Category Archives: Events and jobs

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

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 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 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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February 28, 2016

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Viral sequences in cancers, COPD, and EDGE, an easy online tool for metagenomics analysis.

Jobs

Researcher for a project on the effect of gut microbiome in human behavior – Radboud UMC Nijmegen, The Netherlands

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants – Natalia Zeber-Lubecka – PLOS ONE

Human respiratory microbiome

Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations – Zhang Wang – European Respiratory Journal

Human gut microbiome

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer – Shegan Gao – BMC Infectious Agents and Cancer

Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy – Ai-Hua Wang – Scientific Reports

Review: Gut Microbiota of Nonalcoholic Fatty Liver Disease – Reham M. Abdou – Digestive Diseases and Sciences

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: Beyond the gut bacterial microbiota: The gut virome – Paola Columpsi – Journal of Medical Virology

Human tissues and infection

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers – Jens Friis-Nielsen – MDPI Viruses

Models of microbiome research

Maternal Weaning Modulates Emotional Behavior and Regulates the Gut-Brain – Pamela Farshim – Scientific Reports

Rats: Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State – Hong Lin – Scientific Reports

Animal microbiome

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species – Aitor Albaina – Ecology and Evolution

Plant, root and soil microbiome

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming – Kai Xue – Nature Climate Change

Online Springer Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book chapter: Soil Effects of Genetically Modified Trees (GMTs) – Fernando Gallardo – Biosafety of Forest Transgenic Trees

Borderline Products between Bio-fertilizers/ Bio-effectors and Plant Protectants: The Role of Microbial Consortia – Marco Nuti – David Publishing Company

Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity – Tobias Bölscher – Biology and Fertility of Soils

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon – Andre Mancebo Mazzetto – Brazilian Journal of Microbiology

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests – Zhiqin Pei – Soil Biology and Biochemistry

Water and extremophile microbiome

Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community – Alexander Crits-Christoph – Environmental Microbiology

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water – Dimitri Kalenitchenko – The ISME Journal

Chapter One – Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes – M. Itävaara – Advances in Applied Microbiology

Waste and pollution microbiology

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor – Linda Jabari – Brazilian Journal of Microbiology

High-Resolution Phylogenetic Analysis of Residual Bacterial Species of Fouled Membranes after NaOCl Cleaning – Ronald R. Navarro – Water Research

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis – Firouz Abbasian – Biotechnology Progress

Bioinformatics

Now peer reviewed: cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies – John H. Chase – mSystems

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation – Cecilia Noecker – mSystems

Assessing the performance of DNA barcoding using posterior predictive simulations – Anthony J. Barley – Molecular Ecology

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform – Po-E Li – BioRxiv

GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data – João Marcelo P. Alves – Frontiers in Microbiology

Metabolomics

Human microbial metabolites as a source of new drugs – Somdutta Saha – Drug Discovery Today

More microbiology

Microbiota–mitochondria inter-talk: consequence for microbiota-host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities – Clara Moreno-Fenoll – bioRxiv

Accurate and semi-automated analysis of bacterial association with mammalian cells – C.M. Murphy – Journal of Microbiological Methods

Microbes in the news

Fungal DNA, mycotoxins, cat allergens and fatigue in classrooms – Holly Ganz – MicroBEnet

Gum Disease Bacteria Linked to Esophageal Cancer Risk – Newsmax

Video: Virginia Tech scientists turn poo into power – Virginia Tech

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February 24, 2016

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Women in space, cacti, celiac disease, and traveling dust.

