Category Archives: Human oral

March 31, 2016

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A special mBio issue discussing the Holobiont concept, salivary microbiota in oral cancer, truffles, sinuses in germ-free mice, and Wolbachia in cave spiders.

General microbiome

Special Issue: The Holobiont Concept- mBio
Introduction to the Hologenome Special Series – Margaret McFall-Ngai
Microbes Drive Evolution of Animals and Plants: the Hologenome Concept – Eugene Rosenberg
Speciation by Symbiosis: the Microbiome and Behavior – J. Dylan Shropshire
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts – Angela E. Douglas

Pregnancy and birth

Research Highlight: Baby steps towards the microbiome – Andrea Du Toit – Nature Reviews Microbiology

Oral microbiome

Changes in the salivary microbiota of oral leukoplakia and oral cancer – Xiaosheng Hu – Oral Oncology

Human respiratory microbiome

Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome – M. V. Tejesvi – European Journal of Clinical Microbiology & Infectious Diseases

Conference abstract: Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites – Catherine Igartua – Annals of the American Thoracic Society

Conference abstract: Gut Microbiota and Allergic Disease. New Insights
Susan V. Lynch- Annals of the American Thoracic Society

Human gut microbiome

Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes – Claudio Maffeis – Diabetes/Metabolism Research and Reviews

Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection – Braden Millan – Clinical Infectious Diseases

Special issue with reviews: Gastric and Gut Microbiota in Health and Disease – Digestive Diseases

Animal models

Effect of a long-term high-protein diet on survival, obesity development and gut microbiota in mice – Pia Kiilerich – American Journal of Physiology

Differences in the paranasal sinuses between germ-free and pathogen-free mice – Ravi Jain – International Forum of Allergy & Rhinology

Effects of taurine on gut microbiota and metabolism in mice – Haining Yu – Amino Acids

Animal microbiome

Research Highlight: Microbiome ‘coral’ations – Ursula Hofer – Nature Reviews Microbiology

Classification of Wolbachia (Alphaproteobacteria, Rickettsiales): No evidence for a distinct supergroup in cave spiders – Michael Gerth – BioRxiv

Not a great title: Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis – L. A. Ilina – Doklady Biochemistry and Biophysics

Plant, root, and soil microbiome

Screening of soil bacteria as potential agents for drugs biodegradation: a case study with clofibric acid – Claudia Popa Ungureanu – Journal of Chemical Technology and Biotechnology

Metagenomes provide valuable comparative information on soil microeukaryotes –
Samuel Jacquiod – Research in Microbiology

The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales – Gian Maria Niccolò Benucci – Microbial Ecology

Bioreactor microbiology

The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments – O. Podolich – Origins of Life and Evolution of Biospheres

Food microbiology

Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques – Hana Šuranská – Folia Microbiologica

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening – Oylum Erkus – International Journal of Food Microbiology

Bioinformatics and metagenomics

Predicting microbial interactions through computational approaches – Chenhao Li – Methods

Microbes in the news

A Hidden Factor in Stroke Severity: The Microbes in Your Gut : A new study in mice demonstrates that manipulating the microbiome can influence the extent of brain damage caused by a stroke – Jordana Cepelewic – Scientific American

Pushing and Pulling on the Mosquito Microbiome – Kevin Bonham – Scientific American

Sampling an animal shelter – Holly Ganz – MicroBEnet

Intestinal Microbiome of Children with Cystic Fibrosis Promotes Gut Inflammation, Study Finds – Patricia Inacio – Cystic Fibrosis News Today
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March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 28, 2016

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Oral microbiome and smoking, a bacterial genome from a germ-free mouse isolate, semi-arid soils, jellyfish, OTU picking methods, and the best hypervariable regions in the 16S rRNA gene.

Human oral microbiome

Cigarette smoking and the oral microbiome in a large study of American adults – Jing Wu – The ISME Journal

Human gut microbiome

Persisting changes of intestinal microbiota after bowel lavage and colonoscopy – Drago, Lorenzo – European Journal of Gastroenterology & Hepatology

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations – Rashmi Sinha – PLOS ONE

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India – Saurabh Kedia – Journal of Gastroenterology

Review: Gut Microbiota and Lifestyle Interventions in NAFLD – David Houghton – MDPI International Journal of Molecular Sciences

Review: Microbiota-gut-brain signalling in Parkinson’s disease: Implications for non-motor symptoms – Valeria D. Felice – Parkinsonism & Related Disorders

PhD Thesis: Development and analysis of molecular methods for functional metagenomics of the human gut microbiome – Kathy Lam – University of Waterloo

