Category Archives: Animal microbiome

April 3, 2015

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Check out today’s #PLOSBuzzFeed on Twitter for some Friday fun.

Human general microbiome

Only 10 microbes are designated by the International Agency for Cancer Research (IACR) as carcinogenic to humans (Review): Cancer and the microbiota – Wendy S. Garrett – Science

Microbiome of pregnancy and birth

Administration of a multistrain probiotic product (VSL#3) to women in the perinatal period differentially affects breast milk beneficial microbiota in relation to mode of delivery – Paola Mastromarino – Pharmacological Research

Conference abstract: Preterm Infant Gut Microbiome and Weight at 36 Weeks Corrected Gestational Age – Diana Taft – The FASEB Journal

Still in press: Should Infants Cry Over Spilled Milk? Fecal Glycomics as an Indicator of a Healthy Infant Gut Microbiome – Steven A Frese – Journal of Pediatric Gastroenterology & Nutrition

Human respiratory microbiome

Conference abstract: Correlative Changes in Macrophage Polarization and Pulmonary Microbiota in Lung Transplant Recipients – E. Bernasconi – The Journal of Heart and Lung Transplantation

Harder to breathe (Review): The changing face of asthma and its relation with microbes – Chris S. Earl – Trends in Microbiology

Human gut microbiome / functional foods

Metabolic and physiologic effects from consuming a hunter-gatherer (Paleolithic)-type diet in type 2 diabetes – U Masharani – European Journal of Clinical Nutrition

Findings from a Randomized Controlled Trial of Fecal Transplantation for Patients with Ulcerative Colitis – Noortje G. Rossen – Gastroenterology

Correlation between gut microbiota composition and parasitic infection of pre-adolescence in Malaysia – Chun-Wie Chong – Journal of Microbiology, Immunology and Infection

Fit to the bone (review): The intestinal microbiome and skeletal fitness: connecting bugs and bones – Julia F. Charles – Clinical Immunology

Poster abstract: Effect of Prebiotic Fiber Intake on Adiposity and Inflammation in Overweight and Obese Children: Assessing the Role of the Gut Microbiota – Alissa C. Nicolucci – Canadian Journal of Diabetes

Animal models of microbiome

Poster abstract: Parallel Improvement in Body Weight, Glycemia, and Intestinal Permeability but not Body Fat with Prebiotic- and Antibiotic-Induced Gut Microbiota Modification – Marc Bomhof – Canadian Journal of Diabetes

Animal microbiome

Drosophila: The Impact of Host Diet on Wolbachia Titer in Drosophila – Laura R. Serbus – PLOS Pathogens

Soil and compost microbiome

Soil plots in Burgundy (but no vineyards!): Mapping and determinism of soil microbial community distribution across an agricultural landscape – Florentin Constancias – MicrobiologyOpen

Molecular profile of microbiota of Finnish commercial compost suppressive against Pythium disease on cucumber plants – D. Yu – Applied Soil Ecology

Wildfire effects on the properties and microbial community structure of organic horizon soils in the New Jersey Pinelands – Robyn A. Mikita-Barbato – Soil Biology and Biochemistry

Extremophile microbiome (see also “Microbes in the news” below)

Microbial dwarves in the mines: Use of Phosphate Solubilizing Bacteria to Leach Rare Earth Elements from Monazite-Bearing Ore – Doyun Shin – Minerals

Food microbiology

This study smells: Microbiological spoilage and volatiles production of gutted European sea bass stored under air and commercial modified atmosphere package at 2oC – Foteini F. Parlapani – Food Microbiology

Viable cells differentiation improves microbial dynamics study of fermented milks – Davide Porcellato – International Dairy Journal

Wine electrophoresis? Inactivation of wine associated microbiota by continuous pulsed electric field treatments – Lucía González-Arenzana – Innovative Food Science & Emerging Technologies

Bioreactor microbiome

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters – Wanfeng Wang – Science of the Total Environment

Bioinformatics

PhyloRelief: Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting – Davide Albanese – PLOS Computational Biology

One of the figures has the Giant Microbes in it! Personalized microbial network inference via co-regularized spectral clustering – Sultan Imangaliyev – Methods

Microbes in the news

“Life at the Limits” shows extremophiles aren’t just bacteria – AMNH exhibit includes live axolotls, nautiluses, and mantis shrimp – John Timmer – Ars Technica

uBiome’s Dental Campaign to Give Portion of Proceeds to Charitable Dental Organization
Partnering with Oral Health America’s Smiles Across America – PR Web

No Bonferroni correction but: Is The Microbiome Correlated with Income? The Answer Will Surprise You – Alexandra Carmichael – uBiome

Cross-posting this week’s contribution for MicroBE.net: Gently down the stream: the microbiome along a river’s course – Elisabeth Bik – MicroBE.net

Cleaning with Bleach May Lead to Childhood Infections – Laura Geggel – Live Science

How the guts of poultry affect performance – Jake Davies – FWI

Cigarette Smoke Makes Superbugs More Aggressive – Heather Buschman – UC San Diego

The Plague Bacteria Found in Flea Samples Near Flagstaff – NAZ Today

Travelers Bringing Drug-Resistant Bacteria to U.S.: Strain of Shigella is easily transmitted and causes tough-to-treat diarrhea, CDC says – WebMD

France bans imports of Puglia vegetables as olive bacteria starts mini trade war – Nicole Winfield – US News

Science, publishing, and career

Hoax-detecting software spots fake papers – John Bohannon – Science

A career is like a love affair – Madeleine Jacobs – Science

Ten Simple Rules to Win a Nobel Prize – Richard J. Roberts – PLOS Computational Biology

Science and art

This is gorgeous: A Sprawling New Cut Paper Bacterium by Rogan Brownby – Christopher Jobson – Colossal

Bik’s Picks

All animal phyla in 35 photos – Melissa Hogenboom – BBC

Shelled Out: 5 Egg-Citing Facts – Laura Geggel – Live Science

My Real-Time Response To Learning What The Rock Eats Every Day – Mallory Ortberg

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April 2, 2015

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Animal models of microbiome research

Dietary fat intake and age influence gut microbiota and colonic inflammation in C57BL/6J mice – Su Jeong Kim – The FASEB Journal

Maternal obesity alters gut microbial ecology in offspring of NOD mice – Meijun Zhu – The FASEB Journal

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Animal microbiome

Cheetah (not microbiome but could not resist): Dietary Factors Associated with Faecal Consistency and Other Indicators of Gastrointestinal Health in the Captive Cheetah (Acinonyx jubatus) – Katherine M. Whitehouse-Tedd – PLOS ONE

Ants: Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini – Laura E. Williams, Jennifer J. Wernegreen – PeerJ

Sponges: Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea – Valliappan Karuppiah – Applied Microbiology and Biotechnology

Editorial: Sponge symbionts and the marine P cycle – Albert S Colman – PNAS USA

Soil and plant root communities

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert – Klára Řeháková – Frontiers in Microbiology

Soil microbial functional diversity and biomass as affected by different thinning intensities in a Chinese fir plantation – Xin-Li Chen – Applied Soil Ecology

Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients – Ramesh R. Pokharel, Rick Zimmerman – Organic Agriculture

Impact of preferential methane flow through soil on microbial community composition
Julia Gebert, Mirjam Perner – European Journal of Soil Biology

Characterization of bacterial strains and their impact on plant growth promotion and yield of wheat and microbial populations of soil – Ashok Kumar – African Journal of Agricultural

Metabolomics

Gut Commensal Immunomodulatory Factors: Identification and Structure-Function Studies – Sungwhan Oh – The FASEB Journal

Review: Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems – Stephen A Jackson – Current Opinion in Biotechnology

Techniques

Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents – E. Tournier

Other articles of interest

Dengue: Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference – Sam H. Shen – PNAS USA

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes – David Roy Smith and Patrick J. Keeling – PNAS USA

Bioinformatics

A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments – Nicholas A. Bokulich – PeerJ Preprint

Microbes in the news

I enjoyed reading this: Microbiome Blues in E – Michael Tanner – Clinical Correlations
“You haven’t been squeaky clean since you were bunking with a placenta. “

Drinking water microbiology — from measurement to management – David Coil – MicroBEnet

Movie Night at Bozeman Public Library, April 7th: Bugs with Benefits, an Intro to the Human Microbiome – Bozeman Daily

Do Antibiotics Raise Diabetes Risk via Gut Microbiota? – Liam Davenport – Medscape

About Genome Biology study: Longer DNA fragments reveal rare species diversity – Phys.org

Editorial about mBio study: Soil source for vine bacteria – Nature

Treating the Root Cause of IBS: Small Intestine Bacterial Overgrowth – Maura Henninger – Huffington Post

Origin Sciences Ltd: Newly-Published Data Shows the Effectiveness of OriCol™ for Sampling the Gut Microbiome – BusinessWire

Smart phone diagnosis? Biosensing platform quickly and accurately diagnoses disease and monitors treatment remotely – Science Daily

Science, publishing, and career

Peer review with Elizabeth Marincola (CEO of PLOS) – Royal Society

Fighting Plagiarism In Scientific Papers – Tommaso Dorigo – Science 2.0

Editor’s point of view: Science’s Big Scandal: Even legitimate publishers are faking peer review – Charles Seife – Slate

Stanford Graduate student charged with poisoning labmates’ drinks – Kylie Jue – Stanford Daily

Four simple tools to promote gender balance at conferences – Julie Pfeiffer – The Tree of Life

Bik’s Picks

The human sex ratio from conception to birth – Steven Hecht Orzack – PNAS USA

Failed synchronization of the womb’s clock with mother’s body clock critical in miscarriages – Science Daily

Watch the century’s fastest lunar eclipse Saturday – CBS News

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April 1, 2015

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April 1st science

Want to live chemical free? Try Doctor Bacfarc’s Dark Matter Diet™! – Galileo’s Pendulum

Zoology: Here be dragons – Andrew J Hamilton – Nature

CERN researchers confirm existence of the Force, with scientist Ben Kenobi – Cian O’Luanaigh – CERN

Against April Fools’ in Science Journalism – Lee Billings – Scientific American

Human oral microbiome

Comparison of Oral Microbial Profiles between Children with Severe Early Childhood Caries and Caries-Free Children Using the Human Oral Microbe Identification Microarray – Chen Ma – PLOS ONE

Like pulling teeth: Microbiota at teeth and implants in partially edentulous patients. A 10-year retrospective study – Sigrun Eick – Clinical Oral Implants Research

Human respiratory microbiome

The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation – Lisa A Carmody – Microbiome

Human gut microbiome

Fate, activity, and impact of ingested bacteria within the human gut microbiota – Muriel Derrien, Johan E.T. van Hylckama Vlieg – Trends in Microbiology

Gut Microbiota and Tacrolimus Dosing in Kidney Transplantation – John R. Lee – PLOS ONE

Gut microbiota: Optimal sampling of the intestinal microbiota for research – R. Balfour Sartor – Nature Reviews Gastroenterology & Hepatology

Review: Towards a more comprehensive concept for prebiotics – Laure B. Bindels – Nature Reviews Gastroenterology & Hepatology

Pregnancy and birth microbiome

Antibiotic Exposure in Infancy and Risk of Being Overweight in the First 24 Months of Life – Antti Saari – Pediatrics

Animal microbiome

Bats: External Microbiota of Western United States Bats: Does It Matter Where You Are From? – Ara Kooser – BioRxiv

Aphids: Infection Dynamic of Symbiotic Bacteria in the Pea Aphid Acyrthosiphon pisum Gut and Host Immune Response at the Early Steps in the Infection Process – François Renoz – PLOS ONE

Plant microbiome

Presentation: Mining the Agave Microbiome for Adaptations to Arid Environments – Devin Coleman-Derr – JGI

Soil and plant root microbiome

Baseline Survey of Root-Associated Microbes of Taxus chinensis (Pilger) Rehd – Qian Zhang – PLOS ONE

Extremophile microbiome

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics – Gabriel G. Perron – PLOS ONE

Built environment microbiome

Influence of a Non-Hospital Medical Care Facility on Antimicrobial Resistance in Wastewater – Mathias Bäumlisberger – PLOS ONE

Metagenomics

Staph in staff: Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission – Gavin K. Paterson

Metabolomics

Marine sequestration of carbon in bacterial metabolites – Oliver J. Lechtenfeld – Nature Communications

Ecology

Not microbial, but of interest: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity – Francesco Carrara – Methods in Ecology and Evolution

Techniques

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform – Melanie Schirmer – Nucleic Acids Research

Microbes in the news

Apparently, this is not a joke: #Kryptonia: Hiding in Plain Sight: Researchers using metagenomics and single-cell sequencing identify a potential new bacterial phylum – Kim Smuga-Otto – The Scientist

Can ‘ghosts’ cause bad air? Poor indoor air quality and ‘sightings’ – Science Daily

Cool Jobs: The Cave Microbiologist – Scientiflix

Bacteria are plural, Smithsonian. Found: The Bacteria That’s Making You Stink – Erin Blakemore – Smithsonian

Duke-UNC Collaboration Creating ‘Gut-on-a-Chip’ – Marla Vacek Broadfoot – Duke Translational Medicine Institute

Researchers Discover New Source Of Airborne Antibiotic-Resistant Bacteria – Erin Schumaker – Huffington Post

Research proves that intestinal bacteria can be used to classify the effects of different diseases – Medical Xpress

Vanillin: Are Microbes the Taste-Makers of the Future? – Jeffrey Marlow – Wired.com

Your Microbiome “Tree” – Spectrum MIT
Microbiome Research: A New Frontier in Medicine – Elizabeth Dougherty – Spectrum MIT

Manipulative Microbiomes – Gut bacteria control tumor growth via the mammalian immune system – Jenny Rood – The Scientist

This might be April 1st joke, but realistic results: Scientists reveal the thousands of bacteria colonies growing on dirty coins and notes – Sarah Griffiths – Daily Mail