Event

Not endorsing – full of quackery and folks trying to sell their books and food supplements, little science: Microbiome Medicine Summit

Human oral microbiome

Review: Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line – Kah Yan How – Frontiers in Microbiology

Human reproductive tract microbiome

The potential influence of the microbiota and probiotics on women during long spaceflights – Camilla Urbaniak – Future Medicine

Human gut microbiome

Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease versus non celiac disease controls – Esther Nistal – Journal of Applied Microbiology

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk – Yanan Wang – Frontiers in Microbiology

Review: A glance at … dietary emulsifiers, the human intestinal mucus and microbiome, and dietary fiber – Michael J. Glade – Nutrition

Review: Chemical conversations in the gut microbiota – Jessica A. Thompson – Gut Microbes

Review: Atopic dermatitis and the intestinal microbiota in humans and dogs – J. Mark Craig – Veterinary Medicine and Science

Animal models

Composition of fecal microbiota of laboratory mice derived from Japanese commercial breeders using 16S rRNA gene clone libraries – Ryoko Nozu – Journal of Veterinary Medical Science

Animal microbiome

News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Plant, root, and soil microbiome

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity – Citlali Fonseca-García – Frontiers in Microbiology

Comparison of Fungal Community in Black Pepper-Vanilla and Vanilla Monoculture Systems Associated with Vanilla Fusarium Wilt Disease –
Wu Xiong – Frontiers in Microbiology

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere – Marco Kai – Frontiers in Microbiology

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil – François Thomas – Frontiers in Microbiology

Changes in rhizosphere bacterial gene expression following glyphosate treatment – Molli M. Newman – Science of the Total Environment

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area – Jinxiang Hu – Scientific Reports

Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment – Michelle Cleary – Scientific Report

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts – Candida Vannini – New Phytologist

Water and extremophile microbiome

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway) – Alejandro Mateos-Rivera – FEMS Microbiology Ecology

Water level changes affect carbon turnover and microbial community composition in lake sediments – Lukas Weise – FEMS Microbiology Ecology

Evaluation of the treatment performance and microbial communities of a combined constructed wetland used to treat industrial park wastewater – Ming Xu – Environmental Science and Pollution Research

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps – Marco Meola – Frontiers in Microbiology

Review: Bridging the divide: a model-data approach to Polar and Alpine microbiology – James A. Bradley – FEMS Microbiology Ecology

Bioinformatics and metagenomics

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

More microbiology

Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species – Kathrin Moor – Frontiers in Immunology

Microbes in the news

Bacteria From the Sahara Desert Found on Swiss Glaciers – Nellie Van Driska – GlacierHub

Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates – NDTV

Student Research Focus: Drew Gukeisen discovers and visualizes new virus – Indiana University SouthEast

Bacteria swabbing trend for newborns medically in doubt – Carina Storrs – CNN

Microbes and art

Navel gazing: portraits of the bacteria in our belly buttons – in pictures by Joana Ricou – The Guardian

Science, publishing, and career

Activism: Frustrated postdocs rise up – Paul Smaglik – Nature

Don’t trust an image in a scientific paper? Manipulation detective’s company wants to help – Retraction Watch
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February 23, 2016

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An introduction to 16S rRNA gene sequencing, gut microbiome disruptions in long-term care, microbial responses to oil contamination, colors and k-mers, and how to build your own Winogradsky column.

Jobs and events

PhD position on metagenomics-driven natural product discovery from plant microbiomes – Wageningen University, The Netherlands

Festival of Genomics: Has microbiome session, 27-29 June 2016, Boston

Human skin microbiome

Good introduction for other sample types too! Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research – Jay-Hyun Jo – Journal of Investigative Dermatology

Human gut microbiome

Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention – Alison Laufer Halpin – American Journal of Infection Control

Association of dietary type with fecal microbiota and short chain fatty acids in vegans and omnivores – Alina Reiss – Journal of International Society of Microbiota

Microbiome models

Aging and serum MCP-1 are associated with gut microbiome composition in a murine model – Melissa N. Conley – PeerJ Preprint

Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line – Reed S. Shabman – mSphere

Animal microbiome

Review: Molecular trophic markers in marine food webs and their potential use for coral ecology – Miguel Costa Leal – Marine Genomics

Plant, root, and soil microbiome

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Responses of microbial community from tropical pristine coastal soil to crude oil contamination – Daniel Morais – PeerJ

Zinc treatment increases the titer of ‘Candidatus Liberibacter asiaticus’ in HLB-affected citrus plants while affecting the bacterial microbiomes – Muqing Zhang – Journal of Applied Microbiology

Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment – Ruth D. Lee – Genome Announcements

Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina – Alexandra Alexiev – Genome Announcements

Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues – Sandeep Chakraborty – AMB Express

Water microbiome

Environmental heterogeneity among lakes promotes hyper β-diversity across phytoplankton communities – Selma Maloufi – Freshwater Biology

Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production – A. Belila – Water Research

Bimodal occupancy-frequency distributions uncover the importance of regional dynamics in shaping marine microbial biogeography – Markus V. Lindh – BioRxiv

Microbial Ecology

Eco-evolutionary dynamics in a coevolving host–virus system – Jens Frickel – Ecology Letters

Bioinformatics and metagenomics

Succinct Colored de Bruijn Graphs – Keith Belk – BioRxiv preprint

Metapalette: A k-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation – David Koslicki – ArXiv

Microbes in the news

Grow a bacterial zoo in a bottle: How to build your own Winogradsky column – Steph Yin – Popular Science

Exploring the Humane and Canine Microbiome: Q&A with Dr. Robynne Chutkan – Claudia Kawczynska – The Bark

Ancient bacteria in Utah waters blamed for deaths of pets, people – Todd Tanner – Fox13

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February 17, 2016

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Microbial biomarkers for diabetes, gut sialidases,  pathogens in stranded sea turtles, microbial biodeterioration of an ancient staircase, and how bacterial stay in shape.

Events

‘Microbiome-based Foods for Health and Sustainability’ workshop, 23 February, Brussels – APC Microbiome Institute

Call for Entries! ASM’s 2016 Agar Art Contest. Deadline: May 6.

Human oral microbiome

Intracerebral hemorrhage and deep microbleeds associated with cnm-positive Streptococcus mutans; a hospital cohort study – Shuichi Tonomura – Scientific Reports

Review: Oral Microbiome: Contributions to Local and Systemic Infections – Kerri T. Simpson – Current Oral Health Reports

Human gut microbiome

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes – Moran Yassour – Genome Medicine

Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass – Vania Patrone – Frontiers in Microbiology

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments – Rima M Shobar – Clinical and Translational Gastroenterology

Registered report: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma – John Repass – eLIFE

Review: Sialidases from gut bacteria: a mini-review – Nathalie Juge – Biochemical Society Transactions

Review: Akkermansia muciniphila and its role in regulating host functions – Muriel Derrien – Microbial Pathogenesis

Models of microbiome research

Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice – Jun Li – PNAS

The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility – Cory A Gall – ISME Journal

Have clay will lay: Chicken: Dietary supplementation with the clay mineral palygorskite affects performance and beneficially modulates caecal microbiota in laying pullets – S. Chalvatzi – Journal of Applied Microbiology

Animal microbiome

Bacterial agents in 248 ticks removed from people from 2002 to 2013 – Camille Aubry – Ticks and Tick-borne Diseases

Bacterial and viral pathogens detected in sea turtles stranded along the coast of Tuscany, Italy – G. Fichi – Veterinary Microbiology

Poor English (but US lab): Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria – Zhenyu Shen – Omics’ Journal of Data Mining in Genomics & Proteomics

Editorial: Developmental biology: Females have a lot of guts – Justin Fear – Nature

The sexual identity of adult intestinal stem cells controls organ size and plasticity – Bruno Hudry – Nature

Plant, root, and soil microbiome

Bacterial predator–prey dynamics in microscale patchy landscapes – Felix J. H. Hol – Proceedings of the Royal Society B

Variation in soil microbial communities associated with critically endangered Wollemi pine affects fungal, but not bacterial, assembly within seedling roots – J.L. Rigg – Pedobiologia

The Effects of Nitrogen Fertilizer on Soil Microbial Communities Under Conventional and Conservation Agricultural Managements in a Tropical Clay-Rich Ultisol – Miura, Toshiko – Soil Science

Cover Crop and Irrigation Effects on Soil Microbial Communities and Enzymes in Semiarid Agroecosystems of the Central Great Plains of North America – Francisco J. Calderón – Pedosphere

Effect of soil disinfection with chemical and biological methods on bacterial communities – Md Rokunuzzaman – Egyptian Journal of Basic and Applied Sciences

