Category Archives: Built Environment Microbiology

July 14, 2016

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Gut microbes and diabetes risk, llama sausages, urban greenness, and the sea turtle microbiome.

Pregnancy and birth

The Infant Gut Bacterial Microbiota and Risk of Pediatric Asthma and Allergic Diseases – Christine Cole Johnson – Translational Research

Human gut microbiome

Human gut microbes impact host serum metabolome and insulin sensitivity – Helle Krogh Pedersen – Nature

Press: Gut bacteria imbalance increases diabetes risk – EurekAlert
Gut bacteria imbalance increases diabetes risk – BioMed Central blog

Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial – Dorien Reijnders – Cell Metabolism

The Gut Microbiota from Lean and Obese Subjects Contribute Differently to the Fermentation of Arabinogalactan and Inulin – Marisol Aguirre – PLOS ONE

Review: The esophageal microbiota in health and disease – Vincenzo Di Pilato – Annals of the New York Academy of Sciences

Review: Colon microbiota fermentation of dietary prebiotics towards short-chain fatty acids and their roles as anti-inflammatory and antitumour agents: A review – Javier Fernández – Journal of Functional Foods

Animal and other experiments

Microbial Mat Functional and Compositional Sensitivity to Environmental Disturbance –
Eva Christine Preisner – bioRxiv

Gut microbiota directs PPARγ-driven reprogramming of the liver circadian clock by nutritional challenge – Mari Murakami – EMBO Reports

Preview: Microbially Produced Acetate: A “Missing Link” in Understanding Obesity? – Chad M. Trent – Cell Metabolism

Plant, root, and soil microbiome

Glyphosate and aminomethylphosphonic acid chronic risk assessment for soil biota – Georg von Mérey – Environmental Toxicology and Chemistry

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization – Mengxin Zhao – mSystems

Built environment microbiome

Urban greenness influences airborne bacterial community composition – Gwynne Mhuireach – Science of The Total Environment

Research Watch: Dirty environment for adult life: the bad, the good, the unknown – Jun Sun – Genes & Diseases

Food microbiology

Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity – Fontana Cecilia – International Journal of Food Microbiology

Metabolomics

Free eBook: Metabolomics – A Key Technology for Microbiome Research – Kirk Beebe – Metabolon

Techniques

Evaluation of VITEK matrix-assisted laser desorption ionization–time of flight mass spectrometry for identification of anaerobes – Zheng Xiao – Microbiology and Immunology

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Rapid and Selective Detection of Pathogenic Bacteria in Bloodstream Infection with Aptamer-based Recognition – Haijing Shen – Applied Materials and Interfaces

Microbes in the news

Project to study sea turtle microbiomes in captivity and in the wild – Holly Ganz – MicroBEnet

Gonorrhea may soon become resistant to all antibiotics and untreatable – Helen Branswell – STAT news

Bacteriophage Therapy Grows as Alternative to Antibiotics – Michael McGrady – Heartland

Getting to the guts: Studying the gut microbiome to manage pain – Shay Stowell – Missouri State University

Career

Men cite themselves more than women do. The apparent trend has been on the rise over the past two decades – Dalmeet Singh Chawla – Nature

Bik’s non-microbiology Picks

A Gathering of Giants. A photographer slips into the ocean to swim among hundreds of sperm whales – witnessing a rarely seen social spectacle – Tony Wu – Biographic

The people who don’t get ‘Eleanor Rigby’. Happy music and sad sounds are not universal. – Nature

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

July 8, 2016

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The highly anticipated microbiome statistical workflow from the Holmes lab at Stanford, lichen planus, chronic lung disease, and the beneficial microbes of buildings.

Bioinformatics

Preprint, awaiting peer review: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses  – Ben J. Callahan – F1000 Research

Human oral microbiome

The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus – Yun Sik Choi – Scientific Reports

Human respiratory microbiome

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx – R. L. Marsh – Microbiome

Review: Commensal–Pathogen Interactions along the Human Nasal Passages – Silvio D. Brugger – PLOS Pathogens

Animal experiments

Structural Change in Microbiota by a Probiotic Cocktail Enhances the Gut Barrier and Reduces Cancer via TLR2 Signaling in a Rat Model of Colon Cancer – Eugene Dogkotenge Kuugbee – Digestive Diseases and Sciences

Adaptive immunity against gut microbiota enhances apoE-mediated immune regulation and reduces atherosclerosis and western-diet-related inflammation – Diego Saita – Scientific Reports

Animal microbiome

The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni – Dong Hee-Jin – Foodborne Pathogens and Disease

Press: Microbiology of cattle poop – Doug Powell – BarfBlog

Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyroseqencing analysis – Jin Wang – Asian-Australasian Journal of Animal Sciences

