Category Archives: Science – Career – Publishing

November 21, 2015

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Human respiratory microbiome

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation – Sang Hu Kim – PLOS Pathogens

Human gut microbiome

Review: Immune Interactions with Pathogenic and Commensal Fungi: A Two-Way Street – David M. Underhill – Immunity

Animal and other models

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes – Tiffany C. Scharschmidt – Immunity

Animal microbiome

Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing – Maren Witzig – PLOS ONE

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama – Cole G. Easson – PeerJ

Water microbiome

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

Built environment microbiology

Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea – C. An – Indoor Air

Characterization of Microbial Communities in Household Washing Machines – Ilka D. Nix – Tenside Surfactants Detergents

Metagenomics and Bioinformatics
DUDE-Seq: Fast Universal Denoising of Nucleotide Sequences – Byunghan Lee – ArXiv

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads – Xiao Zhu – BMC Bioinformatics

Viruses and phages

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing – Donatien F. Chedom – PLOS Computational Biology

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity – Magdalena Calusinska – Environmental Microbiology

Microbes in the news

Entering the Natural Antibiotic Arms Race – Anne Estes – Mostly Microbes

This Synthetic Bio Company Is Hacking Microbes to Build the Smells of the Future – Britt Wray – Motherboard

U of T researchers discover mysterious fungus that defends against neighbouring bacteria – News Medical

The Secret is Out! Review of “The Secret World Inside You” at the American Museum of Natural History in New York. – Anne Estes – Mostly Microbes

Innovative microbiome technology may help fight certain infections – News Medical

Science, publication, and career

America’s science legacy – Neil deGrasse Tyson – Science

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November 18, 2015

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

Animal models

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

Plant, root, and soil microbiome

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

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

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

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

Water / extremophile microbiome

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

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

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

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

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

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

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

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

Waste and built environment microbiology

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

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

Infection microbiology

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

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

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

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

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

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

Bioinformatics and metagenomics

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

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

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

Microbial Ecology

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

Microbes in the news

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

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

Bacteria Hysteria

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

Science, publishing, and career

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

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

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November 16, 2015

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Saturday’s post had a lot  of recent papers, so we’ll keep it short today.

Events

Future podcast: The social life of bacteria: collapse of a culture – January 20, 2016, with E. Peter Greenberg

Extremophile microbiome

Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic lake – Anne D. Jungblut – Applied and Environmental Microbiology

Techniques

Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics – Kwangmin Son – Nature Reviews Microbiology

Microbes in the news

Ignorance about antibiotics propelling global ‘superbug’ crisis – Helen Branswell – STAT

Viruses lurking in lab freezers could trigger next outbreak – Helen Branswell – STAT

The Mysterious Rise of Valley Fever: An outbreak investigation spotlights a common regional illness that’s become more prevalent – US News

Broomfield Enterprise Gardening Nov. 15: Soil is much more than dirt – Ann Montague – Broomfield Enterprise

Insurer for Broad Institute suing MIT over infected mice – Travis Anderson – Boston Globe

Student group successfully pushes Subway to go antibiotic-free – Daily Emerald

Book Review: ‘The Microbiome Solution’ asks, ‘are you too clean?’ – Alysa Selby – Steamboat Today

Science, publishing, and career

Stanford researchers uncover patterns in how scientists lie about their data – Bjorn Carey – Stanford News

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November 13, 2015

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Happy Friday the 13th! Today’s post features a gut-vascular barrier implicated in celiac disease, bison microbiota, 16S rRNA genes in metagenomics data, soil communities at neighboring sites, enriching microbial DNA, and lots of gut microbiota reviews.

