March 24, 2017

Complex glycan degradation in the gut; role of LPS-binding protein in NAFLD; contribution of environmental factors to arbuscular mycorrhizal fungi community composition and structure; and ResistoMap, a new web-based bioinformatic tool for visualizing the human gut resistome.

 

Events and jobs
Visiting Professor (Part Time) Microbiology – Chamberlain College of Nursing – Arlington, VA

Scientific Officer (Full Time) Microbiology – Australian Clinical Labs – Sydney, AU

Human respiratory microbiome
Understanding the Lung Abscess Microbiome: Outcomes of Percutaneous Lung Parenchymal Abscess Drainage with Microbiologic Correlation – Christopher Duncan – Cardiovascular and Interventional Radiology

Human oral microbiome
Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Joice Dias Correa – Microbiome

Candida albicans alters the bacterial microbiome of early in vitro oral biofilms – M. M. Janus – Journal of Oral Microbiology

Human skin microbiome
Injections through skin colonized with Staphylococcus aureus biofilm introduce contamination despite standard antimicrobial preparation procedures – Yi Wang – Scientific Reports

Compartmentalized Control of Skin Immunity by Resident Commensals – Shruti Naik – Science

Human gut microbiome
Complex pectin metabolism by gut bacteria reveals novel catalytic functions – Didier Ndeh – Nature

Protective Factors in the Intestinal Microbiome Against Clostridium difficile infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation – Yeon Joo Lee – The Journal of Infectious Diseases

Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure – Takehiro Kamo – PLoS One

Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis – Tung Hiu Li – Scientific Reports

Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation – Benoit Chassaing – Gut

Review: Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia – Sabrina Tamburini & Jose C. Clemente – Nature Reviews Gastroenterology & Hepatology

Proteobacteria explain significant functional variability in the human gut microbiome – Patrick S. Bradley & Katherine S. Pollard – Microbiome

Antigen-Presenting Human γδ T Cells Promote Intestinal CD4+ T Cell Expression of IL-22 and Mucosal Release of Calprotectin – Christopher J. Tyler – Journal of Immunology

Odd Chain Fatty Acids; New Insights of the Relationship Between the Gut Microbiota, Dietary Intake, Biosynthesis and Glucose Intolerance – Benjamin J. Jenkins – Scientific Reports

Review: The gut microbiome in human neurological disease: A review – Helen Tremlett – Annals of Neurology

Animal experiments
Loss of lipopolysaccharide-binding protein attenuates the development of diet-induced non-alcoholic fatty liver disease in mice – Cheng Jun Jin – Journal of Gastroenterology and Hepatology

Animal microbiome
Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Plant, root, and soil microbiome
The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation – Xihui Xu – Scientific Reports

Intercropping maize and common bean enhances microbial carbon and nitrogen availability in low phosphorus soil under Mediterranean conditions – Mourad Latati – European Journal of Soil Biology

The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites – Julien P. Guyonnet – FEMS Microbiology Ecology

Water and extremophile microbiome
Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident – Ming Jiang Zhang – Scientific Reports

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Small Molecules Belowground: The Role of Specialized Metabolites in the Rhizosphere – Massalha H – The Plant Journal

Food microbiology
Rice- or pork-based diets with similar calorie and content result in different rat gut microbiota – Xiaozhe Qi – International Journal of Food Sciences and Nutrition

Bioinformatics
ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

March 21, 2017

Events and jobs

Microbiology Department Manager – Medlab Pathology – Sydney

General microbiome

The ecology of human microbiota: dynamics and diversity in health and disease – A Karkman – Annals of the New York Academy of Sciences

Human gut microbiome

The gut microbiome in human neurological disease: A review – H Tremlett – Annals of Neurology

Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health – DR Covian – Frontiers in Microbiology

Animal microbiome

Effects of a protected inclusion of organic acids and essential oils as antibiotic growth promoter alternative on growth performance, intestinal morphology and gut microflora in broilers – Y Liu – Animal Science Journal