Microbial Composition in Different Gut Locations of Weaning Piglets Receiving Antibiotics – Kaifeng Li – Asian-Australasian Journal of Animal Sciences

Plant, root, and soil microbiome

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities – James P. J. Hall – PNAS

Built environment microbiome

Review: Buildings, Beneficial Microbes, and Health – Jordan Peccia – Trends in Microbiology

Press: Invite good bacteria into home: scientists – MSN
Should architecture take our microbial health into account? – Coby McDonald – Popular Science

Microbes in the news

Gut Bacteria Are Different in People With Chronic Fatigue Syndrome – Nicholas Bakalar – NY Times

An Algorithm To Predict Which Bacteria Are Good For You. For a more targeted microbiome fix than a fecal transplant – Alexandra Ossola – Vocativ

Purdue students hope new bacteria stops toxic algae blooms – Washington Times

Japanese and Chinese scientists team up against infectious diseases – Tetsuya Abe – Nikkei Asian Review

The Microbiome’s New Frontier: The Rest of the Animal Kingdom – Conservation Magazine

July 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

July 1, 2016

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NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.

General microbiome

Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine

Pregnancy and birth

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE

Human oral microbiome

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology

Human respiratory microbiome

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE

Human skin microbiome

The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology

Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control

Human gut microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome

Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology

Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases

Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski

Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research

Animal experiments

Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes

Animal microbiome

Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology

The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology

Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology

Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology

Plant, root, and soil microbiome

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology

Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology

Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology

Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos

Water microbiome

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology

Built environment microbiome

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE

Microbes in space

Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews

Techniques

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes

Microbes in the news

The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot

Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire

uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web

Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal

Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical

Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist

Large Grant to Research on Bacteria in the Nose – Statens Serum Institute

Science, publishing, and career

Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone

June 29, 2016

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Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.

Human respiratory microbiome

Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy

Human skin microbiome

The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology

Human gut microbiome

Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications

Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation

Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International

Animal and in vitro experiments

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio

Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert

Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports

Animal microbiome

Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution

In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters

Plant, root, and soil microbiome

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology

Perspective: Soil immune responses – Jos M. Raaijmakers – Science

Water and extremophile microbiome

Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment

Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology

Built environment microbiome

Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems

Press: ‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – EurekAlert

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Food microbiology

Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology

Metagenomics and bioinformatics

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE

Proteomics and metabolomics

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems

Techniques

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Microbes in the news

Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times

An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India

Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn

 

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 15, 2016

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Microbiome evolution in vertebrates, post-antibiotic microbial competition for sugars, microbial networks in respiratory infections, bacteria in snow from Australian and Swiss Alps, Yucatan Black and Red soil microbes.

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv

Human skin microbiome

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis – Akiomi Tanaka – Microbiology and Immunology

Review: Can molecular DNA-based techniques unravel the truth about diabetic foot infections? – M. Malone – Diabetes/Metabolism Research and Reviews

Human respiratory microbiome

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota – Heping Wang – Journal of Thoracic Disease

Human gut microbiome

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer – Atsuki Tsuruya – Scientific Reports

Research highlight: Intimate gut interactions: helminths and the microbiota – Nicola L Harris – Cell Research

Review: Human Gut-on-a-Chip technology: Will this revolutionize our understanding of IBD and future treatments? – Jaewon Lee – Expert Review of Gastroenterology & Hepatology

Review: Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel – Damien Stark – Clinical Microbiology Reviews

Review: Akkermansia muciniphila: a novel functional microbe with probiotic properties – C. Gómez-Gallego – Beneficial Microbes

Review: Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis – Xiaojun Zhuang – Journal of Gastroenterology and Hepatology

Animal and tissue culture experiments

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion – Franziska Faber – Nature

News and Views: Microbiology: The dark side of antibiotics – Thibault G. Sana & Denise M. Monack – Nature

Genetic and transcriptional analysis of human host response to healthy gut microbiome – Allison L Richards – bioRxiv

The Microbiota Determines Susceptibility to Experimental Autoimmune Uveoretinitis – Jarmila Heissigerova – Journal of Immunology Research

Animal microbiome

Invited Review: Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What’s Known and Unknown – Timothy J. Colston – Molecular Ecology

Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity – Swapnil Gaikwad – AMB Express

Plant, root, and soil microbiome

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) – Wenfeng Wang – Microbiological Research

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State – Héctor Estrada-Medina – Microbiological Research

Water and extremophile microbiome

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps – Tina Wunderlin – FEMS Microbiology Ecology

Waste, pollution, drinking water microbiology

Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria – Mendoza-Hernández José Carlos – Microbiological Research

Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants – Devin B. Holman – PLOS ONE

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities – Lucélia Cabral – Environmental Pollution

