Category Archives: Infection and transplantation

December 10, 2015

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The microbiome quality control project, proton pump inhibitors, microbiome models are useful, and Cryoconites in glaciers.

General microbiome

The microbiome quality control project: baseline study design and future directions – Rashmi Sinha – Genome Biology

Human gut microbiome

Proton pump inhibitors affect the gut microbiome – Floris Imhann – Gut

Microbiome models

Your gut microbiome, deconstructed: Probing microbiome functions through simple models – Dylan Dodd, Carolina Tropini & Justin L Sonnenburg – Nature Biotechnology

Baby, It’s Cold Outside: Host-Microbiota Relationships Drive Temperature Adaptations –
Sol Gomez de la Torre Canny, John F. Rawls – Cell Host & Microbe

N-Acetyl-l-cysteine effects on multi-species oral biofilm formation and bacterial ecology –
K. Rasmussen – Letters in Applied Microbiology

Plant, root, and soil microbiome

The molecular diversity of arbuscular mycorrhizal fungi in the arsenic mining impacted sites in Hunan province of China – Yuqing Sun – Journal of Environmental Sciences

Incorporating biotic factors in species distribution modeling: are interactions with soil microbes important? – Clifton P. Bueno de Mesquita – Ecography

Water and extremophile microbiome

Temperature and trophic structure are driving microbial productivity along a biogeographical gradient – Sarah M. Gray – Ecography

Review: Cryoconite: The dark biological secret of the cryosphere – Joseph Cook – Progress in Physical Geography

Infection and transplantation microbiology

Review: The Microbiome, Systemic Immune Function, and Allotransplantation – Anoma Nellore – Clinical Microbiology Reviews

Built environment microbiology

Microbiological testing of pharmaceuticals and cosmetics in Egypt – Hend Zeitoun – BMC Microbiology

Bioinformatics and metagenomics

Influence of tree shape and evolutionary time-scale on phylogenetic diversity metrics – Florent Mazel – Ecography

Microbes in the news
Germ Warfare: Turns out that, sometimes, Mr. Microbe is your friend – Christianna McCausland – Baltimore

A gut feeling: there’s a connection between your intestines and your health – Carrie Dennett – Seattle Times

Agilent Technologies Presents Thought Leader Award to Human Microbiome Expert Jeffrey Gordon – Business Wire

Getting the Hologenome Concept Right – Seth Bordenstein – Symbionticism

A microbiologist reveals what would go wrong if all bacteria disappeared – with Jack Gilbert – Tech Insider

Microorganism Devours Its Prey in Award-Winning Video – Carl Engelking – Discover

Illumina Invests in Four Startups Through Accelerator Program – Genome Web

Phage Hunters: New biology course transforms Virginia Tech students into young scientists, research contributors – Augusta Free Press

Lab staple agar hit by seaweed shortage: Dwindling algae harvest imperils reagent essential for culturing microbes – Ewen Callaway – Nature

Lab ‘NERD’ receives $1M funding from Taiwan ministry for microbiome research – Michelle Yeomans – Cosmetics Design

uBiome Releases Predictive Engine for Over 100 Metabolic Functions Based on Microbiome Data – Virtual Strategy

Science, publishing, and career

Blog, tweet, and avoid the pitfalls – Sharon Ann Holgate – Science
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December 9, 2015

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Student activity about the microbiome that uses pasta, nutritional supplementation in Malawian infants, fungi and drywall, and microbial aerosols from soiled hospital linens.

General microbiome

Cool student activity: Modeling the Dynamic Digestive System Microbiome – Anne M. Estes – Journal of Microbiology & Biology Education

Pregnancy and birth

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery – Elizabeth A. Baldwin – PeerJ

No effect of supplementation: Gut microbiota in Malawian infants in a nutritional supplementation trial – Yin Bun Cheung – Tropical Medicine & International Health

Human vaginal microbiome

Bacterial vaginosis and inflammatory response showed association with severity of cervical neoplasia in HPV-positive women – Juçara Maria de Castro-Sobrinho – Diagnostic Cytopathology

Human gut microbiome

Review: Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin – Loris R. Lopetuso – Mini-Reviews in Medicinal Chemistry

Animal microbiome

The effects of omeprazole therapy on bacterial colonization of the pharynx in healthy dogs – Lauren A. Sullivan – Journal of Veterinary Emergency and Critical Care