Extreme drought, host density, sex, and bullfrogs influence fungal pathogen infection in a declining lotic amphibian – AJ Adams – Ecosphere

Neoagarotetraose protects mice against intense exercise-induced fatigue damage by modulating gut microbial composition and function – N Zhang – Molecular Nutrition and Food Research

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Die –  L Zhang – Scientific Reports

Plant, root and soil microbiome

*ReviewRhizogenic agrobacteria in hydroponic crops: epidemics, diagnostics and control – L Bosmans – Plant Pathology

Mn accumulation in a submerged plant Egeria densa (Hydrocharitaceae) is mediated by epiphytic bacteria – K Tsuji – Plant, Cell and Environment

Water microbiome and extremophiles

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary – MW Smith – Microbiology Open

Metagenomics of Hyperthermophilic Environments: Biodiversity and Biotechnology – A Strazzulli – Microbial Ecology of Extreme Environments

Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment – DFR Cleary – Marine Ecology

Crenarchaeal Viruses of Hot Springs: Diversity, Ecology and Co-evolution –  AC Ortmann – Microbial Ecology of Extreme Environments

*ReviewMarine Prasinoviruses and Their Tiny Plankton Hosts: A Review – KD Weynberg – Viruses

Microbial Electron Transport in the Deep Subsurface – J Hinks – Microbial Ecology of Extreme Environments

New Insights into the Microbial Diversity of Polar Desert Soils: A Biotechnological Perspective – J v Dorst – Microbial Ecology of Extreme Environments

Transcriptomics

Mechanism for microbial population collapse in a fluctuating resource environment – S Turkarslan – Molecular Systems Biology

Techniques

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? – M Balvociute – BMC Genomics

Prediction of virus-host infectious association by supervised learning methods – M Zhang – BMC Bioinformatics

Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq) – L Krakova – International Biodeterioration & Biodegradation

More microbes

*Review: The role of bacillithiol in Gram-positive Firmicutes – P Chandrangsu – Antioxidants & Redox Signaling

The effect of antibiotics and diet on enterolactone concentration and metabolome studied by targeted and non-targeted LC-MS metabolomics – AK Bolviq – Journal of Proteome Research

Exploring the Viral Ecology of High Latitude Aquatic Systems – C Chenard – Microbial Ecology of Extreme Environments

The Nature and Relevance of Solvent Stress in Microbes and Mechanisms of Tolerance – M Manefield – Microbial Ecology of Extreme Environments

Surveillance of Exhibit Associated Aquatic Viruses Using Next Generation Sequencing Technologies – WV Bonn – IAAAM 2016

Microbes in the news

Before you consume billions of live bacteria … – E Cauthorn – Las Vegas Sun

Bacteria between humans and pets? Could improve global health: researchers – M Shah – Toronto Sun

There is a reason dogs like meat – NZ Herald

ANTIBIOTIC APOCALYPSE: Harvard reveals doomsday scenario that could KILL 10 million a year – O Smith – Express

THE ALTERATION OF THE INTESTINAL MICROBIOTA COULD PROTECT METABOLIC DISEASES – Zoe – The Quebec Times

March 18, 2017

Events and jobs

Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017

Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi

General microbiome

Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences

*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer

*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio

Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods

Animal experiments

Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J

Animal microbiome

Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science

Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports

Plant, root, and soil microbiome

Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry

Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil

Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology

Water and extremophile microbiome

Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles

Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology

Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports

A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses

Built environment

Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology

Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment

*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods

Techniques

*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering

*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology

Microbes in the news

Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science

Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times

Study by Irish scientists finds porridge to be good for the heart and gut – RTE

Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today

Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science

Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record

My cats poop for science – Jonathan M. Giltin – ars Technica

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 15, 2017

Today’s digest is full of environmental, soil/plant/root, and water related studies among a few gut microbiome studies and some opinion pieces.