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms – Zsuzsanna Nagymáté – Microbiological Research

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time – Peter A. Noble – Applied Microbiology and Biotechnology

DGGE: Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment – Mohammed Al-Jawasim – FEMS Microbiology Letters

Food microbiology

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space – Marinella Marzano – PLOS ONE

More microbiology

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B – Caroline Chénard – mBio

Press: Virus Hacks Host Genome, Steals CRISPR to Protect Itself – GenEngNews
Virus uses ‘stolen’ CRISPR to hack its host’s immune system – Science Daily

Microbes in the news

Asgard archaea diversity in estuaries – Roy Rodriguez – REU in Subtropical Marine Ecosystems, University of Texas at Austin

Microbes in pressed grapes may predict flavor metabolites in the finished wine – American Society for Microbiology – EurekAlert

Nanoflowers can detect bacteria before they make you sick: The particles can spot even tiny amounts of E. coli – Mariella Moon – Engadget

BacteriaHysteria: Self-cleaning sheets do exist! Silvon launches bacteria-resistant bedding – Julie Pennell – Today

Science, publishing, and career

Predatory journals: Ban predators from the scientific record – Jeffrey Beall – Nature

Data sharing: A code of conduct for data on epidemics – Ilaria Capua – Nature

June 14, 2016

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Breastfeeding protects against antibiotics’ effect in infants, pediatric gut microbiome after surgery, microbial contribution to regional wine characteristics, microbial hotspots on glacial surfaces, foodwebs in your gut, and much more!

Pregnancy and birth

Association of Early-Life Antibiotic Use and Protective Effects of Breastfeeding – 
Role of the Intestinal Microbiota – Katri Korpela – JAMA Pediatrics

Press: Antibiotics May Blunt Breast-Feeding’s Benefits – Infants given the drugs were prone to infections and obesity in childhood, researchers say – WebMD

Human gut microbiome

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease – Minna M. Wieck – Surgery

Press: Culture Crash: How Common Pediatric Diseases Affect the Healthy Intestinal Microbiome – Children’s Hospital Los Angeles

Systematic Review: Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis – Yanqiang Shi – PLOS ONE

Animal and bioreactor experiments

Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection – Edward van Opstal – Journal of Infectious Diseases

The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth – Jingjing Wang – Scientific Reports

MALDI-TOF: Investigation of the interactions between Chrysanthemum morifolium flowers extract and intestinal bacteria from human and rat – Jin-hua Tao – Biomedical Chromatography

Substrate-driven convergence of the microbial community in lignocellulose-amended enrichments of gut microflora from the Canadian beaver (Castor canadensis) and North American moose (Alces americanus) – Mabel Ting Wong – Frontiers in Microbiology

Animal microbiome
Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics – Nicholas A. Bokulich – mBio

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm – Daiva Domenech Tupinambá – Archaea

Effects of Frangula alnus on soil microbial communities and biogeochemical processes in Wisconsin forests – Joel P. Stokdyk – Plant and Soil

Species-specific effects of plant invasions on activity, biomass, and composition of soil microbial communities – Anna M. Stefanowicz – Biology and Fertility of Soils

Water and extremophile microbiome

Review: Biofilms on glacial surfaces: hotspots for biological activity – Heidi J Smith – NPJ Biofilms and Microbiomes

Press: MSU doctoral student publishes research on microbial biofilms and carbon cycling on glacial surfaces – Montana State University

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4,950 m, in Venezuelan Tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Large differences in bacterial community composition among three nearby extreme waterbodies of the high Andean plateau – Pablo Aguilar – Frontiers in Microbiology

The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu – Xianfang Fan – Archaea

Built environment microbiome / food microbiology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community – Stephan Thies – Scientific Reports

Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies – Agnieszka Piotrowska-Cyplik – Journal of the Science of Food and Agriculture

Metagenomics and bioinformatics

Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics – Tom O Delmont – bioRxiv

Species–function relationships shape ecological properties of the human gut microbiome – Sara Vieira-Silva – Nature Microbiology

Press: Unraveling the food web in your gut – The Flanders Institute for Biotechnology – EurekAlert

Protocol: A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology – Zhanshan (Sam) Ma – Part of the series Springer Protocols Handbook

Review: The evolution of genome mining in microbes – a review – Nadine Ziemert – Natural Product Reports

Transcriptomics, metabolomics

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information – Sandra E. Safo – arXiv

More microbiology

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity – Emanuele Bosi – PNAS

Microbes in the news

Bill Gates, Jennifer Doudna Will Take Podium at ASM Microbe – Ingrid Hein – Medscape

Insights into the ecology of the microbiome: dynamics of the gut, mouth and skin microbiomes of healthy subjects – Science Daily

