechnology

Built environment
The Nosocomial Risk of Bacterial Contamination of Surgical Wards at Saint Francis Hospital in Katete District of Zambia – Frank Mtonga – ARC Journal of Clinical Case Reports

Food microbiology
Preventive effects of a probiotic mixture in an ovalbumin-induced food allergy model – HS Shin -Journal of Microbiology and Biotechnology
No link available yet, linked to PubMed.

Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro by human intestinal microbiota of polysaccharides from Fuzhuan brick tea – Guijie Chen – Food Chemistry

Phages and viruses
Several book chapters from Bacteriophage Therapy:
Book Section: Methods for Bacteriophage Preservation – Małgorzata B. Łobocka
Interaction of Bacteriophages with Mammalian Cells – Zuzanna Kaźmierczak

Perspective: The Intra-Dependence of Viruses and the Holobiont – Juris A. Grasis – Frontiers in Immunology

Bioinformatics
Metagenome sequence clustering with hash-based canopies – Mohammad Arifur Rahman – Journal of Bioinformatics and Computational Biology

Book: UNIT 1E.14 Computational Methods for Human Microbiome Analysis – Matthieu J. Miossec – Current Protocols in Microbiology

Microbes in the news
Enhanced understanding of the microbiome is helping medicine – The Economist

Microbes on the market
Seres Therapeutics to Participate in Three Upcoming November Conferences – Business Wire

Global Microbiome Sequencing Services Market Outlook 2017 Growth, Trends, Forecasts 2022 – Samuel – Talk Daily News

Space travel changes gut bacteria in mice – Science Nordic

New model reveals possibility of pumping antibiotics into bacteria – Phys Org
Paper: New free-exchange model of EmrE transport – Anne E. Robinson – PNAS

EPA approves bacteria-infected insects to kill mosquitoes – Bonnie Burton – CNET

Bacteria Hysteria
Deadly bacterial infections could be coming from your kitchen sink PLUGHOLE – Matt Atherton – Express

Science, publishing, and career
The GOP tax bill could be a disaster for PhD students – Jen Kirby – Vox

November 8, 2017

Photosynthesizing bacteria printed on paper, investigations of microbial communities in water dispensers and mines, a review on the health benefits of natural products from truffles.

Human respiratory microbiome

Review: Airway Microbiota and Allergic Diseases: Clinical Implications – Eman M Fouda – International Journal of Pulmonary and Respiratory Sciences

Human oral microbiome

Proton pump inhibitor alters oral microbiome in gastrointestinal tract of healthy volunteers – Tsuyoshi Mishiro – Journal of Gastroenterology and Hematology

Human gut microbiome

Gut Microbiota Interacts with Markers of Adipose Tissue Browning, Insulin Action and Plasma Acetate in Morbid Obesity – José María Moreno-Navarrete – Molecular Nutrition and Food Research

Is there a relationship between intestinal microbiota, dietary compounds, and obesity? – Joanna Kałużna-Czaplińska – Trends in Food Science and Technology

Animal experiments

Combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota – Le Zhao – Food and Function

Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis – Fionn Dunphy Doherty – Brain, Behavior, and Immunity

Host-microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice – Antonio Molinaro – Molecular Metabolism

Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis – June-Chul Lee – PLOS ONE

Animal microbiome

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica) – Huan Li – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere – Zeno Varanini – Plant and Soil

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface – J R Halliwell – Scientific Reports

Co-existence of Rhizobia and Diverse Non-Rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii,Rhizobium multihospitium–like and Burkholderia pyrrocinia–like Strains – Junkun Lu – Frontiers in Microbiology

Diversity of endophytic bacteria from Piper spp. with antagonistic property against Phytophthora capsici causing foot rot disease in black pepper (Piper nigrum L.) – Nadiya Kollakkodan – Journal of Tropical Agriculture

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests – Sten Anslan – Soil Biology and Biochemistry

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Resource availability underlies the plant-fungal diversity relationship in a grassland ecosystem – Lauren C Cline – Ecology

Water and extremophile microbiome

Microflora Thermarum Atlas project: biodiversity in thermal spring waters and natural SPA pools – F Valeriani – Water Science and Technology: Water Supply

Modes of carbon xation in an arsenic and CO2-rich shallow hydrothermal ecosystem – Nolwenn Callac – Scientific Reports

Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea – Tiantian Yu – Applied Microbiology and Biotechnology

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula – Catherine M Luria – Frontiers in Microbiology

Built environment

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine – Yanping Bao – Science of the Total Environment

Investigation of microbial communities in water dispensers – Sangjung Park – Applied Biological Chemistry

Food microbiology

Review: Potential health benefits of natural products derived from truffles: A review – Seema Patel – Trends in Food Science and Technology

Probiotics/prebiotics

Review: The development of seaweed-derived bioactive compounds for use as prebiotics and nutraceuticals using enzyme technologies – Suvimol Charoensiddhi – Trends in Food Science and Technology

Phages and viruses

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes – Judith Villager – The ISME Journal

Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures – Joana Oliveira – Journal of Dairy Science

Bioinformatics

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks – Zhu Chengsheng – Nucleic Acids Research

Metabolomics

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database – Wailing Huang – Nucleic Acids Research

mVOC 2.0: a database of microbial volatiles – Marie C Lemfack – Nucleic Acids Research

Techniques

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems – Karsten Karczewski – Limnologica Ecology and Management of Inland Waters

More microbes

Review: Our microbes not only produce antibiotics, they also overproduce amino acids – Sergio Sanchez – The Journal of Antibiotics

Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria – José A Gutiérrez-Barranquero – Microbial Biotechnology

Microbes in the news

Bacteria-Activated Wallpaper that Generates Electricity – Katharine Keane – Architect Magazine

US government approves ‘killer’ mosquitoes to fight disease – Emily Waltz – Nature News

Bacteria may help babies’ digestive tracts more than suspected, scientists find – EurekAlert

Using neutrons to study how resistant bacteria evolve – Phys Org

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer – News Medical Life Sciences

New model reveals possibility of pumping antibiotics into bacteria – EurekAlert

Microbes on the market

Seres Therapeutics Awarded Grant from CARB-X to Support Development of Microbiome Therapeutic Candidate – Business Wire

Michael J. Fox Foundation, 23andMe to Jointly Advance Parkinson’s Disease Research – Carolina Henriques – Parkinson’s News Today

November 2, 2017

 

Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

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

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

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

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

November 1, 2017

Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

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

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – Plos One

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

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

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone

 

October 26, 2017

In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

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

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

October 17, 2017

The effects of antimicrobials in household products on the maternal and infant microbiome, water quality of an urban stream network, and using adaptive evolution to improve lager yeast hybrids.

Pregnancy and early life

Household triclosan and triclocarban effects on the infant and maternal microbiome – Jessica V Ribado – EMBO Molecular Medicine

Water and extremophile microbiome

Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations – L M Ward – Geobiology

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole – T L Hamilton – Geobiology

Built environment

Urban infrastructure influences dissolved organic matter quality and bacterial metabolism in an urban stream network – Clay P Arango – Freshwater Biology

Food microbiology

Pre-print: Enhanced wort fermentation with de novo lager hybrids adapted to high ethanol environments – Kristoffer Krogerus – bioRxiv

More microbes

Pre-print: Phosphate starvation induces replacement of phospholipids with the betaine lipid diacylglycerol-N,N,N-trimethylhomoserine in the human fungal pathogen Candida albicans – Surabhi Naik – bioRxiv

Microbes in the news

Infections by C.diff bacteria are on the rise and can cause serious problems – Consumer Reports – The Washington Post

Engineered bacteria build microstructures on their own – Michael Torrice – Chemical & Engineering News

Gut fungi might be linked to obesity and inflammatory bowel disorders – Tina Hesman Saey – Science News

Rare bacteria in dead elephant sparks alarm – Siba Mohanty – The New Indian Express

Woman Contracts Rare Bacterial Infection on 12-Hour Flight – Rachael Rettner – Live Science

Microbial Drug Resistant Mutations Found via Novel Genome Screen – Genetic Engineering and Biotechnology News

One More Small Piece of the Puzzle on the Role of Gut Micro-organisms in MS – Ana Belo Van Wijk – Multiple Sclerosis News Today

Microbes on the market

New Clinical Data and Microbiome Research from Rebiotix’s Phase 2 Program for RBX2660 Highlighted at the World Congress of Gastroenterology at ACG2017 – PR Newswire