Human gut microbiome

(humans and animal models; celiac disease) A gut-vascular barrier controls the systemic dissemination of bacteria – Ilaria Spadoni – Science

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella – Petia Kovatcheva-Datchary – Cell Metabolism

Effect of Antibiotics on Gut Microbiota, Gut Hormones and Glucose Metabolism – Kristian H. Mikkelsen – PLOS ONE

Review: The Enteric Microbiome in Hepatobiliary Health and Disease – James H. Tabibian – Liver International

Review: Microbiota and aging – Stephan C Bischoff – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The impact of gut microbiota on brain and behaviour: implications for psychiatry – Timothy G Dinan – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The gut microbiota keeps enteric glial cells on the move; prospective roles of the gut epithelium and immune system – Panagiotis S. Kabouridis – Gut Microbes

Review: The joint power of sex and stress to modulate brain–gut–microbiota axis and intestinal barrier homeostasis: implications for irritable bowel syndrome – M. Pigrau – Neurogastroenterology & Motility

Review: Microbiome and Health in Past and Present Human Populations – Christina Warinner – American Anthropologist

Animal and bioreactor models

 

Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses – Annah S. Rolig – Cell Host & Microbe

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon – Sophie Fehlbaum – PLOS ONE

Animal microbiome

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison) – Gaddy T. Bergmann – PLOS ONE

Fecal contamination of echinoderms: first report of heavy E. coli loading of sea urchins from a natural growing area – M Bouchoucha – Letters in Applied Microbiology

Plant, root, and soil microbiome

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites – A. L. Gagliano – GeoBiology

Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae – Enrique Lara – Journal of Biogeography

Arsenic uptake, arsenite efflux and plant growth in hyperaccumulator Pteris vittata: Role of arsenic-resistant bacteria – Yong-He Han – Chemosphere

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea – Hanin Alzubaidy – Gene

Review: Current trends in Bt crops and their fate on associated microbial community dynamics: a review – Amit Kishore Singh – Protoplasma

Built environment and waste treatment

Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities – Teofana Chonova – Science of the Total Environment

Bioinformatics and metagenomics

Introducing REAGO: Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Techniques
Enriching microbial DNA: Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA – Angela Glassing – Journal of Microbiological Methods

The Sequence of Sequencers: The History of Sequencing DNA – James M. Heather – Genomics

Microbes in the news

Water Quality in Green Buildings – Katherine Dahlhausen – MicroBEnet

Video: Jonathan Eisen: Microbes in Food and Agriculture: Dr. Jonathan Eisen speaking at UC Davis’s Institute for Food and Ag Literacy round table about the impact the microbiome has made and potential relevance in health, food, and agriculture.

Want a Stronger Defense System against Diseases? Add Some Worms – Sheena Faherty – Scientific American

From garden to gut: New book from UW’s David Montgomery explores an unfolding scientific revolution – Hannah Hickey – University of Washington

Video in Dutch: How many bacteria do you exchange during French Kissing? A demonstration by microbiologist Remco Kort

Bacteria and bacteriophages collude in the formation of clinically frustrating biofilms – Phys.org

Extreme bacteria live in odd corners of the ecosystem – North Country Public Radio

Bacteria Hysteria

Sponsored report: Bacteria, Fecal Matter Found in Rain Puddles on Ground

Science, publishing, and career

In the eye of the Twitterstorm: Social media is shaking up how scientists talk about gender issues – Lauren Morello – Nature
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November 11, 2015

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Red-pigmented haloarchaea in flamingo feathers, cyanobacteria of the Western Himalaya, and read-filtering of HT amplicon reads.

Human respiratory microbiome

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention – Leah Cuthbertson – ISME Journal

Human reproductive tract microbiome

Genital tract colonization with Ureaplasma spp. and its association with abnormal vaginal flora – Ellen Vancutsem – Journal of Medical Microbiology

Impact of Bacterial Vaginosis on Perineal Tears during Delivery: A Prospective Cohort Study – Vincent Letouzey – PLOS ONE

Human gut microbiome

Carriage of enterobacteria producing extended spectrum beta-lactamases and composition of the gut microbiota in an Amerindian community – María José Gosalbes – Antimicrobial Agents and Chemotherapy

Animal microbiome (and archaea)

Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes – Kyung June Yim – Scientific Reports

DGGE: Effect of chemical stress and ultraviolet radiation in the bacterial communities of zebrafish embryos – Jacinta M.M. Oliveira – Environmental Pollution

Plant, root, and soil microbiome

Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya – Kateřina Čapková – Microbial Ecology