Animal models

Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease – Irina A. Kirpich – The American Journal of Pathology

Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse – T. A. Auchtung – Genome Announcements

Animal microbiome

Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes – Daniel F. R. Cleary – FEMS Microbial Ecology

Review: Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases – Mikolaj M. Raszek – Frontiers in Genetics

Plant, root, and soil microbiome

Soil characteristics driving arbuscular mycorrhizal fungi communities in semiarid Mediterranean soils – Maria del Mar Alguacil – Applied and Environmental Microbiology

454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems – Elham A. Kazeeroni – Frontiers in Plant Science

Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis – Zhiyuan Yao – Journal of Soils and Sediments

Soil communities are affected by CO2 belowground emissions at a natural vent in Spain – I. Fernández-Montiel – Soil Biology and Biochemistry

No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium) – Florine Degrune – Agriculture, Ecosystems & Environment

Bacteria play a more important role than nutrients in the accumulation of tetracycline resistance in manure-treated soil – Shuang Peng – Biology and Fertility of Soils

Review: Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism – Sofie Thijs – Frontiers in Microbiology

Water microbiome

Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids – Jean-Paul Baquiran – Frontiers in Microbiology

Streams: Regional and global elevational patterns of microbial species richness and evenness – Jianjun Wang – Ecography

Extremophile microbiome

Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes – Daniel R. Colman – Frontiers in Microbiology

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments – Alexander Crits-Christoph – Frontiers in Microbiology

Bioinformatics and metagenomics

Application of database-independent approach to assess the quality of OTU picking methods – Patrick D Schloss – BioRxiv

MG-Digger: an automated pipeline to search for giant virus-related sequences in metagenomes – Jonathan Verneau – Frontiers in Microbiology

MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices – Dinghua Li – Methods

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis – Bo Yang – BMC Bioinformatics

Absent words and the (dis)similarity analysis of DNA sequences: an experimental study – Mohammad Saifur Rahman – BMC Research Notes

Book chapter: Bidirectional Variable-Order de Bruijn Graphs – Djamal Belazzougui – LATIN 2016: Theoretical Informatics

Transcriptomics

Review: Translating RNA sequencing into clinical diagnostics: opportunities and challenges – Sara A. Byron – Nature Reviews Genetics

Techniques

Modification of a high- throughput automatic microbial cell enumeration system for ship board analyses – Christin M. Bennke – Applied and Environmental Microbiology

More microbiology

Rare-earth elements: Rare-earth separation using bacteria – William Bonificio – Environmental Science & Technology Letters

Expression of HIV-1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus – Angela Marcobal – AIDS Research and Human Retroviruses

Review: Studying Bacterial Multispecies Biofilms: Where to Start? – Henriette L. Røder – Trends in Microbiology

Microbes in the news

Osel scientists engineer vaginal lactobacillus to express neutralizing HIV-1 antibody fragments – EurekAlert

‘Good’ bacteria could save amphibians hit by fungal diseases – Adam Wernick – PRI

Forget Chocolate Rabbits: Microbiologists Celebrate Easter With Bacteria Bunny – ABC News

Psychobiotics Will Use Bacteria to Alter Your Brain Through Your Gut – Ben Guarino – Inverse

Low FODMAP diet may significantly improve IBS symptoms – Healio

Scientists to drill into dinosaur-killing blast – Eric Hand – Science

Rage Disorder Linked with Parasite Found in Cat Feces. Toxoplasmosis may alter brain chemistry is people exhibiting bouts of explosive anger – Christopher Wanjek – Scientific American

Bacteria Hysteria

Would you dare to bacteria-test your entire life? Katherine Keogh did … and the result will shock all house-proud readers – Katherine Keogh – Daily Mail

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March 22, 2016

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Eye microbiota and contact lenses, leaf-cutter ant dumps, bacteria help with platinum transformation, metagenomics from a Swedish cave, extreme habitats at home, bacteria on board the ISS, a special issue on Megaviromes, and a recipe for Poop Peeps.