Events and jobs

Event: Gut Feeling – How bacteria influence our wellbeing – EMBL-EBI – 21-May-2017

Event: Meeting of the Microbiome Minds – Colorado State University

General microbiome

Opinion: The study of microbiota needs both microbiologists and medical doctors – Didier Raoult – CMI

Pregnancy and early life

Review: Distinct Roles of Cervical Epithelia and Stroma in Pregnancy and Parturition – Shanmugasundaram Nallasamy – Seminars in Reproductive Medicine (Thieme)

The shape of the microbiome in early life – Erika von Mutius – Nature Medicine

Multi-site human microbiome

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment – Jeanette M. Carlson – J. Vis. Exp.

Human respiratory microbiome

Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa – Laurence Pages-Monteiro – PLOS One

Human skin microbiome

Review: Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome – Mohammed Ashrafi – Future Microbiology

Human vaginal microbiome

Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, an Sexually Transmitted Diseases – Felicia M. Lewis – Obstetrics & Gynecology

Women view key sexual behaviours as the trigger for the onset and recurrence of bacterial vaginosis – Jade E. Bilardi – PLOS One

Human oral microbiome

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study – Sebastien Boutin – Frontiers in Microbiology

Human gut microbiome

*The altered gut microbiota in adults with cystic fibrosis – D.G. Burke – BMC Microbiology

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: a randomised crossover study – Lee Kellingray – Molecular Nutrition & Food Research

Gastric Acid Suppression Is Associated with an Increased Risk of Adverse Outcomes in Inflammatory Bowel Disease – Shah R – Digestion

NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology

Gut microbiome diversity and high fibre intake are related to lower long term weight gain – Menni C – International Journal of Obesity

We are not alone: a case for the human microbiome in extra intestinal diseases – S. Shivaji – Gut Pathogens

The intestinal microenvironment in sepsis – Katherine T Fay – BBA – Molecular Basis of Disease

The Gut Microbiome and Its Role in Cardiovascular Diseases – W. H. Wilson Tang – Circulation

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion – Wei Sun – Bioresource Technology

Dietary Broccoli Alters Rat Cecal Microbiota to Improve Glucoraphanin Hydrolysis to Bioactive Isothiocyanates – Xiaoji Liu – Nutrients

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens – Eduardo Crisol-Martinez – PeerJ

Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice – Paul M. Ryan – Microbiome

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome – Daniel Aguirre de Cárcer – PLOS One

Animal microbiome (for animals in the wild)

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time – Sheila Torres – PeerJ

Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens – Carolina Ramirez – Frontiers in Microbiology

Use of signature-tagged mutagenesis to identify genes associated with colonization of sheep by E. coli O157:H7 – Nancy A. Cornick – Veterinary Microbiology

The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens – Gerard M. Murray – PLOS One

Plant, root, and soil microbiome

Analysis of microbiota involved in the aged natural fermentation of indigo – Takahiro Okamoto – World Journal of Microbiology and Biotechnology

Microbial solvent formation revisited by comparative genome analysis – Anja Poehlein – Biotechnology for Biofuels

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities – Wepking, C – Proceedings of the Royal Society B-Biological Science

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms – Tobias Weil – Microbiome

Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW) – Chunkai Huang – Biochemical Engineering Journal

Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog – Tomasz Mieczan – European Journal of Protistology

The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands – Dominquez MT – Sci Total Environment

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar – Jaiswal AK – Scientific Reports

Growth and 137Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain – Salem Djedidi – Journal of Environmental Radioactivity

Antibiotic mixture effects on growth of the leaf-shredding stream detritivore Gammarus fossarum – Mirco Bundschuh – Ecotoxicology

Microbial community changes during different empty bed residence times and operational fluctuations in an air diffusion reactor for odor abatement – Elisa Rodriguez – Science of the Total Environment

Response of indigenously developed bacterial consortia in progressive degradation of polyvinyl chloride – Mohammad S Anwar – Protoplasma

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Conference: Effects of simulated deep-sea mining impacts on microbial communities and functions in the DISCOL experimental area – Vonnahme, T – EU FP7 MIDAS final meeting,

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities – Wei Xing – Journal of Environmental Sciences

PrePrint: Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive2 presence of metal resistance genes – Ankita Kothari – bioRxiv

