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

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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 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 9, 2017

Today, we have interesting papers about diet and microbiota both in human and other mammals. We have also papers about urchin and black slug microbiota and gut remediation (use of probiotics to manage metal accumulation).

 

Human Microbiome

State of the art: Manipulating the microbiome: evolution of a strategy to prevent S. aureus disease in children – D F Khamash – Journal of Perinatology

Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications – Shuai Zheng – Scientific Reports

Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota – Gregorio Iraola – Nature Communications

Impact of Lactobacillus reuteri colonization on gut microbiota, inflammation, and crying time in infant colic – Monica L. Nation – Scientific Reports

Outlook: Microbiome: A bag of surprises – Claire Ainsworth – Nature

Research Highlight: Gut microbiota: Oral bacteria: a cause of IBD? – Iain Dickson – Nature Reviews Gastroenterology and Hepatology

Commentary: Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut – Petra Louis – mBio

Opinion: How poverty affects diet to shape the microbiota and chronic disease – Christy A. Harrison – Nature Reviews Immunology

Review: Balancing Herbal Medicine and Functional Food for Prevention and Treatment of Cardiometabolic Diseases through Modulating Gut Microbiota – Ming Lyu – Frontiers in Microbiology

Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients – Matteo Soverini – Frontiers in Microbiology

 

Animal Microbiome

Effect of Dietary Forage to Concentrate Ratios on Dynamic Profile Changes and Interactions of Ruminal Microbiota and Metabolites in Holstein Heifers – Jun Zhang –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Antibiotic-induced Alterations in Gut Microbiota are Associated with Changes in Glucose Metabolism in Healthy Mice – Richard R. Rodrigues – Frontiers in Microbiology

Phylogeny and Antagonistic Activities of Culturable Bacteria Associated with the Gut Microbiota of the Sea Urchin (Paracentrotus lividus) – Marinella Silva Laport – Current Microbiology

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice – Matthew J. Dalby – Cell Reports

Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes – Ryan Joynson – Frontiers in Microbiology

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period – Zhigang Zhu – PLoS ONE

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota – Guolin Li – Cell Metabolism

Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis – Chien-Chao Chiu – Nutrients

 

Beneficial Microbes and Molecules

Gut remediation: a potential approach to reducing chromium accumulation using Lactobacillus plantarum TW1-1 – Gaofeng Wu – Scientific Reports

(Provisionally accepted, Full text available soon) Lactobacillus plantarum MYS6 ameliorates fumonisin B1-induced hepatorenal damage in broilers – B V. Deepthi –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Wuji Wan formula ameliorates diarrhoea and disordered colonic motility in post-inflammation irritable bowel syndrome rats by modulating the gut microbiota – Ying Chen – Frontiers in Microbiology

Polysaccharides from Chrysanthemum morifolium Ramat ameliorate colitis rats by modulating the intestinal microbiota community – Jin-Hua Tao – Oncotarget

 

Environmental Microbiology

Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site – Silvia Crognale – Frontiers in Microbiology

 

Methods

Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota – Fanjing Meng – Molecular Medicine Reports

 

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 6, 2017

Today we have an interesting digest with several articles about human microbiome. Additionally, today we also remark part of the recently release book “Understanding the Gut-Bone Signaling Axis”, with interesting chapters treating the connections between microbiota and bone health.