Water and extremophile microbiome

Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines – Charlotte D. Vavourakis – Frontiers in Microbiology

Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater – Dongqing Zhang – Ecological Engineering

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome – Fabyano Alvares Cardoso Lopes – PLOS ONE

Thesis: Tightly-coupled sulfur-cycling microbial mats of the White Point hydrothermal vent field, CA: An analog for deep-sea vents – Priscilla J Miranda – California State University Long Beach

Thesis: The microbial diversity and function of Arctic supraglacial biomes – Stefanie Lutz – University of Leeds

Built environment microbiome

Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms – Guadalupe Piñar – PLOS ONE

The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens – Jerneja Zupančič – PLOS ONE

Bioinformatics and metagenomics

IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – BioRxiv

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads – Yvan Le Bras – GigaScience

Shannon: An Information-Optimal de NovoRNA-Seq Assembler – Sreeram Kannan – BioRxiv

RECKONER: Read Error Corrector Based on KMC – Maciej Długosz – ArXiv

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Tian-Hao Zhang – BMC Genomics

More microbiology

HT: Liz Costello: Universal resilience patterns in complex networks – Jianxi Gao – Nature

Microbially assisted recording of the Earth’s magnetic field in sediment – Xiangyu Zhao – Nature Communications

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection – Jeroen De Smet – The ISME Journal

Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway – Sung Ryeol Park – Nature Communications

Review: Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments – Desirée C. Yang – Microbiology and Molecular Biology Reviews

Microbes in the news

Oral bacteria linked to risk of stroke – Betty Coffman – University of Louisville

Opportunistic Fungal Pathogens in Dishwashers and Kitchens – Alex Alexiev – MicroBEnet

UVA: Bacteria Overgrowth Could Be Major Cause of Stunting in Children – University of Virginia Health System – NBC29

A new method to dramatically improve the sequencing of metagenomes – EurekAlert

What your gut bacteria can tell you about type 2 diabetes – MedicalXpress

New anti-biofilm compounds show promise against drug-resistant bacteria linked to hospital infections – Ian Demsky – University of Michigan

Crowdfunding project: How Insects and Bacteria Can Solve Murder Mysteries: estimate the time since death (TSD) at a crime scene – Experiment

Crowdfunding project: E pluribus unum: how honey bee bacteria coordinate behaviors – Irene Newton – Experiment

uBiome Named One of World’s Top 10 Most Innovative Companies in Healthcare by Fast Company – PR Web

MIT Spinout Synlogic Grabs $40M To Program Microbes Into Living Drugs – Luke Timmerman – Forbes

Science, publishing, and career

Biologists urged to hug a preprint: ASAPbio meeting discusses the ins and outs of posting work online before peer review – Ewen Callaway – Nature

Accelerating Science with Preprints – Peter Binfield – PeerJ Blog

XY Bias: How Male Biology Students See Their Female Peers. In three large classes, men overrated the abilities of male students above equally talented and outspoken women – Ed Yong – The Atlantic

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February 16, 2016

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Today we’ll go to the extremes: Life in hydrogen sulfide rich environments, subsurface Archaea, subseafloor Fungi, and pit latrines.

Events

NIOO Summer course: identifying terrestrial and freshwater nematodes – June 13-24, Wageningen, The Netherlands

Human respiratory microbiome

Concealed Carry: Hidden Staphylococcus aureus Carriage: Overrated or Underappreciated? – Alex van Belkum – mBio

Human gut microbiome

Review: Imbalance of Gastrointestinal Microbiota in the Pathogenesis of Helicobacter pylori-Associated Diseases – Cong He – Helicobacter

Editorial: We are not alone: Understanding the Contributions of Intestinal Microbial Communities and the Congested Gut in Heart Failure – WH Wilson Tang – JACC Heart Failure

Research Highlight: Microbiota predicts side-effects of immunotherapy – Yvonne Bordon – Nature Reviews Microbiology

Models of microbiome research

Rats: Effects of neutrophils peptide-1 transgenic Chlorella ellipsoidea on the gut microbiota of male Sprague–Dawley rats, as revealed by high-throughput 16S rRNA sequencing – Mingzhang Guo – World Journal of Microbiology and Biotechnology