Water microbiome

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

 

Built environment microbiome

Moisture parameters and fungal communities associated with gypsum drywall in buildings – Sandra Dedesko – Microbiome

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses – Thomas Weinmaier – Microbiome

Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting – Alina Handorean – Microbiome

Phages and viruses

Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo – Janet Y. Nale – Antimicrobial Agents and Chemotherapy

Infection and transplantation

A genetic modifier of the gut microbiome influences the risk of GVHD and bacteremia following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis – Martyn D. Kirk – PLOS Medicine

Functional foods

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods – Remco Kort – Microbial Cell Factories

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences – Tong Zhang – PLOS ONE

Bioinformatics and metagenomics

Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies – Jun Chen – Genetic Epidemiology

Microbes in the news

Questions About the Science Of Beer – Matt Shipman – NC State University News

Guest Post – Stadium Seat Bacteria – PeerJ – David Coil

How microbes in your gut today hold clues to tomorrow’s medicines: For the second episode of “Science Happens,” we hung out with Pamela Silver, a scientist who wants to hack the microbiome – Carl Zimmer – STAT news

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December 2, 2015

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General microbiome

Microbiology: Microbiome studies need local leaders – Victor S. Pylro – Nature

Human skin microbiome

Conclusions not strongly supported by data: Chitosan Coated Textiles May Improve Atopic Dermatitis Severity by Modulating Skin Staphylococcal Profile: A Randomized Controlled Trial – Cristina Lopes – PLOS ONE

Human respiratory microbiome

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome – Robert A Quinn – The ISME Journal

Perspective: In the name of ventilator-associated pneumonia prevention: lung microbiota blown away by colistin! – Saad Nseir – European Respiratory Journal

Human gut microbiome

Better link than yesterday: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Kristoffer Forslund – Nature

Animal microbiome

Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions – Xiaoling Wan – Current Microbiology

Plant, root, and soil microbiome

Commentary: Microbiomes: Curating communities from plants – Gwyn A. Beattie – Nature

Better link than yesterday: Functional overlap of the Arabidopsis leaf and root microbiota – Yang Bai – Nature

Bioinformatics and metagenomics

A New Approach for Scalable Analysis of Microbial Communities – Ehsaneddin Asgari – ArXiv

Microbial ecology

Networks of energetic and metabolic interactions define dynamics in microbial communities – Mallory Embree

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria – João Barroso-Batista – Nature Communications

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils – Christina Kaiser – Nature Communications

Proteomics

Enhancing Metaproteomics – The value of models and defined environmental microbial systems – Florian-Alexander Herbst – Proteomics

Infection microbiology

Nature Supplement: Expanding the role of diagnostic and prognostic tools for infectious diseases in resource-poor settings – Azra C. Ghani – Nature

Microbes in the news

Bacteriophage therapy: an alternative to antibiotics? An interview with Professor Martha Clokie – April Cashin-Garbutt – News Medical

Friends for Life: How Good Bugs Keep You Healthy (Op-Ed) – Jeremy Taylor – LiveScience

Science, publishing, and career

How to build a better PhD: There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved – Julie Gould – Nature

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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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November 28, 2015

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Events

2nd Microbiome R&D and Business Collaboration Congress – Early registration ends Monday – February/March 2016, Kuala Lumpur, Malaysia

Human oral microbiome

Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project – Zongxin Ling – Scientific Reports

Human gut microbiome

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease – Johanna Maukonen – Journal of Crohn’s and Colitis

Microbiome models

Perspective: Could microbial therapy boost cancer immunotherapy? – Alexandra Snyder – Science

Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function – Spenser Reed – Nutrients

Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus – Maurício T. Lima – FEMS Microbiology Ecology

Impacts of Extended Laboratory Rearing on Female Fitness in Florida Colonies of the Parasitoid Spalangia cameroni (Hymenoptera: Pteromalidae) With an Analysis of Wolbachia Strains – E.T. Machtinger – Annals of the Entomological Society of America

Animal microbiome

Fish: Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures – Laetitia G. E. Wilkins – Scientific Reports

Termites: Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites – Karen Rossmassler – Microbiome

Ticks: Emerging horizons for tick-borne pathogens: from the ‘one pathogen–one disease’ vision to the pathobiome paradigm – Muriel Vayssier-Taussat – Future Microbiology

Beetles: Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex – Audrey-Anne Durand – Scientific Reports