New ‘Intraterrestrial’ Virus Found in Ocean Depths – Patrick J Kiger – Discovery

Best date ever: Date syrup shows promise for fighting bacterial infections – Science Daily

Science, publishing, career

How Articles Get Noticed and Advance the Scientific Conversation – Victoria Costello – PLOS Blogs

A Biotic Game Design Project for Integrated Life Science and Engineering Education –
Nate J. Cira – PLOS Biology

Bik’s Picks

Getting away with murder: Global analysis of fungal morphology exposes mechanisms of host cell escape – Teresa R. O’Meara – Nature Communications

Monarch Larva Monitoring Project Helps Citizen Scientists Build Connections to Nature – Eva Lewandowski – PLOS Blogs

Rats see the pain in other rats’ faces – Virginia Morell – Science Mag

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March 31, 2015

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For today’s digest, I screened over 500 papers, and thousands of Tweets for you. Here is my selection:

Pregnancy and birth microbiome

PhD thesis [PDF]: Dynamics of co-existing Escherichia coli lineages in situ of the infant gut – Heidi Kira Gumpert – Technical University of Denmark

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis – Anne G Hoen – The Journal of Pediatrics

Review: Probiotics for Preterm Infants: A Premature or Overdue Necrotizing Enterocolitis Prevention Strategy? – Sharon Anderson – Neonatal Network

Review: Preterm infant nutrition, gut bacteria, and necrotizing enterocolitis – Josef Neu –  Current Opinion in Clinical Nutrition & Metabolic Care

Human oral microbiome

Periodontal Therapy Effects on Nitrite Related to Oral Bacteria: A 6-Month Randomized Clinical Trial – Sheila C Cortelli – Journal of Periodontology

Perspective: Mouthguards: Does the indigenous microbiome play a role in maintaining oral health? – Purnima S. Kumar and Matthew R. Mason – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Nasal Inoculation of the Commensal Neisseria lactamica Inhibits Carriage of Neisseria meningitidis by Young Adults: A Controlled Human Infection Study – Alice M. Deasy – Clinical Infectious Diseases

Human skin microbiome

Molecular cartography of the human skin surface in 3D – Amina Bouslimani – PNAS USA

Human gut microbiome

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection – Alexa Weingarden – Microbiome Journal

Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization – Zhang Lihua – Anaerobe

Review: The microbiota in inflammatory bowel disease – Donal Sheehan – Journal of Gastroenterology

Review: Promoting Health and Longevity through Diet: From Model Organisms to Humans – Luigi Fontana, Linda Partridge – Cell

Review: TLR4 at the crossroads of nutrients, gut microbiota and metabolic inflammation
Licio A. Velloso – Endocrine Reviews

Review: Cultivating Healthy Growth and Nutrition through the Gut Microbiota – Sathish Subramanian – Cell

Review: The human gut microbiome, a taxonomic conundrum – Senthil Alias Sankar – Systematic and Applied Microbiology

Review: The Role of Infectious Mediators and Gut Microbiome in the Pathogenesis of Celiac Disease – Mohammad Rostami-Nejad – Archives of Iranian Medicine

Review: Exercise and the microbiota – Orla O’Sullivan – Gut Microbes

Animal models of microbiome research

Abnormal Pregnancy Outcomes in Mice Using an Induced Periodontitis Model and the Haematogenous Migration of Fusobacterium nucleatum Sub-Species to the Murine Placenta – Sara Stockham – PLOS ONE

Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism – Silvia Falcinelli – Scientific Reports

Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats – Nina L. Cluny – Obesity

Animal microbiome

Editorial to Baboon microbiome paper: Metagenomics: Social behavior and the microbiome – Jack A Gilbert – eLIFE

More baboons: Development, diet, and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons – Tiantian Ren – Environmental Microbiology

Spider monkey: Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks – Vanessa L. Hale – Journal of Microbiological Methods

Cats: Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease – L. Pérez-Salcedo – Journal of Small Animal Practice

Desert wool rat: Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida) – Journal of Mammalogy

Tortoise: Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise – Michael L. Yuan – Molecular Ecology

Trout: Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes
Miray Etyemez, José Luis Balcázar – Research in Veterinary Science

Fruit fly: Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis – Awawing A. Andongma – Scientific Reports

Aphids: Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA – Jean-Pierre Gauthier – PLOS ONE

Plant microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Soil and plant root microbiome

A novel pathway producing ​dimethylsulphide in bacteria is widespread in soil environments – O. Carrión – Nature Communications

Metabolic characteristics of microbial communities of Aeolian sandy soils induced by saline water drip irrigation in shelter forests – Z. Jin – European Journal of Soil Science

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization – Jie Zhao – European Journal of Soil Biology

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus – Jean H. Burns – AoB Plants

Long-term oil contamination causes similar changes in microbial communities of two distinct soils – Jingqiu Liao – Frontiers in Environmental Science

Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments – Sadikshya R. Dangi – Applied and Environmental Soil Science

Water microbiome

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification – C. Harwood Theisen – Geobiology

The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth – Stephen M. Techtmann – PLOS ONE

Planktonic eukaryote molecular diversity: discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina) – Enrique Lara – J. Plankton Research

Extremophile microbiome

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate – B. F. N. Beall – Environmental Microbiology

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep – Stephanie D. Mendes – Journal of Geophysical Research: Oceans

Built environment microbiome

Are microbial communities in green roof substrates comparable to those in post-industrial sites?—a preliminary study – Chloe J. Molineux – Urban Ecosystems

Food microbiology

Some journals just have great titles: Microbial community changes in Makgeolli during brewing – Changhoon Chai – Journal of the Institute of Brewing

Review: Fermented Foods as Experimentally Tractable Microbial Ecosystems – Benjamin E. Wolfe, Rachel J. Dutton – Cell

Metagenomics and bioinformatics

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains
Marie Trussart – Nucleic Acids Research

CRISPR Detection from Short Reads Using Partial Overlap Graphs – Ilan Ben-Bassat, Benny Chor – Research in Computational Molecular Biology

CLARK: fast and accurate classification of metagenomic and genomic sequences using
discriminative k-mers – Rachid Ounit – BMC Genomics

FlowClus: efficiently filtering and denoising pyrosequenced amplicons – John M Gaspar and W Kelley Thomas – BMC Bioinformatics

Review: 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions – Feng Ju, Dr. Tong Zhang – Applied Microbiology and Biotechnology

Book Chapter: Single-Cell Sequencing of Microorganisms – Ying Chen – Single Cell Sequencing and Systems Immunology

Metabolomics

Review: Rumen Nutrition Symposium How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J. L. Firkins and Z. Yu – Journal of Animal Science

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

Body Maps Expose the Chemical Residue That Coats Our Skin – Marcus Woo – Wired.com
Crazy maps reveal colonies of bacteria and chemicals all over the human body – Kevin Loria – Business Insider
3D Human Skin Maps Aid Study of Relationships Between Molecules, Microbes and Environment – Heather Buschman – UC San Diego

Advancing the understanding of the dental microbiome – Maria Perno Goldie – Dentistry IQ