(Each file with an asterisk in the start contains open access to fulltext)

 

Human Microbiome

Bone Mechanical Function and the Gut Microbiota – C. J. Hernandez – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Prebiotics and Bone – Corrie M. Whisner – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Inflammatory Bowel Disease: Effects on Bone and Mechanisms – Francisco A. Sylvester – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Immunology of Gut-Bone Signaling – Fraser L. Collins –  Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota and Bone Health – Darin Quach – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Increased stool immunoglobulin A level in children with autism spectrum disorders – Jiaxiu Zhou – Research in Developmental Disabilities (ScienceDirect)

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

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

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

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota – Rui M Ferreira – Gut (BMJ)

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

Associations Between Microbiota, Mitochondrial Function, and Cognition in Chronic Marijuana Users – Jun Panee – Journal of Neuroimmune Pharmacology

Genetic mannose binding lectin deficiency is associated with airway microbiota diversity and reduced exacerbation frequency in COPD – Alison J Dicker – Thorax (BMJ)

Molecular characterization of Multidrug Resistant Bacteroides isolates from Hungarian clinical samples – Károly Péter Sárvária – Journal of Global Antimicrobial Resistance (ScienceDirect)

* Commentary: Human Intestinal Microbiota and Colorectal Cancer: Moving Beyond Associative Studies – Christian Jobin – Gastroenterology

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. Chena – Steroids (ScienceDirect)

 

Beneficial microbes

(Provisionally accepted, Full text available soon) Probiotic Bacteria Alter Pattern-Recognition Receptor Expression and Cytokine Profile in a Human Macrophage Model Challenged with Candida albicans and Lipopolysaccharide – Victor H. Matsubara – Frontiers in Microbiology

* Butyrate and propionate inhibit antigen-specific CD8+ T cell activation by suppressing IL-12 production by antigen-presenting cells – Claudia Nastasi – Scientific Reports (NPG)

 

Animal Microbiome

(Provisionally accepted, Full text available soon) The Gut Entomotype of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae) and Their Effect on Host Nutrition Metabolism – Abrar Muhammad – Frontiers in Microbiology

Porcine small and large intestinal microbiota rapidly hydrolyze the masked mycotoxin deoxynivalenol-3-glucoside and release deoxynivalenol in spiked batch cultures in vitro – Silvia W. Gratz – Applied and Environmental Microbiology (ASM)

A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon – Knut Rudi – Applied and Environmental Microbiology (ASM)

Fecal microbiota transplant from highly feed efficient donors shows little effects on age-related changes in feed efficiency-associated fecal microbiota in chickens – Sina-Catherine Siegerstetter – Applied and Environmental Microbiology (ASM)

Short communication: The effect of heat treatment of bovine colostrum on the concentration of oligosaccharides in colostrum and in the intestine of neonatal male Holstein calves – Amanda J. Fischer – Journal of Dairy Science

* Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing – Yanfen Cheng – Frontiers in Microbiology

* Neuroprotective effect of Ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals – Jieun Park – Scientific Reports (NPG)

* Gut dysbiosis and impairment of immune system homeostasis in perinatally-exposed mice to Bisphenol A precede obese phenotype development – Yann Malaisé – Scientific Reports (NPG)

Impact of Enteric Health and Mucosal Permeability on Skeletal Health and Lameness in Poultry – L. R. Bielke – Understanding the Gut-Bone Signaling Axis (SpringerLink)

Gut Microbiota Are Disease-Modifying Factors After Traumatic Spinal Cord Injury – Kristina A. Kigerl – Neurotherapeutics (SpringerLink)

 

Food Microbes

(Provisionally accepted, Full text available soon) Extractive Fermentation of Lactic Acid in Lactic Acid Bacteria Cultivation: A Review – Majdiah Othman – Frontiers in Microbiology

* Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

The main spoilage-related psychrotrophic bacteria in refrigerated raw milk – J.C. Ribeiro Júnior – Journal of Dairy Science

* Preprint: Kombucha as a model system for multispecies microbial cooperation: theoretical promise, methodological challenges and new solutions ‘in solution’ – Alexander Niall May – BioRxiv

* New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter – Yuhong Huang – Scientific Reports (NPG)

 

Environmental Microbes

(Provisionally accepted, Full text available soon) Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xueying Tian – Frontiers in Microbiology

Perturbation of seafloor bacterial community structure by drilling waste discharge – Tan T. Nguyen – Marine Pollution Bulletin