Phytostabilization of moderate copper contaminated soils using co-inoculation of Vicia faba with plant growth promoting bacteria – Imen Challougui Fatnassi – Journal of Basic Microbiology

Effects of Common Mycorrhizal Network on Plant Carbohydrates and Soil Properties in Trifoliate Orange–White Clover Association – Ze-Zhi Zhang – PLOS ONE

Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China – Shaorui Wang – Environmental Pollution

Water microbiome

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

Bioinformatics

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences – Vinita Deshpande – Mycologia

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies – Fernando Puente-Sánchez – Nucleic Acids Research

Microbes in the news

One course of antibiotics disrupts gut microbiome for a year – Medical News Today

Science, publishing, and career

Public Data Archiving in Ecology and Evolution: How Well Are We Doing? – Dominique G. Roche – PLOS Biology
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November 10, 2015

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Oral and gut microbiomes respond differently to antibiotics, looking two gifted horses in the mouth, BMIs and Bifidos, Drosophila mating, gut microbes and tumorigenesis, microbial food webs in clay rocks, and don’t forget that Bonferroni correction.

Pregnancy and birth (Probiotics too!)

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit – J. M. Franasiak – Journal of Assisted Reproduction and Genetics

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study – Ulla Uusitalo – JAMA Pediatrics

Human oral microbiome

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces – Egija Zaura – mBio

Crossover clinical trial of different methods of removing a denture adhesive and the influence on the oral microbiota – Élen Massaro Nunes – The Journal of Prosthetic Dentistry

Human gut microbiome

Correlation between body mass index and fecal microbiota from children – A. Ignacio – Clinical Microbiology and Infection

Review: Clostridium difficile infection and intestinal microbiota interactions – C. Rodriguez – Microbial Pathogenesis

Animal and bioreactor models

A Statistical Error in: “Analysis of Caecal Microbiota in Rats Fed with Genetically Modified Rice by Real-Time Quantitative PCR” – Alexander Panchin – Journal of Food Science

In mice: Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis -Joseph P. Zackular – mSphere

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster – Devin Arbuthnott – Journal of Evolutionary Biology

Chemostat culture systems support diverse bacteriophage communities from human feces – Tasha M. Santiago-Rodriguez – Microbiome

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans – Nicholas A. Pudlo – mBio

Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass – Sharon A. Huws – FEMS Microbiology Ecology

Animal microbiome

In-depth snapshot of the equine subgingival microbiome – Wenling Gao – Microbial Pathogenesis

Occurrence and distribution of Malassezia species on skin and external ear canal of horses – Hojjatollah Shokr – Mycoses

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning – Microbiome

Plant, root, and soil microbiome

The effect of altitudinal gradient on soil microbial community activity and structure in moso bamboo plantations – Ed-Haun Chang – Applied Soil Ecology

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

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea – A Metagenomic Approach – Marta Filipa Simões – Genomics, Proteomics & Bioinformatics

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches – Pranitha S. Pandit – Environmental Microbiology

Effects of Sulfamethazine and Zinc on the Functional Diversity of Microbial Communities during Composting – Manli Duan – Environmental Microbiology

Evidence for duplication in title words: Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks – Michael Schloter – Frontiers in Microbiology

A minimalistic microbial food web in an excavated deep subsurface clay rock -Alexandre Bagnoud – FEMS Microbial Ecology

Water microbiome

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms – Sara Kleindienst – PNAS

Extremophile microbiome

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter – Evgeniya Matyugina – Chinese Journal of Oceanology and Limnology

Built environment microbiome

Differences in intertidal microbial assemblages on urban structures and natural rocky reef – Elisa L. Tan – Frontiers in Microbiology

Waste microbiology

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments – Lilian M. Guibert – Environmental Microbiology

Cultivating Microbial Dark Matter in Benzene-Degrading Methanogenic Consortia –
Fei Luo – Environmental Microbiology

Metagenomics and bioinformatics

DESM: portal for microbial knowledge exploration systems – Adil Salhi – Nucleic Acids Research