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria – Daniella Lowenberg – PLOS blogs

Antibiotic-resistant bacteria are not match for medieval potion – Alexandra Ossola – Popular Science

Antibiotic-Resistant Bacteria From Texan Cattle Yards Are Now Airborne, Study Finds
Kevin McSpadden – Time

Growing a Baby Microbiome – Kevin Bonham – Scientific American

Poop Transplants Can Treat Severe Infection In Patients – FPJ Bureau – The Free Press Journal

Poo transplants could save thousands – Geoff Egan – Range News
Healthy Microbiome Changes Last After Fecal Transplant in New Research – Elizabeth Gough-Gordon – MPR

With sample collection videos: GoViral – collecting nasal and saliva samples from sick people – Boston Children’s Hospital

Northwestern leads research on effects of long-term stay in space – Peter Kotecki – The Daily Northwestern
Conference paper: Research from the NASA Twins Study and Omics in Support of Mars Missions – NASA Technical Reports

Podcast (1min30): Donate Your Health Data To Medical Science – Cynthia Graber – Scientific American – American Gut, GoViral

You Act What You Eat: How Gut Microbes Modify Our Behavior – Monica Thunder – ResetMe

Meet The Bacteria That Make A Stink In Your Pits – Poncie Rutsch – NPR
Bacterial genetic pathway involved in body odor production discovered – Science Daily

Should Gut Bugs Influence the 2015 Dietary Guidelines? – Cameron Wells – US News

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

Nearly half of hospital uniforms are washed in temperatures too cool to kill bacteria, says DMU research – De Montfort University
Egyptians Brewed Beer in Tel Aviv 5,000 Years Ago – Megan Gannon – Live Science

Conferences

#IHMC2015: 5th International Human Microbiome Congress, March 31-April 2, 2015, Luxembourg (6/23 plenary speakers are women)

The 2nd Microbiome R&D and Business Collaboration Forum Europe, May 07 – 08, 2015, London, UK (10/36 listed speakers are women)

1st Annual Translational Microbiome Conference, 13–14 May 2015, Boston, United States (5/11 speakers are women)

ASM General Meeting, May 30 – June 2, 2015, New Orleans, LA, USA

Symbiomes: Systems Biology of Host-Microbiome Interactions, 5-10 June 2015, Pultusk, Poland (5/17 speakers are women)

The Human Microbiome, 10-12 Jun 2015, EMBL Heidelberg, Germany (8/23 confirmed speakers are women)

Exploring Human Host-Microbiome Interactions in Health and Disease, June 29 – July 1, 2015 , Cambridge, UK (7/17 speakers are women)

Science, publishing, and career

How Articles Get Noticed and Advance the Scientific Conversation – Victoria Costello – PLOS Blogs

Writing a Good Peer Review to Improve Scholarship: What Editors Value and Authors Find Helpful – H. McLaughlin – Social Work Education: The International Journal

Discussion: Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida – PNAS USA

What if you could replace performance evaluations with four simple questions? – Jena McGregor – Washington Post

Bik’s Picks

What 60 Minutes Got Right And Wrong On Duke’s Polio Virus Trial Against Glioblastoma – David Kroll – Forbes.com

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

What Elephants and Whales Look Like From Space – Robinson Meyer – The Atlantic

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March 30, 2015

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Microbiome in rhinosinusitis patients, microbes in permafrost, and responses of soil to deforestation.

Meetings
London Microbiome Meeting 2015 (LMM2015), St. Thomas’ Hospital, 28 May 2015

Human respiratory microbiome

Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome – Vijay R. Ramakrishnan – Journal of Allergy and Clinical Immunology

Animal microbiome

Antimicrobial resistance in faecal samples from buffalo, wildebeest and zebra grazing together with and without cattle in Tanzania – A.A.S. Katakweba – Journal of Applied Microbiology

Soil and plant root microbiome

Soil microbiome responses to the short-term effects of Amazonian deforestation –
Acacio A. Navarrete – Molecular Ecology

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – B. Ma – Journal of Applied Microbiology

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China – Yucheng Wu – Frontiers in Microbiology

Extremophile microbiome

Structure, mineralogy, and microbial diversity of geothermal spring microbialites associated with a deep oil drilling in Romania – Cristian Coman – Frontiers in Microbiology

Shifts in methanogenic community composition and methane fluxes along the degradation of discontinuous permafrost – Mette M. Svenning – Frontiers in Microbiology

Bioreactor microbiome

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor – Q. Zhang – Journal of Applied Microbiology

Food microbiology

Diffusion of solutes inside bacterial colonies immobilized in model cheese depends on their physicochemical properties: a time-lapse microscopy study – Juliane Floury – Frontiers in Microbiology

Metagenomics

It’s a dirty job — A robust method for the purification and de novo genome assembly of Cryptosporidium from clinical material – Sofia Andersson – Journal of Microbiological Methods

Bioinformatics and statistics

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA – Brendan J. Kelly – Bioinformatics

More microbe papers

Review: Tackling antibiotic resistance: the environmental framework – Thomas U. Berendonk – Nature Reviews Microbiology

Microbes in the news

You Should Know: Kristina Campbell and The Intestinal Gardener – DNLee – Scientific American
Link to blog: The Intestinal Gardener – Kristina Campbell

Video of the February VLAB meeting at Stanford: Gut-Feeling — Ventures into the Microbiome – Colleen Cutcliffe – VLAB videos

Chronic Rhinosinusitis Varies By Bacterial Microbiome – Vijay R. Ramakrishnan – Medical Research

Doctors: How gut bacteria affects obesity, diabetes, child health – Jondi Gumz – Santa Cruz Sentinel

The bacteria that could make your blue jeans greener – Michael Keller – Green Biz

Bacteria power up by using magnets as batteries – Catherine Brahic – New Scientist

Antibiotics from the medieval medicine cabinet: Could medieval medicine provide new antibiotics to treat deadly modern infections? – CrowdFunder

Science, publishing and career

These scientists studied journalists covering science. Whoa, meta. – Suzanne Jacobs – Grist

Let’s compare the backgrounds of science writers for Fox and NPR – Boing Boing

Mind the (gender) gap: Kew’s records show fewer than 3% of land plant species published by women – Lauren Gardiner – Kew Royal Botanical Gardens

I’m an engineer, not a cheerleader. Let’s abandon silly rules about gender roles. – Sara Sakowitz – Washington Post

Bik’s Picks

Velvet Worms, Squirting Slime – James Gorman – New York Times

An apple a day may not keep the doctor away, study says – Lindsey Tanner – Big Story AP

Family income, parental education related to brain structure in children, adolescents – Science Daily

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March 28, 2015

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Screen Shot 2015-03-28 at 1.00.33 AMFeatured video

I had hoped that this would have been a better video. The opening text/visuals are very confusing, and the cartoon human looks like a sad penguin. Is it supposed to be a human? Or human cells inside the human? Or a bacterium? And why is it looking so sad? #SadPenguin

Video (2014): Microbes: The Residents Living On And Inside You – Carl R. Woese Institute for Genomic Biology

 