Podcast: Profile Of A Scientist: Personalized Medicine, Gut Microbes And The Biology Of Space Travel, with Stanford biologist Mike Snyder – WBUR

WPI students may have discovered three new viruses in Worcester soil – Michael D. Kane – MassLive

Electronic sensor that tells dead bacteria from live by measuring ‘osmoregulation’ is potential future tool for medicine and food safety – Purdue University

Oral microbiome rich environment for study, product development, event attendees told – Hank Schultz – Nutraingredients

Take Care of Your Microbiome and Your Microbiome Will Take Care of You – Aaron M. Renn – Urbanophile

Science, publishing, and career

How to make your article easy to review – Part 4 – 25 tips from experienced reviewers on what to look out for before submitting your article – Elsevier

June 11, 2016

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Microbiome and virome of FMT patient over time, how well do animal models predict natural microbial activities, goats!, Neolithic vs. modern soil, truffles, and a medieval church.

Human gut microbiome

Long-term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection – Felix Broecker – Annals of the New York Academy of Sciences

Perspective: Nutrition and the microbiome – Karin Moelling – Annals of the New York Academy of Sciences

Entitled denigrating view of African research, unclear background or IRB approval of volunteers from Africa: Significant pharmacokinetic differences of berberine are attributable to variations in gut microbiota between Africans and Chinese – Raphael N. Alolga – Scientific Reports

Conference report: A Summary of The First HIV Microbiome Workshop 2015 – Brett Williams – AIDS Research and Human Retroviruses

Infection and microbes

No mention of extraction or PCR controls, and most OTUs are shared between samples, so suspicious for contamination. Proceed with caution: High-throughput sequencing of microbial diversity in implant-associated infection – Xin Wang – Infection, Genetics and Evolution

Animal experiments

Metabolomics insights into the modulatory effects of long term low calorie intake in mice – Junfang Wu – Journal of Proteome Research

Perspective: A synthetic ecology perspective: how well does behavior of model organisms in the laboratory predict microbial activities in natural habitats? – Zheng Yu – Frontiers in Microbiology

Animal microbiome

Age and feeding system (supplemental feeding versus grazing) modulates colonic bacterial succession and host mucosal immune maturation in goats – J. Jiao – Journal of Animal Science

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers – Phillip R. Myer – Journal of Microbiological Methods

Plant, root, and soil microbiome

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation – Yong-Guan Zhu – Science Bulletin

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov. – Rosanne A. Healy – Mycorrhiza

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions – Alfonso Navarro-Ródenas – Mycorrhiza

Nutrient limitation drives response of Calamagrostis epigejos to arbuscular mycorrhiza in primary succession – Jana Rydlová – Mycorrhiza
http://link.springer.com/article/10.1007/s00572-016-0712-5

Ectomycorrhizal and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment – Nhu H. Nguyen – Molecular Ecology

Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing – John Farmer – Archives of Agronomy and Soil Science

Resilience of Fungal Communities to Elevated CO2 – Stavros D. Veresoglou – Microbial Ecology

Review: Life in heaps: A review of microbial responses to variable acidity in sulfide mineral bioleaching heaps for metal extraction – D.W. Shiers – Research in Microbiology

Review: Giving back to the community: Microbial mechanisms of plant-soil interactions – Sur Herrera Paredes – Functional Ecology

Perspective: History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Response of a coastal tropical pelagic microbial community to changing salinity and temperature – Gurpreet Kaur-Kahlon – Inter-Research in Aquatic Microbial Ecology

Bacterial communities in Arctic first-year drift ice during the winter/spring transition – E. Eronen-Rasimus – Environmental Microbiology Reports

Diversity and distribution of prokaryotes within a shallow-water pockmark field – Donato Giovannelli – Frontiers in Microbiology

Mainly about animals: Life in a dark biosphere: a review of circadian physiology in “arrhythmic” environments – Andrew David Beale – Journal of Comparative Physiology B

Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds – Matthew A. Saxton – Inter-Research in Aquatic Microbial Ecology

Built environment microbiome

Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing – Guglielmina Chimienti – Applied Microbiology and Biotechnology

Food microbiology

Cascade degradation of organic matters in brewery wastewater using a continuous stirred microbial electrochemical reactor and analysis of microbial communities – Haiman Wang – Scientific Reports

Bioinformatics and computational biology

Advancing microbial sciences by individual-based modelling – Ferdi L. Hellweger – Nature Reviews Microbiology

Microbes in the news

A Portrait of a Building and its External Inhabitants – Makayla Betts – MicroBEnet

Woman meets Winnipeg researchers whose Ebola treatment saved her life – Bill Redekop – Winnipeg Free Press

Tackling healthcare challenges in a changing world: an interview with Professor Jeremy Nicholson – News Medical