Techniques

Coupling dye-integrated polymeric membranes with smartphone detection to classify bacteria – Lígia Bueno – RSC Advances

Microbes in the news

9 Fascinating Facts About The Microbiome, The Trillions Of Microbes Hidden Inside Us — Jessica Leber – Fast Co.Exist

NTU scientists use dead bacteria to kill colorectal cancer – EurekAlert

Science, publishing, and career

(A)Historical Science: why scientists should care more about the history of science – Arturo Casadevall and Ferric C. Fang – Infection and Immunity

November 4, 2015

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Lots of upcoming workshops and seminars, genome-wide association of the human gut microbiota, contamination of cord blood units, and bacteria with the rRNA genes on a plasmid, not on their chromosome.

Events

Webinar: The ageing microbiota by Gemma Walton and Annie-Rose Harrison-Dunn – November 17, 2015 – 10AM Paris

Mothur 3-day workshop organized by Pat Schloss – December 16-18, Detroit.

2nd Microbiome R&D and Business Collaboration Congress: Asia – February 29-March 1 2016, Kuala Lumpur, Malaysia

Early career workshop on Microbiology of the built environment (Chicago, IL) – Jack Gilbert lab – April 26-29 2016

Human oral microbiome

Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes – Meng Zhang – PLOS ONE

Human gut microbiome

In Hutterites: Genome-Wide Association Studies of the Human Gut Microbiota – Emily R. Davenport – PLOS ONE

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

Infection microbiology

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling – Luís França – PLOS ONE

More microbes

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome – Mizue Anda – PNAS

High-throughput 3D tracking of bacteria on a standard phase contrast microscope –
K.M. Taute – Nature Communications

Automated image analysis for quantification of filamentous bacteria – Marlene Fredborg – BMC Microbiology

Microbial ecology

Community rescue in experimental metacommunities – Etienne Low-Décarie – PNAS

Microbes in the news

Family dog lowers kids’ asthma risk, proving dirt and bacteria are good for children – Shelley Hazen – Inquisitr

Microbiome expert Martin Blaser to receive Georgetown’s Cura Personalis Award Nov. 3 – EurekAlert

Microbiomes could prove essential in various fields of science, study suggests – Kimberly Nielsen – The Daily Californian

Salivary microbiome of whitetail deer: Mature doe set the rut timetable – Oak Duke – Wellsville Daily Reporter

Finally! New germ exhibit opening at the American Museum of Natural History – Rebecca Rosenthal – North Jersey

Thank heavens, someone figured out which bacteria live on a donkey’s penis – Discover
http://blogs.discovermagazine.com/seriouslyscience/2015/11/03/thank-heavens-

How was the bacteria at York Hospital found?– Dylan Segelbaum – York Daily Record

Worms (and germs) may be the answer to preventing allergies – Jason Tetro – Popular Science

Two Million-Year-Old Bacteria Used Iron “Sunscreen” – Charlotte Ward – RedBrick

Bacteria infecting orange groves is driving up cost of juice; threatens nation’s supply – Sandy Miller – Fox2Now

Science, publishing, and career

EU urges science publishers to adapt to open access: European research commissioner Carlos Moedas has urged journal publishing companies to reshape their business models to an open access system. – LabNews

Supervision: Clear direction: Managing laboratory members as well as a research strategy can be difficult for early-career principal investigators, but help is at hand. – Boer Deng – Nature

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November 3, 2015

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Dog exposure and childhood asthma, earthworm poop, thermally stressed corals, and cryospheric ecosystems.