Human oral microbiome

Acetaldehyde production by major oral microbes – Keisuke Moritani – Oral Diseases

Prelude to oral microbes and chronic diseases: Past, present and future – Kalina R. Atanasova – Microbes and Infection

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human gut microbiome

Common occurrence of antibacterial agents in human intestinal microbiota – Fatima Drissi – Frontiers in Microbiology

Maintaining gut ecosystems for health: Are transitory food bugs stowaways or part of the crew? – Coline Plé – International Journal of Food Microbiology

Size does not matter: commensal microorganisms forge tumorpromoting inflammation and anti-tumor immunity – Melanie R. Rutkowski – Oncoscience

Review: Time for Food: The Intimate Interplay between Nutrition, Metabolism, and the Circadian Clock – Gad Asher – Cell

Animal microbiome

Horses: Characterization and comparison of the bacterial microbiota in different gastrointestinal tract compartments in horses – M.C. Costa – The Veterinary Journal

Fish: Declining diversity of egg-associated bacteria during development of naturally spawned whitefish embryos (Coregonus spp.) – Laetitia G. E. Wilkins – Aquatic Sciences

Bees (see also under “Other microbiology” below): Characterization of gut bacteria at different developmental stages of Asian honey bees, Apis cerana – Jun Guo – Journal of Invertebrate Pathology

Soil, rock, and marble microbiome

Biofouling of marbles by oxygenic photosynthetic microorganisms – Zeki Karaca – Environmental Science and Pollution Research

Water microbiome

Bacterial diversity of polluted surface sediments in the northern Adriatic Sea determined by pyrosequencing – Marino Korlević – Systematic and Applied Microbiology

Extremophile microbiome

Genomics in a changing Arctic: Critical questions await the molecular ecologist – Stan D. Wullschleger – Molecular Ecology

Microbial diversity on Icelandic glaciers and ice caps – Stefanie Lutz – Frontiers in Microbiology

Other microbiology

Antimicrobial-Induced DNA Damage and Genomic Instability in Microbial Pathogens –
Rebecca S. Shapiro – PLOS Pathogens

Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera) – David A. Galbraith – PLOS Pathogens

News

Planetary Protection Workshop (Forward Contamination) – Jenna Lang – MicroBEnet

How to keep up with microbial ecology and the built environment: microBEnet is your place – Jonathan Eisen – The Tree of Life

Italian Researchers Publish Array Method to Profile Vaginal Microbiome, Gauge Treatment Response – Molika Ashford – Genome Web

Social constructs and behaviors can predict microbiome composition – American Microbiome Institute

Not a good title: Hunter-Gatherers Have Better Guts Than We Do – Cody Brooks – Clapway

The tiny intruders in YOUR home: Researchers reveal the average house has 8,000 different types of bacteria and bugs – Mark Prigg

Drug metabolism: manipulating the microbiome – Sarah DeWeerdt – Pharmaceutical Journal

A High-Fat Diet May Alter Your Behavior and Your Brain with Changed Gut Bacteria – Catherine Griffin – Science World Report

Surfwear founder’s charity backs UQ researcher in superbug war – University of Queensland

Paywalled: Bacteria: Master Microbial Colonizers – Marcia Stone – BioScience

A Farmer Drilled For Water, But What Came Up Turned This Desert Into An Oasis! – OffGridQuest

Science, publishing and career

BioMed Central retracting 43 papers for fake peer review – Cat Ferguson – Retraction Watch

Bik’s Picks

Crossing fingers can reduce feelings of pain – Science Daily

Giant pandas’ secret social life revealed – Bob Holmes – New Scientist

Watch Scientists Try Everything to Put a Camera on a Manatee – Jane J. Lee – National Geographic

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March 26, 2015

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General microbiome

Note: not about metagenomics but 16S rRNA gene: The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies – J Paul Brooks – BMC Microbiology

Human respiratory microbiome

Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography – Robert P. Dickson – Annals ATS

A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients – Mohammad A. Tariq – Frontiers in Microbiology

Perspective: Meningitis in adolescents: the role of commensal microbiota – James W.B. Moir – Trends in Microbiology

Human gut microbiome

An n=1 case report of a child with autism improving on antibiotics and a father’s quest to understand what it may mean – John Rodakis – Microbial Ecology of Health and Disease

Animal microbiome

Sponges: Culturable associated-bacteria of the sponge Theonella swinhoei show tolerance to high arsenic concentrations – Ray Keren – Frontiers in Microbiology

Soil, sediment, and plant root microbiome

Community Dynamics of Arbuscular Mycorrhizal Fungi in High-Input and Intensively Irrigated Rice Cultivation Systems – Yutao Wang – Applied and Environmental Microbiology

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes – Zhichao Zhou – Frontiers in Microbiology

Isolation and characterization of culturable bacteria from bulk soil samples and the rhizosphere of arid-adapted Tylosema esculentum (Burchell). A. Schreiber (Marama bean) in Namibia – Olaf S. Kandjimi – African Journal of Biotechnology

Water microbiome

Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea – Ching-Hung Tseng – BMC Genomics

Spatial distribution of bacterial communities driven by multiple environmental factors in a beach wetland of the largest freshwater lake in China – Xia Ding- Frontiers in Microbiology

Review: Advancing the science of microbial symbiosis to support invasive species management: a case study on Phragmites in the Great Lakes – Kurt P. Kowalski – Frontiers in Microbiology

Extremophile microbiome (by special request!)

Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria – Kamil M. Szafranski – Frontiers in Microbiology

Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines) – Kristin M. Woycheese – Frontiers in Microbiology

Isolation of diverse members of the Aquificales from geothermal springs in Tengchong, China – Brian P. Hedlund – Frontiers in Microbiology

Fatty Acids Profile of Microbial Populations in a Mining Reclaimed Region Contaminated with Metals: Relation with Ecological Characteristics and Soil Respiration – Ramya Narendrula and Kabwe K. Nkongolo – Journal of Bioremediation & Biodegradation

Bioreactor microbiome

Nitrogen addition, not initial phylogenetic diversity, increases litter decomposition by fungal communities – Anthony S. Amend – Frontiers in Microbiology

Food microbiology

Lipidomics as an important key for identification of beer-spoilage bacteria – Tomáš Řezanka – Letters in Applied Microbiology

Metabolomics

Combining reverse genetics and NMR-based metabolomics unravels trypanosome-specific metabolic pathways – Frédéric Bringaud – Molecular Microbiology

Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms – Ellard R. Hunting – Frontiers in Microbiology

Techniques

Enriching distinctive microbial communities from marine sediments via an electrochemical-sulfide-oxidizing process on carbon electrodes – Shiue-Lin Li and Kenneth H. Nealson – Frontiers in Microbiology

Microbes in presentations

Video: Dissertation seminar for Suzanne Ishaq – comparative analysis of the moose rumen microbiota

Video: Vance Kramer of Syngenta discussing microbiome research and comparing soil microbe communities across the US, Europe, and Brazil.