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

Effect of Infant Formula Containing a Low Dose of the Probiotic Bifidobacterium lactis CNCM I-3446 on Immune and Gut Functions in C-Section Delivered Babies: A Pilot Study – L. Baglatzi – Clinical Medicine Insights: Pediatrics

Infection, immunology, and transplantion microbiology

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia – P. Gyarmati – Scientific Reports

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation – D Weber – Bone Marrow Transplantation

Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology

Crosstalk between microbiota, pathogens and the innate immune responses – Claudia Günther – International Journal of Medical Microbiology

Human oral microbiome

Commentary: Microbiota-derived metabolites modulate tissue homeostasis: relevance to the oral cavity? – Hervé Le Moual – Oral Diseases

Human eye and skin microbiome

Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio

Human vaginal microbiome

Improvement and automation of a real-time PCR assay for vaginal fluids – E. De Vittori – Forensic Science International

Human gut microbiome

Conference report: Talking about cross-talk: the immune system and the microbiome: A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, Feb 2016 – David Zeevi – Genome Biology

Review: An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? – Burman S. – Digestive Diseases

Review: Gut Microbiota: The Brain Peacekeeper – Chunlong Mu – Frontiers in Microbiology

Review [PDF]: The intestinal microbiota and its role in human health and
disease – Keiko Kataoka – The Journal of Medical Investigation

Editorial: The microbiome as a possible target to prevent celiac disease – Maureen M Leonard – Expert Review of Gastroenterology & Hepatology

Animal models

Mice: Arthritis-induced alveolar bone loss is associated with changes in the composition of oral microbiota – Jôice Dias Corrêa – Anaerobe

Chickens: Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens – Qin Luo – Biological Trace Element Research

Tilapia: Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis – Zhi Liu – Scientific Reports

Animal microbiome

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability – Gina R. Lewin – PLOS ONE

Plant, root, and soil microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity – Paul Carini – bioRxiv

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities – Megan A. Rúa – Frontiers in Microbiology

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert – Yan Gui Su – CATENA

The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests – Nicholas P. Rosenstock – New Phytologist

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass – Erin E. Nuccio – Ecology

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan – Shunsuke Matsuoka – FEMS Microbiology Ecology

Review: The Functioning of Rhizosphere Biota in Wetlands – a Review – Amir Neori – Wetlands

Water and extremophile microbiome

Experimental evidence that microbial activity lowers the albedo of glaciers – M. Musilova – Geochemical Perspectives Letters

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor – William D. Orsi – Environmental Microbiology Reports

Cave microbiome

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden – Marie Lisandra Zepeda Mendoza – PLOS ONE

Built environment microbiology

Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ preprint

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A. Coil – PeerJ

Food microbiology

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits – Wen Yi W. V – Letters in Applied Microbiology

Bioinformatics, techniques, and metagenomics

Strain-level microbial epidemiology and population genomics from shotgun metagenomics – Matthias Scholz – Nature Methods

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions – Shengqin Wang – Journal of Theoretical Biology

A framework for inferring biological communities from environmental DNA – Andrew Olaf Shelton – Ecological Applications

Review: Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money – Antony T. Vincent – Journal of Microbiological Methods

Metagenomics and viruses

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity – Yu-Nong Gong – PLOS ONE

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics – Daniel Wüthrich – Virology

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets – Oskar E. Karlsson – PLOS ONE

Special issue of Current Opinion in Microbiology: Megaviromes
Review: Giant viruses come of age – Matthias G Fischer
Review: Giant viruses and the origin of modern eukaryotes – Patrick Forterre

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life – Patrick Forterre – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

More microbiology

The mystery of plague in medieval Iceland – Chris Callow – Journal of Medieval History

Microbes in the news

HT: Tomer Altman: Poop Peeps: Today we’re going to make Poop Peeps. Marshmallow Peeps that are shaped like the poop emoji.– Matthew Cetta – Nomageddon

Elizabethkingia, the rare and deadly bacteria that’s sickening people in the Midwest, explained – Julia Belluz – Vox

Forest resilience; can microbes help combat climate change issues faster than genetic adaptations? – Armand Séguin

Controversial New Push to Tie Microbes to Alzheimer’s Disease. A journal article says herpes virus and Lyme disease bacteria are behind the mind-robbing illness, but not all researchers are convinced – Melinda Wenner Moyer – Scientific American

Bacteria Are Revolutionizing Biotech–Here’s Why We Need To Talk About It – Catherine Feuillet – Forbes

Contact Lenses Fill Your Eyes With Bacteria – Mandy Oaklander – Time

Killing Bacteria With Gold Nanodisks And Light – Jennifer Hicks – Forbes

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

Top Science Fair Projects Put Stream Data, Bacteria to Work – Dan Swanson – News Channel Nebraska

The Daily Startup: Startups Look to ‘New Frontier’ of Microbiomes to Fight Disease – Wall Street Journal

The Human Microbiome Handbook – Edited by Jason Tetro, Emma Allen-Vercoe

New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data – Genome Web

Ulcerative Colitis Improves in Multidonor Fecal Transplant Trial – Damian McNamara – MedScape

Blog posts by me:

New papers, March 22, 2016 – Elisabeth Bik – MicroBEnet

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 20, 2016

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Back in the PDT, so catching up with the literature.