General microbiome

From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology – Pierre-Edouard Fournier – Anaerobe

Study from Sweden with patients and dogs registries: Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma – Tove Fall – JAMA Pediatrics

Human gut microbiome

Plagiarism in intro and only CFU data for E. coli and lactic acid bacteria: A Comparative Study of Gut Microbiota Profiles of Children Living in Kulon Progo and West Lombok – Siti Helmyati – Pakistan Journal of Nutrition

Microbial Signatures in Post-Infectious Irritable Bowel Syndrome – Towards Patient Stratification for Improved Diagnostics and Treatment – Jonna Jalanka – Gut Microbes

Review: Genetic Variations in Vitamin D Metabolism Genes and the Microbiome, in the Presence of Adverse Environmental Changes, Increase Immune Dysregulation – Laing BB
and Ferguson LR – Austin Journal of Nutrition & Metabolism

Animal models

In mice: Gut microbe-derived extracellular vesicles induce insulin resistance, thereby impairing glucose metabolism in skeletal muscle – Youngwoo Choi – Scientific Reports

In mice: Influence of whole-wheat consumption on fecal microbial ecology of obese diabetic mice – Jose F Garcia-Mazcorro – PeerJ Preprints

Earthworms: Characterization of the bacterial communities of casts from Eisenia andrei fed with different substrates – Manuel Aira – Applied Soil Ecology

Animals

Viral and Bacterial Epibionts in Thermally-Stressed Corals – Hanh Nguyen-Kim – J Mar Sci Eng

Plant, root, and soil microbiome

Cross-biome comparison of microbial association networks – Karoline Faust – Frontiers in Microbiology

Response of microbial communities from an apple orchard and grassland soils to the first-time application of the fungicide tetraconazole – Sławomir Sułowicz – Ecotoxicology and Environmental Safety

A Chemical Perspective on Microalgal–Microbial Interactions – Erik F.Y. Hom – Trends in Plant Science

Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency – Laura Giagnoni – Applied Soil Ecology

Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change – Ellen L. Fry – Soil Biology and Biochemistry

Copper and temperature modify microbial communities, ammonium and sulfate release in soil – Rui Ferreira – Journal of Plant Nutrition and Soil Science

Review: Mitigating climate change through managing constructed-microbial communities in agriculture – Cyd E. Hamilton – Agriculture, Ecosystems & Environment

Extremophile microbiome

Editorial: Cryospheric ecosystems: a synthesis of snowpack and glacial research – Andy Hodson – Environmental Research Letters

Bioinformatics and metagenomics

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities – Anja Lange – PLOS ONE

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes – Mingjie Wang – Genome Biology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets – Yu-Wei Wu – Bioinformatics

Techniques

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms – Jeongan Choi – Scientific Reports

Microbes in the news

Microbesity: Obesity appears linked to the gut microbiome. How and why is still a mystery—but scientists have plenty of ideas – Jenny Rood – The Scientist

Science, publishing, and career

“There’s No Crying in Academia,” Acknowledging Emotional Labour in the Academy  – Margeaux Feldman – Gender and Society

2015 Life Sciences Salary Survey – Karen Zusi and Amanda B. Keener – The Scientist
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October 23, 2015

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Nasopharyngeal microbiota in infants with CF, antibiotic use makes kids heavier, H7N9 virus infection effects on microbiome, microbial sequence capture in soil, and the microbiology of plumbing. Happy Friday!

Human respiratory microbiome

Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis – Sabine M.P.J. Prevaes – American Journal of Respiratory and Critical Care Medicine

Familial and Microbiological Contribution to the Otitis-Prone Condition – Matthew C. Morris – International Journal of Pediatric Otorhinolaryngology

Human gut microbiome

Antibiotic use and childhood body mass index trajectory – B S Schwartz – International Journal of Obesity

Influence of H7N9 virus infection and associated treatment on human gut microbiota – Nan Qin – Scientific Reports

Plant, root, and soil microbiome

Captured metagenomics: large-scale targeting of genes based on ‘sequence capture’ reveals functional diversity in soils – Lokeshwaran Manoharan – DNA Research

Soil fungi for mycoremediation of arsenic pollution in agriculture soils – M. Singh – Journal of Applied Microbiology

Phylogenetic structure of soil bacterial communities predicts ecosystem functioning – Eduardo Pérez-Valera – FEMS Microbiology Ecology

Food microbiology

DGGE: The Occurrence of Beer Spoilage Lactic Acid Bacteria in Craft Beer Production – Cristiana Garofalo – Journal of Food Science

Built Environment microbiology

Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome – Pan Ji – PLOS ONE

Whole-building decontamination of Bacillus anthracis Sterne spores by methyl bromide fumigation – S. Serre – Journal of Applied Microbiology