Coral: Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Plant, root, and soil microbiome

Illumina High-Throughput Sequencing and Comparative Analysis of Bacterial Communities in Cherry Orchard Soil – Lingzhi Liu – Toxicological & Environmental Chemistry

Water microbiome

Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon – Suchismita Srichandan – Marine Pollution Bulletin

New insights into relationships between active and dormant organisms, phylogenetic diversity and ecosystem productivity – Jacob A. Cram – Molecular Ecology

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS – Rafael R. C. Cuadrat – International Journal of Molecular Sciences

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality – K. Jordaan – Environmental Science and Pollution Research

Extremophile microbiome

The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China – Haizhou Li – Scientific Reports

Built environment microbiome

Characterizing the Bacterial Communities in Retail Stores in the United States – A Hoisington – Indoor Air

Viruses and phages

A New Zamilon-like Virophage Partial Genome Assembled from a Bioreactor Metagenome – Meriem Bekliz – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – ArXiv

Microbial Ecology

Resource limitation drives spatial organization in microbial groups – Sara Mitri – The ISME Journal

Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Biofilms / Infection microbiology

Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Review: The limitations of in vitro experimentation in understanding biofilms and chronic infection – Aled E L Roberts – BioRxiv

Review: The Application of Metagenomic Approaches in the Management of Infectious
Diseases – Jinhua Wu – Tropical Medicine & Surgery

Food microbiology

Sourdough microbial community dynamics: An analysis during French organic bread-making processes – Emilie Lhomme – Food Microbiology

Bacteria in the news

Woolly rhino bacteria cleans up oil spills – Energy Global

A personal touch to wine microbiology – Kyanah Lawson – Food Magazine

Arizona inspectors find Theranos lab issues – AZ Central

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November 20, 2015

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Dog licking and microbe sharing, glycemic response and gut microbiome, fungi in the Amazon, and separating the bacteria from the poop. And an image I could not resist creating:

 

Screen Shot 2015-11-20 at 10.13AM, Nov 20

 

Human gut microbiome

Personalized Nutrition by Prediction of Glycemic Responses – David Zeevi – Cell

DNA fingerprinting approaches to trace E. coli sharing between dogs and owners – Zahra Naziri – Journal of Applied Microbiology

Metabolomic fingerprint of severe obesity is dynamically affected by bariatric surgery in a procedure-dependent manner – Ewa Gralka – American Journal of Clinical Nutrition

Review: T Lymphocyte Dynamics in Inflammatory Bowel Diseases: Role of the Microbiome – C. B. Larmonier – BioMed Research International

Animal models

Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice – Alice Chaplin – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Fungal Community Assembly in the Amazonian Dark Earth – Adriano Reis Lucheta – Microbial Ecology

Molecular diversity and distribution of marine fungi across 130 European environmental samples – Thomas A. Richards – Proceedings of the Royal Society B

Extremophile microbiome

Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria – Guillaume Tahon – Microbial Ecology

Infection microbiology

The role of biofilms as environmental reservoirs of antibiotic resistance – José L. Balcázar – Frontiers in Microbiology

Elucidating Host–Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches – Vaishnavi Ravikumar – Frontiers in Microbiology

Techniques

Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof – Arancha Hevia – Scientific Reports

Microbes in the news

Different parasitic worms can raise or lower female fertility – Sam Wong – New Scientist

The Secret World of Museums: How Hidden Science Becomes Public Exhibit – Katharine Trendacosta – IO9
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November 18, 2015

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My sincere apologies: the website was down most of today. I am not sure what it was – the problem was on the host server site. But I’m back, with tea rhizobacteria, bacteria reporting explosives in the soil, fungi in a glacier, and a bacterial protein preventing ice cream drip.