Pregnancy and birth

In mice: The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Review: New techniques to characterise the vaginal microbiome in pregnancy – George L. Mendz – AIMS Microbiology

Perspective: The Placental Microbiome: A New Site for Policing Women’s Bodies – Saray Ayala – International Journal of Feminist Approaches to Bioethics

Review: Building a Beneficial Microbiome from Birth – Esther Castanys-Muñoz – Advances in Nutrition

Human oral microbiome

Microbiome associated with severe caries in Canadian First Nations children – EurekAlert

Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults – Theresa Wan-Chen Yap – PLOS ONE

FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial – Keith McIntosh – Gut

Tumour-associated and non-tumour-associated microbiota in colorectal cancer – Burkhardt Flemer – Gut
Review: Microbiota and lifestyle interactions through the lifespan – Simone Rampelli – Trends in Food Science & Technology

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanism and Application of Metabolomics – Xuyun He – Int J Mol Sci

Animal models

Effect of artesunate supplementation on bacterial translocation and dysbiosis of gut microbiota in rats with liver cirrhosis – Yun-Xia Chen – World Journal of Gastroenterology

Long-term effects of early life microbiota disturbance on adaptive immunity in laying hens
K. Simon – Poultry Science

Animal microbiome

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

Review: Microbial diversity associated with ascidians: a review of research methods and application – Lei Chen – Symbiosis

Plant, root, and soil microbiome

Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity – Binu M. Tripathi – Frontiers in Microbiology

Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field – Muhammad Naveed – Applied Soil Ecology

Microbial community structure and nutrient dynamics in forest soils colonized by bracken fern (Pteridium aquilinum) – Manuel Aira – PeerJ Preprint

Evidence of horizontal gene transfer between obligate leaf nodule symbionts – Marta Pinto-Carbó – The ISME Journal

Bacteria-Soil-Plant Interaction: This Relationship to Generate can Inputs and New Products for the Food Industry – Jeremias Pakulski Panizzon – Rice Research

Microbial growth and community structure in acid mine soils after addition of different amendments for soil reclamation – R. Zornoza – Geoderma

Water and extremophile microbiome

Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy – Amy R. Smith – Geomicrobiology Journal

Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy – Emil S. Ruff – Frontiers in Microbiology

Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge – Xinxu Zhang – Frontiers in Microbiology

Built environment microbiology

Qualitative and Quantitative Analysis of Microbial Communities in Household Dishwashers in Germany – Britta Brands – Tenside Surfactants Detergents

Waste and pollution microbiology

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure – Halil Coban – Bioprocess and Biosystems Engineering

Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils – Santonu Kumar Sanyal

Techniques

Example used in this review paper: kombucha (?): DNA metabarcoding of microbial communities for healthcare – Zaets I. Ye – Biopolym Cell

Next-Generation Sequencing in the Mycology Lab – Jan Zoll – Current Fungal Infection Reports

Metagenomics

Identification of virulence factors and antibiotic resistance markers using bacterial genomics – Sofiane Bakour – Future Medicine

Microbes in the news

Gut health: Stanford researchers explain how what’s in our bellies affects myriad health issues – Martha Ross – Contra Costa Times

Inflamed, noninflamed mucosal microbiota differ between patients with Crohn’s disease, UC – Healio

Video: Six Strange Things Bacteria Eat – Wall Street Journal

Bacteria in your mom’s gut may have influenced the way you fight off infections today
Katherine Ellen Foley – Quartz

New technique for rapidly killing bacteria using tiny gold disks and light – Nanowerk

Bacteria-powered Bio-Bots Avoid Obstacles on Way to Target – MedGadget

Pneumonia, middle ear infections might be prevented by diverse bacteria in gut microbiome – Emily Lunardo – Belmarra Health

Going viral: IU Southeast student, teacher discover a new type of virus
Student, professor find new bacteriophage in Ohio River – Jerod Clapp – News and Tribune

Brucellosis-causing bacteria could be dropped from bioterrorism list – Helenair

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March 19, 2016

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General microbiome

Prospect: Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology – Felix Sommer – BioEssays

Review: Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance – Andrés Moya – Trends in Microbiology

Human oral microbiome

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus – Andrew T. Ozga – American Journal of Physical Anthropology

Oral microbiota species in acute apical endodontic abscesses – Noelle George – Journal of Oral Microbiology

Human gut microbiome

Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment – Bumjo Oh – Helicobacter

Gut microbiota produce alcohol and contribute to NAFLD – Lixin Zhu – Gut

Probiotics

Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili – Hanne L. P. Tytgat – PLOS ONE