Video: Dr. Jan Jones from AgBiome discussing the plant-soil microbiome

Microbes in the news
Hidden Life Forms: Investigating Microbial Diversity on Our Bodies and in Our Homes – Jennifer Cutraro – New York Times

My uBiome Sleep Hacking Update – Alexandra Carmichael – uBiome

Antimicrobial CRISPR-Cas systems may be better weapons against bacteria than antibiotics – The Conversation

Secret Science Club Post-Lecture Recap: Big Data, Genomics and Urban Microbiomes – Big Bad Bald Bastard

Antibiotics For Gut Bacteria Show Surprising Results In Treating Autism – Dianne Depra – Tech Times

Harmless bacteria may be helpful against meningococcal outbreaks – Eureka Alert

New Software Offers Improved Read-based Identification in Metagenome Studies – Andrew P. Han – Genome Web

Not sure which one, but here it is: I am the bacterium that lives in your intestine – MicrobeWorld

FMT: Update on OpenBiome – Paul Levy – Not Running A Hospital

Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro) – Jenna Lang – Microbe.net

Microbes and art

A Dress Made From Beer And Bacteria: C’est Chic Or C’est Ick? – Charles Poladian – IB Times

Science, publishing, and career

Developing microbiological learning materials for schools: best practice – James Redfern – FEMS Microbiology Letters

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights – Claire Bertelli – Frontiers in Microbiology

Calling attention to poor speaker gender ratio – even when it hurts – Jonathan Eisen – The Tree of Life

The 5 Biases Pushing Women Out of STEM – Joan C. Williams – Harvard Business Review

Bik’s Picks

Jurrassic Park, but then with more fur: Woolly mammoth could be revived after scientists paste DNA into elephant’s genetic code – Andrew Griffin – The Independent

The Fitness Guru of the Trucking Industry – The Atlantic

On Friday, half a pair of twins leaves for a year in space. Here’s why that’s awesome. – Rachel Feltman – Washington Post

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March 25, 2015

Posted on by

General microbiome

Introducing npj Biofilms and Microbiomes – Staffan Normark – NPJ Biofilms and Microbiomes – includes:

Clinical Implications of Basic Science Discoveries: Immune Homeostasis and the Microbiome—Dietary and Therapeutic Modulation and Implications for Transplantation – J. A. Fishman, and A. W. Thomson – American Journal of Transplantation

Human respiratory microbiome

Clinical Outcomes and Microbiological Characteristics of Severe Pneumonia in Cancer Patients: A Prospective Cohort Study – Ligia S. C. F. Rabello – PLOS ONE

Human gut microbiome

Subsistence strategies in traditional societies distinguish gut microbiomes – Alexandra J. Obregon-Tito – Nature Communications

Variation in rural African gut microbiomes is strongly shaped by parasitism and diet – Elise R Morton – BioRxiv

Some problems with JAMA website, not sure if link works: Association of Gastrointestinal Symptoms With Autism – JAMA Psychiatry

Contrasting effects of fresh and fermented kimchi consumption on gut microbiota composition and gene expression related to metabolic syndrome in obese Korean women – Kyungsun Han – Molecular Nutrition & Food Research

Review: Alcohol and gut microbiota – the possible role of gut microbiota modulation in the treatment of alcoholic liver disease – G. Vassallo – Alimentary Pharmacology & Therapeutics

Perspective: Studies of the Gut: Overhyped or Underappreciated? – Tom Bartlett – The Chronicle of Higher Education

Review: Microbial biofilms and the human intestinal microbiome – Willem M de Vos – NPJ Biofilms and Microbiomes

Review: Microbial endocrinology: host-bacteria communication within the gut microbiome – Sara Sandrini – Journal of Endocrinology

Dead body microbiome

Potential Use of Bacterial Community Succession in Decaying Human Bone for Estimating Postmortem Interval – Franklin E. Damann – Journal of Forensic Sciences

Life after death: shallow-water Mediterranean invertebrate communities associated with mammal bones – Sergi Taboada – Marine Ecology

Animal microbiome

Monkeys: Adenovirus and Herpesvirus Diversity in Free-Ranging Great Apes in the Sangha Region of the Republic of Congo – Tracie A. Seimon – PLOS ONE

Birds (not birds and bees): Pathogenic bacteria and timing of laying – Anders Pape Møller – Ecology and Evolution

Arthropods: Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan, China – Han Xia – PLOS ONE

Nematodes: Associated bacteria of different life stages of Meloidogyne incognita using pyrosequencing-based analysis – Yi Cao – Journal of Basic Microbiology

Corals: Microbial Communities Associated with Healthy and White Syndrome-Affected Echinopora lamellosa in Aquaria and Experimental Treatment with the Antibiotic Ampicillin – David Smith – PLOS ONE

Water microbiome

Plant pathogenic bacteria in open irrigation systems: what risk for crop health? – J. R. Lamichhane and C. Bartoli – Plant Pathology

Elements of metacommunity structure and community-environment relationships in stream organisms – Jani Heino – Freshwater Biology

Opportunistic Pathogens and Elements of the Resistome that Are Common in Bottled Mineral Water Support the Need for Continuous Surveillance – Maria Fernanda Falcone-Dias – PLOS ONE

Bioinformatics

MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome – Ohad Manor and Elhanan Borenstein – Genome Biology

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome – Stephen Nayfach and Katherine S Pollard – Genome Biology

Novel R Pipeline for Analyzing Biolog Phenotypic Microarray Data – Minna Vehkala – PLOS ONE

Ecology

Probabilistic Models to Describe the Dynamics of Migrating Microbial Communities – Joanna L Schroeder – PLOS ONE

Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 Vibrio cholerae by Whole Genome Mapping Reveals Extensive Population Genetic Diversity – Carol Chapman – PLOS ONE

Archaea

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis – Guanghong Zuo – Life

Techniques

Open Labware: 3-D Printing Your Own Lab Equipment – Tom Baden – PLOS Biology

Microbes in the news

Treponema are not “ancient” but absence from some human’s guts is very interesting – Jonathan Eisen – Tree of Life
Refers to:
Ancient bacteria found in hunter-gatherer guts – Ann Gibbons – Science

With recipes: Upcoming book by Justin and Erica Sonnenburg: “The Good Gut” – Amazon

The ‘intraterrestrials’: New viruses discovered in ocean depths – National Science Foundation

Martian Microbes Could Be Eating Carbon Monoxide From the Atmosphere – Popular Mechanics

Kids with Autism Are More Likely to Have Gastrointestinal Problems – Rachael Rettner – LiveScience

Examining the connection between infant gut bacteria and food allergies – HealthCanal

Repeated Use of Antibiotics May Raise Diabetes Risk – Agata Blaszczak-Boxe – LiveScience

Bacteria in bud prompts B.C. medical marijuana firm to recall product – Canadian Press

Twin astronauts provide Earth-bound control for orbital health study – Phys.org

Baylor College of Medicine: Certain makeup can cause bacterial infections – John Brannen – Click2Houston

The Bathroom Blast Radius (And Your Toothbrush) – Dollar Shave Club

The Antibiotics Problem in Meat – Olga Khazan – The Atlantic

Satire: Biotechnology pressure group calls for an end to Saccharomyces abuse – The Allium