Climate, soil and plant functional types as drivers of global fine-root trait variation – Gregoire T. Freschet – Journal of Ecology

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function – Konstantin Gavazov – Science of the Total Environment

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes – Emily B. Graham – Environmental Microbiology

Review: Microbiome involved in microbial electrochemical systems (MESs): A review – Saratale RG – Chemosphere

Chapter Four – Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings – Xinli An – Environmental Science and Pollution Research

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis – Niranjan Nitin Parulekar – PLOS One

Food microbiology

Editorial: Inner Workings: Fermented foods offer up a versatile microbial model system – Alla Katsnelson – PNAS

Probiotics / prebiotics

News article: IBS cure? Probiotics could REDUCE irritable bowel syndrome symptoms AND stress – Olivia Lerche – express.co.uk

 Bioinformatics

Applied Metagenomics for Biofuel Development and Environmental Sustainability – Antonio Djalma Nunes Ferraz Junior – Advances of Basic Science for Second Generation Bioethanol from Sugarcane

DEMOGRAPHICS INDUCE EXTINCTION OF DISEASE IN AN SIS MODEL BASED ON CONDITIONAL MARKOV CHAIN – XIAOFENG LUO – Journal of Biological Systems

Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters – Yu Shang – PLOS One

Techniques

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods – Beibei Wang – Science of The Total Environment

*How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity – Camille Truong – New Phytologist

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research – Shaocun Zhang – Frontiers in Cellular and Infection Microbiology

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

Ed’s non-microbiology picks (news articles)

First Time Ever: Gene Therapy Reverses Sickle Cell Disease

Earth’s oceans are warming 13% faster than thought, and accelerating

MIT researchers create new form of matter

Gene therapy treats muscle-wasting disease in dogs

World’s oldest plant fossil discovered by student pushes evolution of complex life back 400 million years

 

March 10, 2017

Ancient microbial DNA in Neanderthal dental calculus; the role of fungus in inflammatory bowel disease; symbiotic bacteria in the Hawaiian bobtail squid reproductive system; and a colorimetric/electrochemical device for detection of food and waterborne bacteria.

Events and jobs
Microbiology/Immunology Faculty – West Virginia School of Osteopathic Medicine – Lewisburg, West Virginia

Pregnancy and early life
Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota – Alyssa Robinson – Journal of Pediatric Gastroenterology and Nutrition

Review: Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – Mohan Pammi – Microbiome

Human oral microbiome
New approach for studying mobile genes using metagenomic analysis – K. Ishihara – Oral Diseases

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus – Laura S. Weyrich – Nature

In the News: Prehistoric ‘Aspirin’ Found in Sick Neanderthal’s Teeth – National Geographic

Human skin microbiome
Using Shotgun Metagenomics to Examine the Use of Hand Microbiome as a Forensic Tool – Ning Chin – ProQuest Dissertations Publishing

Human vaginal microbiome
Review: The role of the vaginal microbiome in gynecological cancer: a review – Champer M. – BJOG

Human gut microbiome
A translational investigation into the role of dietary fatty acids in modulating endotoxemia and associated inflammation – Joshua Mark Lyte – ProQuest Dissertations Publishing

Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity – Malini Ahuja – Cell Metabolism

Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – Herbert Tilg – Cell Metabolism

Low-dose penicillin exposure in early life decreases Th17 and the susceptibility to DSS colitis in mice through gut microbiota modification – Shuang Jin – Scientific Reports

Gut microbiota modulation of chemotherapy efficacy and toxicity – James. L. Alexander – Nature Reviews Gastroenterology & Hepatology

CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – Christian Barthels – Nature Communications

Faecal microbiota transplantation in clinical practice – E M Terveer – Gut

Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder – Ruth Ann Luna – Cellular and Molecular Gastroenterology and Hepatology
Animal experiments
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – Romeo Batacan – Journal of Applied Microbiology

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice – Chiaro TR – Science Translational Medicine

Animal microbiome
Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen – Henk J. Van Lingen – Frontiers in Microbiology

Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and developing eggs – Allison H. Kerwin – Environmental Microbiology

Plant, root, and soil microbiome
Arsenic Transport in Rice and Biological Solutions to Reduce Arsenic Risk from Rice – Yanshan Chen – Frontiers in Plant Science

Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress – Shalaka Shinde – Frontiers in Plant Science

Short-term exposure of paddy soil microbial communities to salt stress triggers different transcriptional responses of key taxonomic groups – Jingjing Peng – Frontiers in Microbiology

Fertilization of Phaseolus vulgaris with the Tunisian rock phosphate affects richness and structure of rhizosphere bacterial communities – Darin Trabelsi – Applied Soil Ecology

Bioprospecting plant-associated microbiomes – Christina A. Muller – Journal of Biotechnology

Water and extremophile microbiome
Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation – MA Jebelli – Ecotoxicology and Environmental Safety

Performance and kinetics of membrane and hybrid moving bed biofilm-membrane bioreactors treating salinity wastewater – Alejandro Rodriguez-Sanchez – AlChE Journal

Metabolomics
Technological development of high-performance MALDI mass spectrometry imaging for the study of metabolic biology – Adam D. Feenstra – ProQuest Dissertations Publishing

Food microbiology
The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products – Solimar G. Machado – Frontiers in Microbiology

Culturable microorganisms during fermentation of Veltlínske zelené (Grüner Veltliner) ice wine – K. Ženišová – Journal of Food and Nutrition Research

Metabolomics for empirical delineation of the traditional Korean fermented foods and beverages – Digar Singh – Trends in Food Science & Technology

Probiotics/prebiotics
Case Study: Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study – Elisa Salvetti – Applied Microbiology and Biotechnology

Techniques
Colorimetric and Electrochemical Bacteria Detection Using Printed Paper- and Transparency-Based Analytic Devices – Jaclyn A. Adkins – Analytical Chemistry

Microbes in the news
Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – The New York Times

Garrett’s non-microbiology picks
‘Plan bee’ drone artificially pollinates flowers on behalf of bees – Design Boom

March 8th, 2017

Today is the International Women’s Day! This is a day for awareness about the importance of support equality in rights and opportunities for women.

About International Women’s Day

Gender at Nature Ecology & Evolution

Helping women progress in traditionally male dominated fields

Rosalind Franklin: Navigating workplace politics to gain recognition in science

International Women’s Day 2017: pursuing a career in science

BMC Series Blog: International Women’s Day

Events and Webinars

3rd Annual Translational Microbiome Conference, April 12-13, 2017 in Boston, MA

Webinar: Nomadic nanopore sequencing of metagenomes with the MinION

Microbiome research

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island – Jiro Nakayama – Frontiers in Microbiology

Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora – Shirali Pandya – Journal of Medical Microbiology

Effect of predatory bacteria on the gut bacterial microbiota in rats – Kenneth Shatzkes – Scientific Reports

Methods article: Critical Issues in Mycobiota Analysis – Bettina Halwachs – Frontiers in Microbiology

Microbiota alteration is associated with the development of stress-induced despair behavior – Ioana A. Marin – Scientific Reports

Review: Beyond Hygiene: Commensal Microbiota and Allergic Diseases – Sung-Wook Hong – Immune Network

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens – Sandra Pinto-Cardoso – Scientific Reports

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Probiotics

Lactobacillus rhamnosus GG supernatant enhance neonatal resistance to systemic Escherichia coli K1 infection by accelerating development of intestinal defense – Xiaolong He – Scientific Reports

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat  – Elaine Patterson – Scientific Reports

Timely use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: a Systematic Review with Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Metagenomics

Review: Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Yu – bioRxiv

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Pathogens

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus – Ilse Vandecandelaere – PLoS ONE

Review: Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium – David Taylor-Robinson – Research in Microbiology

Case report: Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus – Emilie Sitterlé – Frontiers in Microbiology

The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes – Helena M.B. Seth-Smith – Genome Biology and Evolution