Animal microbiome

Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals – Mariana Kluge – PLOS ONE

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla) – Klára Vlčková – Microbial Ecology

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia – H.N. Su – Letters in Applied Microbiology

Plant, root, and soil microbiome

The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots – Larry M. York – Journal of Experimental Botany

Impact of an invasive N2-fixing tree on arbuscular mycorrhizal fungi and development of native species – Alejandra, Guisande-Collazo – AoB Plants

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado? – Renata Carolini Souza – BMC Microbiology

Water microbiome

High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling – Tomàs Llorens-Marès – Microbial Ecology

Food and medicine microbiology

Characterization of malolactic bacteria isolated from Aosta Valley wines and evidence of psychrotrophy in some strains – I. Vigentini – Journal of Applied Microbiology

A review of melanized (black) fungal contamination in pharmaceutical products—incidence, drug recall and control measures – R. Vijayakumar – Journal of Applied Microbiology

Microbes in the news

Researchers Extract and Sequence Ancient DNA From Biofilm Coating Teeth – Genome Web

New green toothpaste reveals biofilm – Maria Perno Goldie – Dentistry IQ

Video: Pink Lake Mystery Solved: Lake Hillier Bacteria – SciShow – YouTube

SlideShow: Experiments with my Microbiome – Richard Sprague – LinkedIn

Video: #GMFH2016 (5th Gut Microbiota for Health World Summit ) Interviews: Prof. Joël Doré – YouTube
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March 16, 2016

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Events

Strategies & Techniques for Analyzing Microbial Population Structures (STAMPS) Course 8/3-8/13 – MicroBEnet

Human skin microbiome

An in Vitro Model for the Human Cutaneous Microbial Ecosystem – Danique A. van der Krieken – Acta Dermato-Venereologica

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – I.M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory tract microbiome

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines – Chinelo Ebruke – BMC Microbiology

Human gut microbiome

Note: data segregate according to study: Gene expression profiling gut microbiota in different races of humans – Lei Chen – Scientific Reports

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman

Review: Gut Microbiota and Obesity: Potential Therapeutic Targets and Probiotic 
Nicole D. White – American Journal of Life Sciences

Animal models

Fuzhuan tea consumption imparts hepatoprotective effects and alters intestinal microbiota in high saturated fat diet-fed rats – Michelle T. Foster – Molecular Nutrition & Food Research

Long-term effects of early life microbiota disturbance on adaptive immunity in laying 
K. Simon – Poultry Science

Rapid evolution of microbe-mediated protection against pathogens in a worm host –
Kayla C King – ISME Journal

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Hongxing Han – Scientific Reports

Animal microbiome

Genomic Analysis of Companion Rabbit Staphylococcus aureus – Mark A. Holmes – PLOS ONE

Plant, root, and soil microbiome

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants – Tao Ding – PLOS ONE

Water and extremophile microbiome

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats – David Velázquez – Scientific Reports

Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters – Richard A. Haugland – Journal of Microbiological Methods

Built environment microbiome

Potentially harmful secondary metabolites produced by indoor Chaetomium species on artificially and naturally contaminated building materials – I. Došen – Indoor AIr

Food microbiology

Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties – Reza Ranjbar – BMC Microbiology

Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce – Ji Young Jung – PLOS ONE

Viruses and phages

The Formulation of Bacteriophage in a Semi Solid Preparation for Control of Propionibacterium acnes Growth – Teagan L. Brown – PLOS ONE

News & Views: Microbial oceanography: Viral strategies at sea – T. Frede Thingstad – Nature

Lytic to temperate switching of viral communities – B. Knowles – Nature

Microbial Ecology

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla – Judith Zimmerman – Molecular Ecology

Bioinformatics

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to 
Yanming Zhang – Nucleic Acids Research

Techniques

The US Culture Collection Network lays the foundation for progress in preservation of valuable microbial resources – Kevin McCluskey – Phytopathology

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

A modified micro chamber agar spot slide culture technique for microscopic examination of filamentous fungi – Peralam Yegneswaran Prakash – Journal of Microbiological Methods

Microbes in the news

uBiome is World’s First Company to Appoint Citizen-Scientist-in-Residence – PR Web

Incredible images reveal bacteria motor parts in unprecedented detail – Science Codex

Ancient Bacteria With Photosynthesis Were Much More Common Than Previously Thought, Study Finds – Catherine Griffin – HNGN

Viral Remnants Help Regulate Human Immunity: Endogenous retroviruses in the human genome can regulate genes involved in innate immune responses – Jyoti Madhusoodanan – The Scientist