Microbes in the news

The Microbial Neighbors in Your Tap Water Episode 1: Say Hello to the Building Plumbing Microbiome – Pan Ji – MicroBEnet

Star biologist pinpoints role of microbes in disease: Interview with Rob Knight -Gary Robbins – San Diego Union Tribune

Microbiome Signature Can Predict Risk of C. difficile Treatment Failure. Interview with
Dr. Sahil Khanna – Medical Research

Too Many Antibiotics May Make Children Heavier – Alice Park – Time

Nano Power Grids Discovered Between Bacteria – Controlled Environments

The secret behind kimchi’s sour taste: Kimchi doesn’t just contain bacteria, but viruses as well – Veronique Greenwood – BBC

Ancient Safety Valve Linking Pollen To Bacteria Discovered – Science2.0

Scientists say deep-sea bacteria could neutralize CO2 – Brooks Hays – UPI

Science, publishing, and career

The power of mentoring – Carol Lynn Curchoe – Science

The Odds That a Panel Would ‘Randomly’ Be All Men Are Astronomical – Lauren Bacon – The Atlantic

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October 22, 2015

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Digesting from LAX: Risk of childhood asthma, antibiotic effects on fish microbiome, and interactions between the gut microbiome and Clostridium difficile.

Pregnancy and birth

Claims that placenta has a rich microbiome, which I disagree with. The maternal microbiome and pregnancy outcomes – Chelsea Fox – Fertility and Sterility

Human gut microbiome

Altered fecal short chain fatty acid composition in children with a history of Hirschsprung-associated enterocolitis – Farokh R. Demehri – Journal of Pediatric Surgery

Gut microbiota and the risk of childhood asthma – Priya Venkatesan – The Lancet Respiratory Medicine

Can Helminth Infection Reverse Microbial Dysbiosis? – P’ng Loke – Trends in Parasitology

Can a Bug in the Gut Act Like a Drug in the Brain? – Robert H. Howland – Journal of Psychosocial Nursing

Review: Interactions Between the Gastrointestinal Microbiome and Clostridium difficile – Casey M. Theriot – Annual Review of Microbiology

Animal models

Risperidone-induced weight gain is mediated through shifts in the gut microbiome and suppression of energy expenditure – Sarah M. Bahr – EBioMedicine

Fish: The host effects of Gambusia affinis with an antibiotic-disrupted microbiome – Jeanette M. Carlson – Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology

Host and microbiota interactions are critical for development of murine Crohn’s-like ileitis – M Roulis – Mucosal Immunology

Plant, root, and soil biology

Drought-induced piñon mortality alters the seasonal dynamics of microbial activity in piñon–juniper woodland – Daniel D. Warnock – Soil Biology and Biochemistry

Long-term oil contamination increases deterministic assembly processes in soil microbes – Yuting Liang – Ecological Applications

Water microbiome

A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor Igneous Crust – Magnus Ivarsson – PLOS ONE

Food microbiology

Review: Microbial terroir and food innovation: the case of yeast biodiversity in wine – Vittorio Capozzi – Microbiological Research

Review: Microbiome profiling in fresh-cut products – Chiara Gorni – Trends in Food Science & Technology

Infection

Why Do We Feel Sick When Infected—Can Altruism Play a Role? – Keren Shakhar, Guy Shakhar – PLOS Biology

Microbes in the news

Gut researcher issues warning on DIY poo transplants: Q&A with Dr Paul Bertrand on the pros and cons of poo transplants to treat bacterial infections – Jess Davis
– SBS

Surprising source for ancient life biomarker found: It was thought that tetrahymanol was produced primarily by eukaryotes, but a new study suggests many bacteria might also produce the lipid – Stanford

Science, publishing, and career

Why biomedical superstars are signing on with Google. Tech firm’s ambitious goals and abundant resources attract life scientists – Erika Check Hayden – Nature

The Rise of “Quit Lit”: Soon-to-be former academics are taking their grievances public – Colleen Flaherty – Slate
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