November 17, 2017

Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

Advertisements

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

November 12, 2017

General microbiome

Rapid colonization of artificial endolithic uninhabited habitats – Charles S. Cockell, International Journal of Astrobiology

A bacterial pioneer produces cellulase complexes that persist through community succession – Sebastian Kolinko, Nature Microbiology

Endoglucanase and Xylanase Production by Chryseobacterium Species Isolated from Decaying Biomass – Asisipho Nkohla, Polish Journal of Environmental Studies

Human gut microbiome

Extended screening costs associated with selecting donors for fecal microbiota transplantation for treatment of metabolic syndrome-associated diseases – Laura J Craven, Open Forum Infectious Diseases

Fecal microbiota signatures of adult patients with different types of short bowel syndrome – Yuhua Huang, Gastroenterology

Association Between Small Intestinal Bacterial Overgrowth by Glucose Breath Test and Coronary Artery Disease – Andre Fialho, Digestive Diseases and Sciences

Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions – Jiayan Li, Microbial Ecology

Animal experiments

Transcriptomics-driven lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism – Anirikh Chakrabarti, npj Systems Biology and Applications

Vitamin A deficiency in mice alters host and gut microbial metabolism leading to altered energy homeostasis – Yuan Tian, The Journal of Nutritional Biochemistry

Subtle Microbiome Manipulation Using Probiotics Reduces Antibiotic-Associated Mortality in Fish – Victor Schmidt, mSystems

Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows – E. Castillo-Lopez, Journal of Applied Microbiology

How gut transcriptional function of Drosophila melanogaster varies with the presence and composition of the gut microbiota – Alyssa Bost, Molecular Ecology

Gut microbiomes and reproductive isolation in Drosophila – Philip T. Leftwich, PNAS

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages – Shenzheng Zeng, PeerJ

Animal microbiome

FVD: The fish-associated virus database – Yaxin Chen, Infection, Genetics and Evolution

Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat–swine interspecies transmission –  Susanna K. P. Lau, Journal of General Virology

Forest canopy, water level, and biopesticide interact to determine oviposition habitat selection in Aedes albopictus – Christopher A. Binckley, Journal of Vector Ecology

Ecological characterization of Aedes aegyptilarval habitats (Diptera: Culicidae) in artificial water containers in Girardot, Colombia – Diana C. Garcia-Sánchez, Journal of Vector Ecology

Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water – Renata Medina-Silva, Antonie van Leeuwenhoek

Plant, root, and soil microbiome

Changes in the soil bacterial community along a pedogenic gradient – Manuel Sánchez-Marañón, Scientific Reports

 

Rhizosphere activity and atmospheric methane concentrations drive variations of methane fluxes in a temperate forest soil – Jens-Arne Subke, Soil Biology and Biochemistry

The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley – Divyashri Baraniya, Microbial Ecology

The temperature sensitivity of soil organic matter decomposition is constrained by microbial access to substrates – Gabriel Y.K. Moinet, Soil Biology and Biochemistry

Application of Aspergillus aculeatus to rice roots reduces Cd concentration in grain – Yan Xie, Plant and Soil

Screening Bacillus species as biological control agents of Gaeumannomyces graminis var. tritici on wheat – Lirong Yang, Biological Control

Soil geochemical factors regulate Cd accumulation by metal hyperaccumulating Noccaea caerulescens (J. Presl & C. Presl) F.K. Mey in field-contaminated soils – Carla E. Rosenfeld, Science of The Total Environment

Antibiotics in the Soil: Sources, Environmental Issues, and Bioremediation – Umesh B. Jagtap, Antibiotics and Antibiotics Resistance Genes in Soils

Water and extremophile microbiome

Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach – Paula M. Tribelli, Journal of Industrial Microbiology & Biotechnology

Potential Role of Halophile in Crude Glycerol Based Biorefinery – Noopur Singh, Biorefining of Biomass to Biofuels

Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein – Chen Wang, PLOS one

Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp. – Jake V. Bailey, mBio

Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation – Jonathan Botha, Extremophiles

Prospects of Solvent Tolerance in Butanol Fermenting Bacteria – Shuvashish Behera, Biorefining of Biomass to Biofuels

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead – Susanna M. Blunt, Science of the Total Environment

Effect of TiO2 and CeO2 nanoparticles on the metabolic activity of surficial sediment microbial communities based on oxygen microelectrodes and high-throughput sequencing – Lingzhan Miao, Water Research

Performance and microbial communities in a combined bioelectrochemical and sulfur autotrophic denitrification system at low temperature – Dan Chen, Chemosphere