Animal models

Editorial: Worming Their Way into the Picture: Microbiota Help Helminths Modulate Host Immunity – Lisa A. Reynolds, B. Brett Finlay – Immunity

Plant, root, and soil microbiome

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change Biology

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains – Remo Freimann – Frontiers in Microbiology

Resistance of Undisturbed Soil Microbiomes to Ceftriaxone Indicates Extended Spectrum β-Lactamase Activity – Joao Gatica – Frontiers in Microbiology

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars – Jintu Dutta – Frontiers in Microbiology

Water / extremophile microbiome

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea – Meng Li – Nature Communications

Fungal biodiversity in the periglacial soil of Dosdè Glacier (Valtellina, Northern Italy) – Marinella Rodolfi – Journal of Basic Microbiology

Winter severity determines functional trait composition of phytoplankton in seasonally ice-covered lakes – Deniz Özkundakci – Global Change Biology

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria – Katrin Zwirglmaier – Frontiers in Microbiology

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities – Kemal Sanli – Frontiers in Microbiology

Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin – Ying He – Frontiers in Microbiology

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing – Neng Fei Wang – Frontiers in Microbiology

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust – Everett C. Salas – Frontiers in Microbiology

Waste and built environment microbiology

Review: Genetically engineered microorganisms for the detection of explosives’ residues – Benjamin Shemer – Frontiers in Microbiology

Self-healing of early age cracks in cement-based materials by mineralization of carbonic anhydrase microorganism – Chunxiang Qian – Frontiers in Microbiology

Infection microbiology

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness – Matthew J. Binnicker – Journal of Clinical Microbiology

FilmArray Respiratory Panel Assay: Comparison of Nasopharyngeal Swabs and Bronchoalveolar Lavage Samples – Natalya Azadeh – Journal of Clinical Microbiology

Editorial: Variability in Antibiotic Prescribing: An Inconvenient Truth – Lauri A. Hicks and Martin J Blaser – Journal of the Pediatric Infectious Diseases Society

Variation in Antibiotic Prescribing Across a Pediatric Primary Care Network – Jeffrey S. Gerber – Journal of the Pediatric Infectious Diseases Society

Innate Immune Signaling Activated by MDR Bacteria in the Airway – Dane Parker – Physiological Reviews

Tropheryma whipplei, a Potential Commensal Detected in Individuals Undergoing Routine Colonoscopy – M. E. Grasman -Journal of Clinical Microbiology

Bioinformatics and metagenomics

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes – Samuel C. Forster – Nucleic Acids Research

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics – Matthias Willmann – Antimicrobial Agents and Chemotherapy

Current and future resources for functional metagenomics – Kathy N. Lam – Frontiers in Microbiology

Microbial Ecology

Slow and Fast Evolving Endosymbiont Lineages: Positive Correlation between the Rates of Synonymous and Non-Synonymous Substitution – Francisco J. Silva – Frontiers in Microbiology

Microbes in the news

How the Western Diet Has Derailed Our Evolution: Burgers and fries have nearly killed our ancestral microbiome – Moises Velasquez-Manoff – Nautilus

Bacterial biofilm protein prevents ice cream drip – Elisabeth Bik – NPJ Biofilms Community
and
Ice cream designed to drip slowly – Lydia Chain – Popular Science

Bacteria Hysteria

You Don’t Know Where That’s Been: Part 2 – KGNS TV

Science, publishing, and career

Racial bias continues to haunt NIH grants – Minorities still less likely to win biomedical funding – Erika Check Hayden – Nature

Ask Me Anything on Reddit with Carl Zimmer, science journalist at The New York Times, National Geographic and STAT.

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November 17, 2015

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Detecting bacteriophage DNA in mummies, microbiome depletion reduces obesity (in mice), viruses in city rats, microbes in alkaline hotsprings and in glaciers.

Events

European Microbiome Congress 2015: 18-19 November 2015, London.

Human respiratory tract microbiome

Viral aetiology of common colds of outpatient children at primary care level and the use of antibiotics – Janete Kamikawa – Mem. Inst. Oswaldo Cruz

Human reproductive tract microbiome

A DNA tool for early detection of vaginal dysbiosis in African women – Vicky Jespers – Research in Microbiology

Human gut microbiome

Natural mummification of the human gut preserves bacteriophage DNA – Tasha M. Santiago-Rodriguez – FEMS Microbiology Letters

Review: Inhibition of methanogenic archaea by statinsas a targeted management strategy for constipation andrelated disorders – K. Gottlieb

Review: Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Opinion: The Microbiome and Cancer: Is the ‘Oncobiome’ Mirage Real? – Ryan M. Thomas – Trends in Cancer

Review: The effect of gut microbiota on drug metabolism – Mi Jeong Kang – Expert Opinion on Drug Metabolism & Toxicology

Animal and bioreactor models

Microbiota depletion promotes browning of white adipose tissue and reduces obesity –
Nicolas Suárez-Zamorano – Nature Medicine