Plastic That Mimics Insect Wings Kills Bacteria, University of California, Irvine Study – Biospace

Early heavy metal exposure can cause permanent changes to gut microbiome and cause a host of diseases – Dave Mihalovic – SOTT

Slice of PLOS: Bacteria’s Social Media – Lauren Richardson – PLOS ONE

“Unsurprisingly, Perlmutter has his critics.” Neurologist David Perlmutter gets to the guts of brain health with surprising advice – SMH.com

Opinion: A Mother’s Microbes: On “vaginal seeding” and the challenge of evidence-based parenting – Rob Knight and Jack Gilbert – The Scientist

Australian Scientists Discover How Gut Bacteria May Prevent Stomach Cancer – MSN

Reduction in dietary diversity impacts richness of human gut microbiota – Science Codex
http://www.nature.com/articles/srep23075

Press might be overinterpreting Mouse seminal microbiome study:
Scientists discover microbiome that may be responsible for male reproductive disorders – EurekAlert

Seminal work. How unruly data led MU scientists to discover a new microbiome – Roger Meissen – Decoding Science

Microbiome: This Type Of Bacteria May Increase Risk Of Reproductive Disorders – Kathleen Lees – HNGN

Science, publishing, and career

Handful of Biologists Went Rogue and Published Directly to Internet – Amy Harmon

Peer-Led Team Learning Helps Minority Students Succeed – Julia J. Snyder – PLOS Biology

Video parody: PloS ANNA VS ELSAvier – For The First Time – Luisa Hugerth -YouTube

Bik’s Picks

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

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March 12, 2016

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Microbiomes of farmland frogs and grape vine, and functional structures in acid mine drainage microbes.

Human oral microbiome

Ecological changes in oral microcosm biofilm during maturation – Young-Seok Kim – Journal of Biomedical Optics

Human gut microbiome

Review: Consequences of bile salt biotransformations by intestinal bacteria – Jason M. Ridlon – Gut Micobes

Review: The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder – Q. Li,- Neuroscience

Animal models

Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology – Qingqing Wang – PLOS ONE

Animal microbiome

Changes of diet and dominant intestinal microbes in farmland frogs – Chun-Wen Chang – BMC Microbiology

Plant, soil, and microbiome

Vitis vinifera microbiome: from basic research to technological development – Cátia Pinto – BioControl

Water and extremophile microbiology

Predicting taxonomic and functional structure of microbial communities in acid mine drainage – Jialiang Kuang – The ISME Journal

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences – Martin W Hahn – The ISME Journal

Waste and pollution microbiology

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing analyses – Yiwen Lin – Frontiers of Environmental Science & Engineering

Metabolomics

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease – Qiang Feng – Scientific Reports

Bioinformatics and metagenomics

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences – Alexey M Kozlov – BioRxiv

Microbial Ecology

Challenges in microbial ecology: building predictive understanding of community function and dynamics – Widder, S – White Rose Research Online

Microbes in the news

A cloud of distinction – Could the trails of microbes we leave behind be used to solve crimes? Julian Smith picks up the scent – Julian Smith  – New Scientist

Stick Out Your Tongue: Citizen science project draws up the first oral microbiome map for the youth: Over 4,000 people have taken part in this hands-on scientific project in Barcelona- EurekAlert

Biologicals in quest for 2050: BioConsortia is evaluating microbes that could help protect seedlings emerging in cold and wet conditions. – AgriView

Gut Microbiome Analysis for Detecting Colon Cancer Mutations – Univesrity of Minnesota

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March 11, 2016

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Posting from the airport – flying home to my folks for a week. I will try to keep you all updated, though! Fecal microbiota from dolphins (by another group!), microbes and Alzheimer’s, plastic-eating bacteria, and lead exposure.

Pregnancy and birth

State Scope of Practice Laws, Nurse-Midwifery Workforce, and Childbirth Procedures and Outcomes – Y. Tony Yang – Women’s Health Issues

Human oral microbiome

Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans – Xuelian Huang – Applied and Environmental Microbiology

The Microbiome of the Oral Mucosa in Irritable Bowel Syndrome – Nicolaas H. Fourie – Gut Microbes

Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus
Kun Wang – Scientific Reports

Human respiratory microbiome

Review: The lung microbiome and exacerbations of COPD – Dy, Rajany – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis – Hanneke Borgdorff – PLOS ONE

Human gut microbiome

The Microbiome, Intestinal Function, and Arginine Metabolism of Healthy Indian Women Are Different from Those of American and Jamaican Women – CC Kao – Journal of Nutrition