Ongoing biodegradation of Deepwater Horizon oil in beach sands: Insights from tracing petroleum carbon into microbial biomass – Joel T. Bostic, Marine Pollution Bulletin

Antibiotic degradation and microbial community structures during acidification and methanogenesis of swine manure containing chlortetracycline or oxytetracycline – Fubin Yin, Bioresource Technology

Metagenomics profiling for assessing microbial diversity in both active and closed landfills – Mohamad Yusof Zainun, Science of The Total Environment

Development of a microbial community-based index of biotic integrity (MC-IBI) for the assessment of ecological status of rivers in the Taihu Basin, China – Lihua Niu, Ecological Indicators

Microbial community response to silver nanoparticles and Ag+in nitrifying activated sludge revealed by ion semiconductor sequencing – Carley A. Gwin, Science of The Total Environment

Anaerobic co-digestion of pig manure and food waste; effects on digestate biosafety, dewaterability, and microbial community dynamics – C. Dennehy, Waste Management

Evaluating the impacts of triclosan on wastewater treatment performance during startup and acclimation – R. M. Holzem, Water Science and Technology

Nitrifier Gene Abundance and Diversity in Sediments Impacted by Acid Mine Drainage – Bhargavi Ramanathan, Frontiers in Microbiology

Live Faecalibacterium prausnitzii induces greater TLR2 and TLR2/6 activation than the dead bacterium in an apical anaerobic co-culture system – Eva Maier, Cellular Microbiology

Food microbiome

A mathematical model to predict early quality attributes in hake during storage at low temperature – C. Vilas, Journal of Food Engineering

Chemical, Physiochemical, and Microstructural Properties, and Probiotic Survivability of Fermented Goat Milk Using Polymerized Whey Protein and Starter Culture Kefir Mild 01 – Hao Wang, Food Microbiology & Safety

Re-evaluation of mono- and di-glycerides of fatty acids (E 471) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

Opportunities and hurdles of edible insects for food and feed – D. Dobermann, Nutrition Bulletin

Re-evaluation of alginic acid and its sodium, potassium, ammonium and calcium salts (E 400–E 404) as food additives – EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS), European Food Safety Authority

The SALAMANDER project: SALivAry bioMarkers of mediterraneAN Diet associated with long-tERm protection against type 2 diabetes – G. B. Proctor, Nutrition Bulletin

Polyphenols and health: Interactions between fibre, plant polyphenols and the gut microbiota – C. A. Edwards, Nutrition Bulletin

Techniques

Optimization of Culture Conditions for the Production of Halophilic Protease by Newly Isolated Bacillus sonorensis – S. Sankaralingam, American-Eurasian Journal of Agricultural & Environmental Science

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 5, 2017

 

A shorter digest today, but includes a lot of human gut microbiome studies and a cool study on microbes used to treat snake bites!

General microbiome

Comparison of two Jatropha species (Euphorbiaceae) used popularly to treat snakebites in Northeastern Brazil: Chemical profile, inhibitory activity against Bothrops erythromelas venom and antibacterial activity – Juliana Félix-Silva, Journal of Ethnopharmacology

Multi-site human microbiome

A slippery slope: On the origin, role and physiology of mucus – Farhan Taherali, Advanced Drug Delivery Reviews

Human gut microbiome

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial –  Peter Holger Johnsen, The Lancet Gastroenterology & Hepatology

Estrogens and Female Liver Health – Karen L. Chen, Steroids

Safety and Efficacy of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection in Patients With Cancer Treated With Cytotoxic Chemotherapy: A Single-Institution Retrospective Case Series – Mehrdad Hefazi, Mayo Clinic Proceedings

Gut Microbiota and Cancer Patients: A Broad-Ranging Relationship – Giovanni Cammarota, Mayo Clinic Proceedings

Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies – Yongbo Kang, Clinics and Research in Hepatology and Gastroenterology

Preface to “Gut microbiome in health and disease” – Maikel P. Peppelenbosch, Best Practice & Research Clinical Gastroenterology

Results of the implementation of a multidisciplinary programme of faecal microbiota transplantation by colonoscopy for the treatment of recurrent Clostridium difficile infection – Antonio López-Sanromán, Gastroenterología y Hepatología (English Edition)

Animal experiments

Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows – D.W. Pitta, Journal of Dairy Science

Chronic chlorpyrifos exposure elicits diet-specific effects on metabolism and the gut microbiome in rats – Bing Fang, Food and Chemical Toxicology

Housing influences tissue cytokine levels and the fecal bacterial community structure in rats – Padmaja Shastri, Journal of Functional Foods