Extremophiles

Reducing salinity by flooding an extremely alkaline and saline soil changes the bacterial community but its effect on the archaeal community is limited – Arit S de León-Lorenzana – Frontiers in Microbiology

Early life

Paleoproterozoic sterol biosynthesis and the rise of oxygen – David A. Gold – Nature

March 7, 2017

Events and jobs

Professor Of Microbiology – University of Western Australia – Last date: Friday, May 12, 2017

 

General microbiome

Biofilms: Microbial Cities Wherein Flow Shapes Competition – Su Chuen Chew – Trends in Microbiology

*ReviewCritical Streptococcus suis Virulence Factors: Are They All Really Critical? – Mariela Segura – Trends in Microbiology

*Review: Collective Infectious Units in Viruses – Rafael Sanjuán – Trends in Microbiology

*Review: KSHV microRNAs: Tricks of the Devil – Jie Qin – Trends in Microbiology

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

 

Human oral microbiome

Chemotherapeutic decontamination of dental implants colonized by mature multispecies oral biofilm – Sebastien Dostie – Journal of Clinical Periodontology

 

Human vaginal microbiome

The presence of vaginal Lactobacillus species does not contribute to a measureable difference in amniotic fluid lactate levels collected from the vaginal tract of laboring women – Beverley Hall – AOGS

 

Animal microbiome

Effects of Pediococcus pentosaceus supplementation on growth performance, intestinal microflora and disease resistance of white shrimp, Litopenaeus vannamei – M. Adel – Aquaculture Nutrition

 

Plant, root and soil microbiome

Effects of the Inoculant Strain Pseudomonas sp. SPN31 nah + and of 2-Methylnaphthalene Contamination on the Rhizosphere and Endosphere Bacterial Communities of Halimione portulacoides – V Oliveira – Current Microbiology

Microbial-enhanced lindane removal by sugarcane (Saccharum officinarum) in doped soil-applications in phytoremediation and bioaugmentation. – J A Salam – Journal of Environmental Management

Immobilization remediation of Cd-polluted soil with different water condition – J Li – Journal of Environmental Management

Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat – Yudi M Lozano – New Phytologist

A long-term study of burning effects on a plant pathogen in tallgrass prairie – S. P. Dendy – Plant Pathology

 

Water and extremophile microbiome

Temperature–nutrient interactions exacerbate sensitivity to warming in phytoplankton – Mridul K. Thomas – Global Change Biology

 

Metagenomics and Bioinformatics

Omics for Understanding the Gut-Liver-Microbiome Axis and Precision Medicine – Jag Khalsa – Clinical Pharmacology in Drug Development

 

Techniques

Drug–Drug Interactions and Diagnostics for Drug Users With HIV and HIV/HCV Coinfections: Introduction – Jag H. Khalsa – Clinical Pharmacology in Drug Development

 

More Microbes

Influence of key physicochemical and hydrodynamic specifications of three packing materials on both performance and bacterial community structure of gas-biofilters – Luc Malhautier – Journal of Chemical Technology and Biotechnology

Metabolic coupling in bacteria – Shraddha Shitut – bioRxiv

Fungal derived 15-keto-prostaglandin E2 and host peroxisome proliferator-activated receptor gamma (PPAR-γ) promote C. neoformans growth during infection – Robert J Evans – bioRxiv

 

Microbes in news

Parkinson’s Linked to Changes in Gut Bacteria – T Pedersen – Psych Central

3.77 billion year old bacteria fossil may be Earth’s oldest, scientists say – J Leone – Journal-News

Bacterial vaginosis: A common health concern women must not take lightly – S Kantengwa – The New Times

This Drugstore Face Cream Is A Game Changer For People With Dry Skin – L Lebsack – Refinery29

UT researchers take new approach in cholera prevention – C Deangelis – The Blade

Bacteriophages Offer Potential for Helping Reduce Dependence on In-Feed Antibiotics – The Pig Site

Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – AE Carroll – The Upshot

Human Microbiome Market Worth 899.1 Million USD by 2025 – PRNewswire

Native Squid Used in Research of Environment and Human Health – Maui Now