Fish: Correlation between microbiota and growth in Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Gadus morhua) – Torunn Forberg – Scientific Reports

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Plant, root, and soil microbiome

Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development –
Eline H. Verbon – Trends in Plant Science

Water and extremophile microbiome

Mechanisms underlying adaptation to life in hydrogen sulfide rich environments – Joanna L. Kelley – Molecular Biology and Evolution

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces – William Orsi – PLOS ONE

Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment – Elisa Korenblum – Microbial Biotechnology

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea – Brett J. Baker – Nature Microbiology

Built environment microbiome

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines – Belen Torondel – Microbial Biotechnology

Efficacy of dental unit waterlines disinfectants on a polymicrobial biofilm – Damien Costa – Water Research

Food microbiology

Warning: contains graphic images: Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport – Sarah Temmam – Transboundary and Emerging Diseases

Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization – Miki Okuno – DNA Research

Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres – Elina Jääskeläinen – International Journal of Food Microbiology

More microbiology

My favorite structure: Ribosomal small subunit domains radiate from a central core – Burak Gulen – Scientific Reports

Selection favors incompatible signaling in bacteria – Alfonso Pérez-Escudero – PNAS

Microbes in the news

Bacteria Can Convey Electrical Messages the Same Way Neurons Do – Diana Kwon – Scientific American

40 Trillion Bacteria on and in Us? Fewer Than We Thought – Nicholas Bakalar – New York Times

Scientists discover new microbes that thrive deep in the earth – Phys.org

Europe’s Richest Microbiome Biotech Acquires Irish Start-up To Accelerate – Labiotech

There are always bacteria lurking in dental equipment, suggests research – MedicalXpress

Genes, bugs and radiation: WHO backs new weapons in Zika fight – Ben Hirschler – Reuters

Gene Linked to Patients’ Response to Infectious Diseases – GenEngNews

Science, publishing, and career

Poisoning your lab mates? Simulating Scientific Sabotage, For Fun: With a card game, researchers make light of the “wacky aspects of scientific research.” – Tracy Vence – The Scientist

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February 13, 2016

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Fungal communities of bark beetles, microbiome in rhinosinusitis, deep-sea chemolithoautotrophic communities, talking walls (microbes in houses), and, for Valentine’s Day: cocoa bean fermentation. 

Jobs and events

Postdoc opportunity, University of Notre Dame: 20,000 longitudinal gut microbiome samples from wild baboons

Pregnancy and birth

Review: Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant – Kannikar Vongbhavit – Clinical Therapeutics

Human oral microbiome

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing – Kwan Hee Yun – International Journal of Paediatric Dentistry

Human respiratory microbiome

Composition and dynamics of the respiratory tract microbiome in intubated patients – Brendan J. Kelly – Microbiome Journal

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity – Simon J. S. Cameron- PLOS ONE

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes – Edward John Cleland – American Journal of Rhinology & Allergy

Review: Microbiome of the paranasal sinuses: Update and literature review – Jivianne T. Lee – American Journal of Rhinology & Allergy

Editorial: The microbiome of the sinuses and its relevance in health and disease – Simon A. Carney

Human reproductive tract microbiome

Molecular detection of intrauterine microbial colonization in women with endometriosis – Khaleque N. Khan – European Journal of Obstetrics & Gynecology and Reproductive Biology

Review: The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine – Deepak S. Ipe – Frontiers in Cellular and Infection Microbiology

Review: The Human Microbiome during Bacterial Vaginosis – Andrew B. Onderdonk – Clinical Microbiology Reviews

Human gut microbiome

Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project – Xing Hua – EBioMedicine

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection – Vijay C. Antharam – PLOS ONE

Review: The Role of Probiotics on the Microbiota: Effect on Obesity – Esther Nova – Nutrition in Clinical Practice

Editorial: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Perspective: The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders? – Javier Ochoa-Repáraz – Current Obesity Reports

Review: Butyrate, Neuroepigenetics and the Gut Microbiome: Can a High Fiber Diet Improve Brain Health? – Megan W. Bourassa – Neuroscience Letters