Fecal Microbiota Transplantation Inhibits Multidrug-Resistant Gut Pathogens: Preliminary Report Performed in an Immunocompromised Host – Jarosław Biliński – Archivum Immunologiae et Therapiae Experimentalis

The Intersection of TNF, IBD and the Microbiome – Yava L. Jones-Hall – Gut Microbes

Review: Bacterial species involved in the conversion of dietary flavonoids in the human gut – Annett Braune – Gut Microbes

Review: Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism – Douglas J. Morrison – Gut Microbes

Microbiome models

Perinatal lead (Pb) exposure alters gut microbiota composition and results in sex-specific bodyweight increases in adult mice – Jianfeng Wu – Toxicological Sciences

Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice – Naoki Harada – Scientific Reports

Animal microbiome

The bottlenose dolphin (Tursiops truncatus) fecal microbiota – Matteo Soverini – FEMS Microbiology Ecology

Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes – Moritz Buck – Scientific Reports

Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil – Janira Prichula – Marine Pollution Bulletin

Targeting eukaryote mitochondrial 16S rRNA gene: Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing – Kyle Logue – PLOS Neglected Tropical Diseases

Characterization of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16s rRNA gene – S. Saxena – British Poultry Science

Plant, root, and soil microbiome

Nitrogen-fixing bacterial communities in invasive legume nodules and associated soils are similar across introduced and native range populations in Australia – Christina Birnbaum – Journal of Biogeography

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors? – José A. Siles – Microbial Ecology

Interactions between Bacteria And Aspen Defense Chemicals at the Phyllosphere – Herbivore Interface – Charles J. Mason – Journal of Chemical Ecology

Long-term effects of multi-walled carbon nanotubes and graphene on microbial communities in dry soil – Yuan Ge – Environmental Science and Technology

Air and space station microbiome

Airborne Bacterial Diversity from the Low Atmosphere of Greater Mexico City – Jaime García-Mena – Environmental Microbiology

Characterization of Fungi Isolated from the Equipment Used in the International Space Station or Space Shuttle – Kazuo Satoh – Microbiology and Immunology

Water, waste, and pollution microbiology

A bacterium that degrades and assimilates poly(ethylene terephthalate) – Shosuke Yoshida – Science

The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities – Brian T. Murphy – Marine Pollution Bulletin

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – Microbiology Ecology

Microbial Ecology

Phylogenetic organization of bacterial activity – Ember M Morrissey – The ISME Journal

Infection and microbiology

Editorial: Microbes and Alzheimer’s Disease – Ruth F. Itzhaki – Journal of Alzheimer’s Disease

Treatment of in vitro enterohemorrhagic E. coli infection using phage and probiotics – Cecilia Dini _ Journal of Applied Microbiology

Microbes in the news

These plastic-eating bacteria could help cut down on waste – Rachel Feltman – Washington Post

Some bacteria think plastic is fantastic – Nicholas S. Wigginton – Science

Science: Newly Identified Bacteria Break Down Tough Plastic – Michelle Hampson – AAAS News

Scientists identify a virus and two bacteria that could be causing Alzheimer’s – Fiona MacDonald – Science Alert

Lead exposure changes gut microbiota, increases chance for obesity – Laurel Thomas Gnagey – University of Michigan

These newly discovered bacteria can help prevent cavities, and scientists want to put them in a pill – Peter Dockrill – Science Alert

Viral infections may affect respiratory microbiome of patients with CF – Healio

Emollient Treatment Improves Skin Microbiome in Atopic Dermatitis: Interview with Sophie Seite – Medical Research

Science, publishing, and career

The Frequency of “Brilliant” and “Genius” in Teaching Evaluations Predicts the Representation of Women and African Americans across Fields – Daniel Storage – PLOS ONE

Papers with simpler abstracts are cited more, study suggests – Dalmeet Singh Chawla – Retraction Watch
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March 10, 2016

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Signals within microbial communities, feeding the microbiome with milk, gut metagenomes of Japanese subjects, multiethnic cohorts, biogeography of viruses in the sea, and finding transcription start sites.