Science, publishing, and career

The 2015 Salary Survey Is Here – The Scientist

Women still find it tough to reach the top in science – Sharon Bell – The Conversation

Bik’s Picks

Ancient Egyptian skeleton shows signs of breast cancer – Elahe Izadi – Washington Post

Unravelling the hidden ancestry of American admixed populations – Francesco Montinaro – Nature Communications

Short Circuit in Magnets Postpone Re-Launch of CERN Collider – InsightTicker

Why the world needs biodiversity – Scientists have engineered the food that will help save a starving, warming planet – Jack Aldwinckle – Quartz

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March 24, 2015

Posted on by

General microbiome

Review: Biomarkers for the 21st Century: Listening to the Microbiome – Rodney Reynolds Dietert* and Ellen Kovner Silbergeld – Toxicological Sciences

Nice overview [PDF]: FASEB Releases “The Human Microbiome: Your Own Personal Ecosystem” – FASEB

Microbiome of pregnancy and birth

Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis – Valarie E McMurtry – Microbiome

Human vaginal microbiome

Vaginal Microbiota of Adolescent Girls Prior to the Onset of Menarche Resemble Those of Reproductive-Age Women – Roxana J. Hickey – mBio

Human gut microbiome

The detection of vector-borne-disease-related DNA in human stool paves the way to large epidemiological studies – Alpha Kabinet Keita – European Journal of Epidemiology

Animal and other models

A Modified R-Type Bacteriocin Specifically Targeting Clostridium difficile Prevents Colonization of Mice without Affecting Gut Microbiota Diversity – Dana Gebhart – mBio

Effects of Irradiation on Epithelial Wound Healing and Microbial Diversity in an
in-vitro Oral Mucosa Model – Tine De Ryck – Nuclear Medicine & Radiation
Therapy

Microbes on Mars? Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith – Gary M. King – PNAS USA

Animal microbiome

Rabbit: The bacterial communities associated with fecal types and body weight of rex rabbits – Bo Zeng – Scientific Reports

Plant microbiome

Lots of omics words in this book: Microbiomics: An Approach to Community Microbiology – Pankaj Sharma – In: PlantOmics

Soil and plant root microbiome

The Soil Microbiome Influences Grapevine-Associated Microbiota – Iratxe Zarraonaindia – mBio

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem – Jinbo Xiong – Scientific Reports

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust – Ulisses Nunes da Rocha – Frontiers in Microbiology

Nucleotide Sequences of Giant Viruses Found in Soil Samples of the Mojave Desert, the Prairie, the Tundra and the Antarctic Dry Valleys – Csaba Kerepesi – ArXiv

Impacts of bulk soil microbial community structure on rhizosphere microbiomes of Zea mays – Matthew G. Bakker – Plant and Soil

Pyrosequencing Reveals Changes in Soil Bacterial Communities after Conversion of Yungas Forests to Agriculture – Marcela S. Montecchia – PLOS ONE

Priority effects during fungal community establishment in beech wood – Jennifer Hiscox – The ISME Journal

Water microbiome

Very cool, with longitudinal plots: The Source of the River as a Nursery for Microbial Diversity – Luiz Felipe Valter de Oliveira, Rogério Margis – PLOS ONE

Evidence of active methanogen communities in shallow sediments of the Sonora Margin cold seeps – Adrien Vigneron – Applied and Environmental Microbiology

Site history and edaphic features override the influence of plant species on microbial communities in restored tidal freshwater wetlands – Christine E. Prasse – Applied and Environmental Microbiology

Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance – Silvia Pajares – PLOS ONE

Physiological and evolutionary potential of microorganisms from the Canterbury Basin subseafloor, a metagenomic approach – Frédéric Gaboyer – FEMS Microbiology Ecology

Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source – Eleftheria Antoniou – Frontiers in Microbiology

Built environment microbiome

Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments – Christine Moissl-Eichinger – Scientific Reports

Effect of Monochloramine Treatment on the Microbial Ecology of Legionella and Associated Bacterial Populations in a Hospital Hot Water System – Julianne L. Baron – Systematic and Applied Microbiology

Non-culturable bioaerosols in indoor settings: impact on health and molecular approaches for detection – Pascale Blais-Lecours – Atmospheric Environment

Probiotics

Development and Utility of the FDA “GutProbe” DNA Microarray for Identification, Genotyping, and Metagenomic Analysis of Commercially Available Probiotics – Jennifer N. Patro – Journal of Applied Microbiology

Antibiotics

Global trends in antimicrobial use in food animals – Thomas P. Van Boeckel – PNAS USA

Metagenomics and bioinformatics

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly – Tarini Shankar Ghosh – Journal of Bioinformatics and Computational Biology

Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors – Jeremy G. Owen – PNAS USA

Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis – Pushpendra Singh – PNAS USA

Metabolomics / Ecology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Microbes in the news

With a picture you will never forget: Acne and the Microbiome: Christi Investigates – Alexandra Carmichael

Vineyard’s soil microbes shape grapes’ microbial community – Science Daily

Crohn’s Disease: Gut Microbial Collaborations Trigger Inflammatory Diseases – PR NewsWire

Feed the microbes so they don’t feed on you: Fiber-Famished Gut Microbes Linked to Poor Health – Katherine Harmon Courage – Scientific American

Harnessing The Microbiome To Curb Hunger – Chemical and Engineering News

New Research On Appetite-Suppressing Bacteria Could Help Fight Obesity – Anna Almendrala

The MinION Access Programme (MAP) for portable DNA sequencing – Science Daily

Viruses, Archaea Self-mutate to Survive – Laboratory Equipment

Engineering and waterborne bacteria in building water systems – Colum Ó Bric -EngineersJournal

Gut and Mood: The Microbiome in Anxiety and Depression – Nina Weisbroth – Translational Microbiome

Not so fast, FastTree – Darling lab

Satire: Each bioinformatician to have their own personal short-read aligner by 2016 – The Science Web

Not about Dr. Who: The Doctor Who Tested Infectious Bacteria On Himself, And Won A Nobel – Ria Misra

Comparing the genomes of the leprosy bacteria – Phys.org

#BacteriaHysteria: “Beer Pong” Associated with Frequent Bacterial Transmissions – Jacquelyn Gray – HCPlive

#BacteriaHysteria: Clean machines: how to look after your tech and avoid bacteria bombs – David Howell – TechRadar

Science and art

Workshop, April 6, 2015: Paint with Bacteria – GenSpace, New York City’s Community Biolab

Science, publishing, and career

Opinion: Lay summaries needed to enhance science communication – Lauren M. Kuehne and Julian D. Olden – PNAS USA

50 min podcast: Women in Oceanography: Lots of Students, Not So Many Professors – Heather Goldstone – Capeandislands.com

This is why you shouldn’t believe that exciting new medical study – Julia Belluz – Vox.com

Stubborn Pay Gap Is Found in Nursing – Catherine Saint Louis – Catherine Saint Louis – New York Times

It’s time to reboot bioinformatics education – Todd Harris

Bik’s Picks

Macaques Exhibit a Naturally-Occurring Depression Similar to Humans – Fan Xu – Scientific Reports