Variable responses of human and non-human primate gut microbiomes to a Western diet –
Katherine R. Amato – Microbiome

Research Highlight: Commensal bacterium prevents wasting – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of a probiotic, inulin, or their combination on the piglets’ microbiota at different intestinal locations – V.A. Sattler – Beneficial Microbes

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro – Alexandra Dostal – mBio

Research Hightlight: Scaling up spatial imaging of the gut microbiota – Naomi Attar – Nature Reviews Microbiology

Metagenomic analysis of anammox communities in three different microbial aggregates – Jianhua Guo – Environmental Microbiology

Microbial community analysis of a full-scale DEMON bioreactor – Alejandro Gonzalez-Martinez – Bioprocess and Biosystems Engineering

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems – Simon J. McIlroy – Environmental Microbiology Reports

Animal microbiome

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics – Thomas Arn Hansen – PLOS ONE

Bleaching of Baikalian sponge affects the taxonomic composition of symbiotic microorganisms – O. V. Kaluzhnaya – Russian Journal of Genetics

Experimental Infection of Snakes with Ophidiomyces ophiodiicola Causes Pathological Changes That Typify Snake Fungal Disease – Jeffrey M. Lorch – mBio

Plant, root, and soil microbiome

Glyphosate effects on soil rhizosphere-associated bacterial communities – Molli M. Newman – Science of the Total Environment

Soil microarthropods support ecosystem productivity and soil C accrual: Evidence from a litter decomposition study in the tallgrass prairie – Jennifer L. Soong – Soil Biology and Biochemistry

Microbial communities and organic matter composition in surface and subsurface sediments of the Helgoland mud area, North Sea – Oluwatobi E. Oni – Frontiers in Microbiology

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation – Toshiko Miura – Biology and Fertility of Soils

Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands, and scrub biome – Andrey M. Yurkov – FEMS Yeast Research

Coal mining practices reduce the microbial biomass, richness and diversity of soil –
Patricia Dorr de Quadros – Applied Soil Ecology

Water microbiome

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities – Zilian Zhang – PLOS ONE

Comparative study on composition and abundance of major planktons and physico-chemical characteristics among two ponds and Lake Tana, Ethiopia – Wondie Zelalem Amanu – Journal of Coastal Life Medicine

Extremophile microbiome

Metagenomics of an alkaline hot spring in Galicia (Spain): microbial diversity analysis and screening for novel lipolytic enzymes – Olalla López-López – Frontiers in Microbiology

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic – Purnima Singh – Journal of Basic Microbiology

Built environment microbiology

Microbiota formed on attached stainless steel coupons correlate with the natural biofilm of the sink surface in domestic kitchens – Birgitte Moen – Canadian Journal of Microbiology

Towards an antimicrobial ‘microglove’ – Ewoud Reilman – Scientific Reports

Infection microbiology

Research Highlight: The Origin of a Killer Revealed by Bronze Age Yersinia Genomes – Shijulal Nelson-Sathi – Cell Host & Microbe

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago – Simon Rasmussen – Cell

Review: The Black Death: Its origin and routes of dissemination – Kristina Lenz – Scandinavian Journal of History

Review: Emerging methodologies for pathogen identification in positive blood culture testing – Grégory Dubourg – Expert Review of Molecular Diagnostics

Microbial ecology

Integrating ecological and engineering concepts of resilience in microbial communities – Hyun-Seob Song – Frontiers in Microbiology

Perspective: Rethinking “mutualism” in diverse host-symbiont communities – Alexandra A. Mushegian – BioEssays

Techniques

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community – Yang Lu – PLOS ONE

Bioinformatics, viruses, and metagenomics

The State of Software in Evolutionary Biology: code quality of 15 highly cited tools – Diego Darriba – bioRxiv

Kaiju: Fast and sensitive taxonomic classification for metagenomics – Peter Menzel – bioRxiv

A novel group of diverse Polinton-like viruses discovered by metagenome analysis – Natalya Yutin – BMC Biology

Microbes in the news

Taking Antibiotics Can Change the Gut Microbiome for Up to a Year. A new study illuminates the problems antibiotic overuse could cause for individual patients – Julie Beck – The Atlantic

Health Experts Are Explaining Drug-Resistant Bacteria Poorly: Their confusing jargon is pushing people toward bad decisions – Ed Yong – The Atlantic