An intact gut microbiota may be required for lactoferrin-driven immunomodulation in rats – Yongping Wen, Journal of Functional Foods

Untargeted metabolomic profiling of urine in Wistar rats reveals enhanced bioavailability of soy isoflavones post short-term consumption of noni (Morinda citrifolia) juice – José-Manuel Fallas-Ramirez, Journal of Functional Foods

Plant, root, and soil microbiome

Long and short term effects of solarization on soil microbiome and agricultural production – Housam Kanaan, Applied Soil Ecology

Water and extremophile microbiome

Microbial communities involved in biogas production exhibit high resilience to heat shocks – Abendroth Christian, Bioresource Technology

Food microbiome

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins, Food Research International

Microbial ecology along the processing of Spanish olives darkened by oxidation – Eduardo Medina, Food Control

Co-fermentation of onion and whey: A promising synbiotic combination – Federica Tinello, Journal of Functional Foods

Diverse yeasts for diverse fermented beverages and foods – Chris Todd Hittinger, Current Opinion in Biotechnology

Techniques

Microbiome measurement: Possibilities and pitfalls – Djawad Radjabzadeh, Best Practice & Research Clinical Gastroenterology

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration – DongFeng Yan, Biological Conservation

Commensal Koch’s postulates: establishing causation in human microbiota research – B Anne Neville, Current Opinion in Microbiology

Microbes in the news

Disease outbreak at Marine Corps boot camp abates in San Diego – Carl Prine, The San Diego Union-Tribune

November 4, 2017

Events and jobs

Microbiology Lab Technician – Manpower – Evansville

Research Associate in Plant and Arthropod Microbiome – Indiana University

 

General microbiome

Review: New Insights into Graft-Versus-Host Disease and Graft Rejection – E Perkey – Annual Review of Pathology

Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete. – J Zhang – Scientific Reports

Review: A Call to Arms: Quest for a Cryptococcal Vaccine – MC Caballero Van Dyke – Cell

 

 

Human respiratory microbiome

Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection. – M Pichon – Vaccines

 

 

Human gut microbiome

Review: Atherosclerosis: Association between the gut microbiome and atherosclerosis – WT Barrington – Nature Reviews

Improvement in cardiometabolic risk markers following a multifunctional diet is associated with gut microbial taxa in healthy overweight and obese subjects. – N Marungruang – European Journal of Nutrition

Opinion: NOD2 and bacterial recognition as therapeutic targets for Crohn’s disease. – M de Bruyn – Expert Opinion on Therapeutic Targets.

 

Animal experiments 

Microbial diversity and composition in different gut locations of hyperlipidemic mice receiving krill oil. – C Lu – Applied Microbiology and Biotechnology

Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration. – X Huang – Scientific Reports

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. – B Routy – Science

 

Animal microbiome 

The bacterium Wolbachia exploits host innate immunity to establish a symbiotic relationship with the dengue vector mosquito Aedes aegypti. – X Pan – The ISME Journal

Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment. – B Ordoñez-Arévalo – Environmental Science and Pollution Research International

Microbial community and ovine host response varies with early and late stages of Haemonchus contortus infection. – S El-Ashram – Veterinary Research Communications

 

Plant, root and soil microbiome

The spent culture supernatant of Pseudomonas syringae contains azelaic acid – SG Javvadi – bioRxiv

Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Z Zhou – Frontiers in Microbiology

Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity – GA Jana – Genome Announcements

A New Proposal for the Pathogenic Mechanism of Non-Coeliac/Non-Allergic Gluten/Wheat Sensitivity: Piecing Together the Puzzle of Recent Scientific Evidence. – V Leccioli – Nutrients

Identification of novel small RNAs in Burkholderia cenocepacia KC-01 expressed under iron limitation and oxidative stress conditions. – S Ghosh – Microbiology

Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments – AE Rotaru – bioRxiv

 

Water and extremophile microbiome

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. – BJ Tully – The ISME Journal

 

 

Phages and viruses

Co-existence of freshwater and marine T4-like myoviruses in a typical subtropical estuary. – L Liu – FEMS Microbiology Ecology

 

Techniques

Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. – C Alcon-Giner – BMC Genomics

Metagenomic analysis reveals potential interactions in an artificial coculture. – M Ren – AMB Express

Review: Phage Hunters: computational strategies for finding phages in large-scale ‘omics datasets – BL Hurwitz – Virus Research

Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing – M Shnayder – bioRxiv

 

Microbes in the news

Can microbiology tell us exactly what killed the Aztecs? – OUP Blog

Tuning the Microbiome Improves Melanoma Immunotherapy Response – GEN

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