Earth’s most powerful physics machine gets back in action – Marcus Woo – Wired.com

Scientists want museums to cut their ties with David Koch – Science Recorder

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March 22, 2015

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Human oral microbiome

Effect of dental cements on peri-implant microbial community: comparison of the microbial communities inhabiting the peri-implant tissue when using different luting cements – Michael Korsch – Clinical Oral Implants Research

Human vaginal microbiome

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. – Helena Mendes-Soares – Pathogens and Disease

Human gut microbiome

Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis – Ratnakar Shukla – Digestive Diseases and Sciences

Review: Psychobiotics and the gut–brain axis: in the pursuit of happiness – Zhou L – Neuropsychiatric Disease and Treatment

Microbiome of pregnancy and birth

The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Colonisation of the gut by bifidobacteria is much more common in vaginal deliveries than Caesarean sections – Sarka Musilova – Acta Paediatrica

Review: The Birth of the Holobiont: Multi-species Birthing Through Mutual Scaffolding and Niche Construction – Lynn Chiu, Scott F. Gilbert – Biosemiotics

Animal models

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota – Jessica Ann Thompson – Cell Reports

Vagotomy prevents the effect of probiotics on caspase activity in a model of postmyocardial infarction depression – M. Malick – Neurogastroenterology & Motility

Faecalibacterium prausnitzii prevents physiological damage in a chronic low-grade inflammation murine model – Rebeca Martín – BMC Microbiology

Peyer’s patch innate lymphoid cells regulate commensal bacteria expansion – Masaaki Hashiguchi – Immunology Letters

Animal microbiome

Review: A Review of Infectious Agents in Polar Bears (Ursus maritimus) and Their Long-Term Ecological Relevance – Anna C. Fagre – EcoHealth

Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH – Neeti Pandey andRaman Rajagopal – Insect Science

Genetic diversity of cyanophages of the myoviridae family as a constituent of the associated community of the Baikal sponge Lubomirskia baicalensis – T. V. Butina – Russian Journal of Genetics

Soil and plant root microbiome

Effects of Thinning and Induced Drought on Microbiological Soil Properties and Plant Species Diversity at Dry and Semiarid Locations – Javier Hedo de Santiago – Land Degradation & Development

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities in Jatropha curcas L. Plantation – Doongar Ram Chaudhary – CLEAN-Soil, Air, Water

Water microbiome

Quantifying the effects of geographical and environmental factors on distribution of stream bacterioplankton within nature reserves of Fujian, China – Yongming Wang – Environmental Science and Pollution Research

Spatial distribution of marine airborne bacterial communities – Jasmin S. Seifried – Microbiology Open

Microbiome of the built environment

Interphase microbial community characteristics in the fermentation cellar of Chinese Luzhou-flavor liquor determined by PLFA and DGGE profiles – Xiaofei Ding – Food Research International

Bioreactor microbiology

Microbial structures and community functions of anaerobic sludge in six full-scale wastewater treatment plants as revealed by 454 high-throughput pyrosequencing – Duntao Shu – Bioresource Technology

Cu and Cr enhanced the effect of various carbon nanotubes on microbial communities in an aquatic environment – Fei Wang – Journal of Hazardous Materials

Review: Utilization of microbial community potential for removal of chlorpyrifos: a review – Maya Yadav – Critical Reviews in Biotechnology

Metagenomics and Bioinformatics

A robust approach for identifying differentially abundant features in metagenomic samples – Michael B. Sohn – Bioinformatics

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe – Tianmin Wang – BMC Bioinformatics

The impact of quality filter for RNA-Seq – Pablo H.C.G. de Sáa – Gene

Poster: MetaGenSense: a web application for analysis and visualization of high throughput sequencing metagenomic data – Damien Correia – F1000 posters

SISPA-Seq for rapid whole genome surveys of bacterial isolates – Meredith S. Wright – Infection, Genetics and Evolution

Metabolomics

The metabolomics of necrotising enterocolitis in preterm babies: an exploratory study – Amy Wilcock – The Journal of Maternal-Fetal & Neonatal Medicine

Deep metabotyping of the murine gastro-intestinal tract for visualization of digestion and microbial metabolism – Silke S Heinzmann and Philippe Schmitt-Kopplin – Journal of Proteome Research

Application of a new Dynamic Gastrointestinal Simulator (SIMGI) to study the impact of red wine in colonic metabolism – C. Cueva – Food Research International

Isolation of dextran-hydrolyzing intestinal bacteria and characterization of their dextranolytic activities – Jin Kyoung Kim – Biopolymers

Diet-induced obesity causes metabolic impairment independent of alterations in gut barrier integrity – Caroline Kless – Molecular Nutrition & Food Research

Other microbial science papers

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals – Thomas Obadia – PLOS Computational Biology

How bacterial pathogens colonize their hosts and invade deeper tissues – David Ribet, Pascale Cossart – Microbes and Infection

Antimicrobial stewardship: the role of scientists? – Laura Bowater – Journal of Antimicrobial Chemotherapy

Cyanobacteria: the bright and dark sides of a charming group – Katia Sciuto, Isabella Moro – Biodiversity and Conservation

Microbes in the news
The ChuckNorrisMicrobiome will get you, and you, and you … – Jonathan Eisen – The Tree of Life

The Oral Microbiota Affects More Than Just the Mouth – Lily Berrin – PLOS blog

This Week in Microbiology #100: Omnis cellula e cellula – MicrobeWorld

Wisconsin Longitudinal Study: Decades later, benchmark study yields data on human condition – Pamela Herd – Madison.com

Special microbes make anti-obesity molecule in the gut – American Chemical Society – Eureka Alert

About the baboon microbiome study: Are our gut bacteria swapped when we snuggle up? – Tim Sandle – Digital Journal

Wireless Sensors Help Scientists Map Staph Spread Inside Hospital – Scott Hensley – NPR

Science spreads antibiotic resistance by genetic experimentation – Karen Hardison – Digital Journal
Great #openaccess collection of papers on RNA – Jonathan Eisen – MicroBEnet

Visualizing the deadly threat of meningitis on campuses – Jamie Lampros – Standard Examiner

Epidemic Predicted by Bill Gates Who Pleads: Microbes Not Missiles – Jeanette Smith – Guardian LV

Science, publishing, and career

Forget Harvard and Stanford. It really doesn’t matter where you go to college – Jeffrey J. Selingo

Wolf Prize for Agricultural Science for Linda Saif: Award shines light on Ohio State scientist – Laura Arenschield – The Columbus Dispatch

Michigan judge asks PubPeer to turn over anonymous user information – Kelly Servick – Science Insider

In science, irreproducible research is a quiet crisis – Carolyn Johnson – Boston Globe

Bik’s Picks

Copy Cat: Someone Keeps Photocopying Their Cat at the University of Wisconsin Library – Samantha Grossman – Time.com

First fine-scale genetic map of the British Isles – Science Daily

Dude, why is my mushroom glowing? Scientists have the answer – Will Dunham – Reuters