General human microbiome

Review: Signaling in Host-Associated Microbial Communities – Michael A. Fischbach and Julia A. Segre – Cell

Review: The microbiome systemic diseases connection – T.A. van der Meulen – Oral Diseases

Review: The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance – Melinda M. Pettigrew – Annals of Epidemiology

Pregnancy and birth

The placental microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis – Amanda L. Prince – American Journal of Obstetrics and Gynecology

It’s in the Milk: Feeding the Microbiome to Promote Infant Growth – Stavros Bashiardes – Cell Metabolism

The Microbiome in Necrotizing Enterocolitis: A Case Report in Twins and Minireview –
Suchitra K. Hourigan – Clinical Therapeutics

Comment: Gut microbiome and necrotising enterocolitis: time for intervention? –
Alessio Fasano – The Lancet

Human oral microbiome

Not sure if I agree with the goal of this paper: Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms – Lamprini Karygianni – Frontiers in Microbiology

Human urinary tract microbiome

The Urinary Microbiome Differs Significantly between Patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as between Patients with Different Clinical Phenotypes – Daniel A Shoskes – Urology

Human gut microbiome

The gut microbiome of healthy Japanese and its microbial and functional uniqueness – Suguru Nishijima – DNA Research

Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype – Tyler, Andrea D. – Inflammatory Bowel Diseases

Perspective: Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease – J. Schulberg – Internal Medicine Journal

FMT Happens: Regulating Fecal Microbiota Therapy in Canada; What You Need to Know – Shahad Salman – World Medical & Health Policy

Review: Characterization of the Gut Microbiome in Epidemiologic Studies: The Multiethnic Cohort Experience – Benjamin C. Fu – Annals of Epidemiology

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Animal models

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes – Chenhong Zhang – ISME Journal

Review: Viruses in Rodent Colonies: Lessons Learned from Murine Noroviruses – Stephanie M. Karst – Annual Review of Virology

Animal microbiome

Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals – Teresita de J. Bello González – Frontiers in Microbiology

Allows the consumption of toxic cabbage: SaxA-mediated isothiocyanate metabolism in phytopathogenic Pectobacteria – Cornelia U. Welte – Applied and Environmental Microbiology

Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-Throughput Sequencing of the V4 Region of the 16S rRNA Gen (sic) – Yiping Zhao – Asian Australian Journal of Animal Sciences

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

I really feel for horses who are sick of grass.  Abstract: Analysis of the large intestinal and faecal microbiota of horses with grass sickness using denaturing gradient gel electrophoresis – D. Nölkes – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Phyllosphere Fungal Communities Differentiate More Thoroughly than Bacterial Communities Along an Elevation Gradient – Corinne Vacher – Microbial Ecology

A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system – Hui Lin – Environmental Pollution

Water and extremophile microbiome

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi – József Geml – FEMS Microbiology Ecology

Review: Biogeography of Viruses in the Sea – Cheryl-Emiliane T. Chow – Annual Review of Virology

DGGE: Oil removal and effects of spilled oil on active microbial communities in close to salt‑saturation brines – Yannick Y. Corsellis – Extremophiles

Bioreactors and waste microbiology

Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures – Haifeng Geng – Microbial Ecology

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters – Arda Gülay – ISME Journal

Bacterial communities in different locations, seasons and segments of a dairy wastewater treatment system consisting of six segments – Kikue Hirota – Journal of Environmental Sciences

Food microbiology

Resistome diversity in cattle and the environment decreases during beef production – Noelle R Noyes – eLIFE

Inactivation of Salmonella on tainted foods: using blue light to disinfect cucumbers and processed meat products – J. Stephen Guffey – Food Science & Nutrition

Bioinformatics and metagenomics

Review: Recovering complete and draft population genomes from metagenome datasets – Naseer Sangwan – Microbiome

Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics – Leandro D. S. Duarte – Methods in Ecology and Evolution

Transcriptomics

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome – Laurence Ettwiller – BMC Genomics

Fungi

Perspective: The invisible dimension of fungal diversity – David Hibbett – Science

Microbes in the news

At Stanford: Center launched to explore, exploit human microbiome – Bruce Goldman – Stanford Medicine

Columbia Expands Its Microbiome Research – Christopher Williams – Columbia University Medical Center

UT professor develops technique to enhance desirable traits of plants, animals through microbiology – Maluly Martinez Benavides – The Daily Texan

5th World Summit “Gut Microbiota For Health”: Media Information on Top Issues Ready for Download

Gut bacteria make cabbage poison harmless – Radboud University

Scientists developed a robust method for analysis of intestinal bacteria – Science Codex

Nukadoko: rich in beneficial bacteria: Nukadoko is made by fermenting rice bran, a byproduct of milling brown rice, with lactic acid bacteria and yeast. – Natsuko Tamaki – The Japan News

A mouse’s house may ruin experiments. Environmental factors lie behind many irreproducible rodent experiments – Sara Reardon – Nature

Viral infections may affect respiratory microbiome of patients with CF – Healio

Science, publishing, and career

German Defense Minister to keep doctoral degree – plagiarism found on 44% – Debora Weber-Wulff – Copy, Shake, and Paste

Bik’s Picks

How long can you chew on goat meat? Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans – Katherine D. Zink – Nature

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