5 Common Myths About Antibiotic-Resistant Bacteria – Alexandra Sifferlin – Time

There’s Life in Rocks Deep Below the Sea Floor. Seriously. – Heather Goldstone – Cape and Islands

More armadillos that carry leprosy bacteria found in Southern US – Amanda Lane – Midday Daily

Blood-Gut Barrier. Scientists identify a barrier in mice between the intestine and its blood supply, and suggest how Salmonella sneaks through it – Ruth Williams – The Scientist

Microbes Play Role in Anti-Tumor Response
Gut microbiome composition can influence the effectiveness of cancer immunotherapy in mice – Anna Azvolinsky – The Scientist

How depleting the gut microbiota protects from obesity – MedicalXpress

A Complex Disorder. Factors that likely contribute to obesity include disruptions to intercellular signaling, increased inflammation, and changes to the gut microbiome – Stephen D. Hursting – The Scientist

 

Effect of feed on microbiota balance in piglets – All About Feed

Skin Must Develop Tolerance to ‘Good’ Bacteria Early In Life, Says New Study: Research Probes How Skin’s Resident Communities of Microbes Are Established – Pete Farley – University of California San Francisco

How You’re Born May Affect Your Brain Development – Stephanie Pappas – Brain Decoder

Bacteria Hysteria

Doctors say to watch out for bacteria in your makeup bag – NBC News

Proper Use Of Wipes Kills Germs, Improper Use Could Spread Them – Maria Simbra – CBS Local

Microbiology and Art

What Lives on the Subway Pole? – Jen Kirby – New York Magazine

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November 12, 2015

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Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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November 7, 2015

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Human oral microbiome

Dental demineralization, radiation caries and oral microbiota in patients with head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: Bacterial interactions in pathogenic subgingival plaque – Hong Min Ng – Microbial Pathogenesis

Human gut microbiome

Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians – Fang Wang – Journal of Microbiology and Biotechnology

Gut colonization with methanobrevibacter smithii is associated with childhood weight development – Catherine A. Mbakwa – Obesity

Review: Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota – Paige V. Bauer – Cellular and Molecular Life Sciences

Animal and other models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Mice: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline – Jérôme Lluch – PLOS ONE

Sheep: Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium – David Collie – PLOS ONE

Human cells: The effect of short-chain fatty acids on human monocyte-derived dendritic cells – Claudia Nastasi – Scientific Reports

Review: Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? – E. Ringø – Aquaculture Nutrition

Animal microbiome

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions –
Katharina Burbach – Microbiology Open

Insects: Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis – Paul R. Johnston – PLOS Pathogens

Plant, root, and soil microbiome

Microbial immigration across the Mediterranean via airborne dust – Riccardo Rosselli – Scientific Reports

The herbaceous landlord: integrating the effects of symbiont consortia within a single host – Roo Vandegrift – PeerJ

Review: The plant microbiome explored: implications for experimental botany – Gabriele Berg- Journal of Experimental Botany

The influence of hydrogeological disturbance and mining on coal seam microbial communities – M. J. Raudsepp – Geobiology

Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards – Paula Baptista – Environmental Microbiology Reports

Water microbiome

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Metagenomics and bioinformatics

Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome – Tanudeep Bhattacharya – PLOS ONE

Kernel-Penalized Regression for Analysis of Microbiome Data – Timothy W. Randolph – ArXiv

Infection and microbial detection

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry – Aleksandra Jakovljev – BMC Microbiology

Copper surfaces are associated with significantly lower concentrations of bacteria on selected surfaces within a pediatric intensive care unit – Michael G. Schmidt – American Journal of Infection Control

Microbial ecology

An equilibrium theory signature in the island biogeography of human parasites and pathogens – Kévin Jean – Global Ecology and Biogeography

Microbes in the news

‘The Secret World Inside You’ Explores the Microbial Human – William Grimes – The New York Times
I Contain Multitudes: Microbiomes at the American Museum of Natural History –
Sean Hutchinson – Inverse
Exploring the Inner Universe. A new American Museum of Natural History exhibit introduces visitors to the microbes within their bodies – Ashley P. Taylor – The Scientist

Sexed-up beer – Nature Biotechnology

Microbes aid cancer drugs – Mitch Leslie – Science

Gut microbiota regulates antioxidant metabolism – EurekAlert

Kitchen utensils can spread bacteria between foods, UGA study finds – Sydney Devine – University of Georgia
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