Gut passage

Colonic response to laxative ingestion as assessed by MRI differs in constipated irritable bowel syndrome compared to functional constipation – C. Lam – Neurogastroenterology & Motility

How do primates affect seed germination? A meta-analysis of gut passage effects on neotropical plants – Lisieux F. Fuzessy – Oikos

Models of microbiome research

Drosophila: Effects of co-occurring Wolbachia and Spiroplasma endosymbionts on the Drosophila immune response against insect pathogenic and non-pathogenic bacteria – Upasana Shokal – BMC Microbiology

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Thesis, mice: The effects of nicotine on the gut microbiome and the serum metabolite profile of mice – Ridwan Amin Mahbub – University of Georgia

Contains several cases of image duplication (might be error): Dietary Fiber Intake Regulates Intestinal Microflora and Inhibits Ovalbumin-Induced Allergic Airway Inflammation in a Mouse Model – Zhiyu Zhang – PLOS ONE

Animal microbiome

Metabarcoding of fungal communities associated with bark beetles – Kirsten E. Miller – Ecology and Evolution

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue-green sharpshooter (Graphocephala atropunctata) – E. E. Rogers – Journal of Applied Entomology

A bacterial filter protects and structures the gut microbiome of an insect – Michele Caroline Lanan – The ISME Journal

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression – Shaikhul Islam – Frontiers in Microbiology

Microbial biomass and soil organic carbon accumulation on a former lakebed near Novosibirsk, Russia – Mikhail. V. Yakutin – Journal of Plant Nutrition and Soil Science

A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition – A.B. Siddique – Fungal Ecology

Primer: Networking in the Plant Microbiome – Marcel G. A. van der Heijden – PLOS Biology

Thesis: Next generation sequencing on soil samples from Etosha National Park: Diversity studies of an anthrax reservoir – Valseth, Karoline

Water and extremophile microbiome

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent – Caroline S Fortunato – The ISME Journal

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt – Sean P Jungbluth – The ISME Journal

Context dependency in biodiversity patterns of central German stream metacommunities – Jonathan D. Tonkin – Freshwater Biology

Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys – Heebok Choi – Journal of Microbiology and Biotechnology

Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community – Enrique Zozaya-Valdés – Frontiers in Microbiology

Using in situ bacterial communities to monitor contaminants in river sediments – Yuwei Xie – Environmental Pollution

DGGE: Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities – J. R. Lawrence – Environmental Science and Pollution Research

Built environment microbiome

Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances

Microbial communities affecting albumen photography heritage: a methodological survey – Andrea Puškárová – Scientific Reports

Food microbiology

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing –
Alessandra Dalmasso – LWT-Food Science and Technology

Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses – Tiong Gim Aw – International Journal of Food Microbiology

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment – Monika Dzieciol

Review: The cocoa bean fermentation process: from ecosystem analysis to starter culture development – L. De Vuyst – Journal of Applied Microbiology

Techniques

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis – Ahmad Paintdakhi – Molecular Microbiology

Viruses and phages

Perspective: A Virological Perspective on Cancer – Blossom Damania – PLOS Pathogens

Bioinformatics and metagenomics

Fast search of thousands of short-read sequencing experiments – Brad Solomon – Nature Biotechnology

Open-Source Sequence Clustering Methods Improve the State Of the Art – Evguenia Kopylova

Editorial: Bacterial Speciation: Genetic Sweeps in Bacterial Species -Frederick M. Cohan – Current Biology

Microbes in the news

Walls talk – or at least hold many secrets a wall whisperer can reveal – Jonathan Eisen – MicroBEnet

Country microbes, city microbes—where you live can change how you get sick – Annalee Newitz – Ars Technica

Urbanization Leads to Change in Type of Bacteria in the Home – Lauran Neergaard – ABC News

Fun list: Ranking the Top 10 Best Bacteria on Earth – Ben Guarino – Inverse

Science, publishing and career

The Research Pirates of the Dark Web – Kaveh Waddell  – The Atlantic

Researcher illegally shares millions of science papers free online to spread knowledge – Science Alert

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