Monthly Archives: April 2015

April 7, 2015

Posted on by

Lots of abstracts today that were published in the FASEB Journal. Although not clearly marked, these appear to be abstracts from an ASBMB meeting held in March 2015 in Boston, called “The Human Microbiome“. None of these have a link to a PDF.

Course: Frontiers in Host-Microbe Interactions – August 2015

Pregnancy and birth microbiome

The FASEB Journal Abstracts:

Review: Normal flora and bacterial vaginosis in pregnancy: an overview – Mathys Jacobus Redelinghuys – Critical Reviews in Microbiology

Review: The Infant Gut Microbiome: Evidence for Obesity Risk and Dietary Intervention – Petya T. Koleva – Nutrients

Human skin microbiome

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin – Jared Liu – The ISME Journal

Human oral microbiome

The Repertoire of Archaea Cultivated from Severe Periodontitis – Hong T. T. Huynh – PLOS ONE

Review: Filifactor alocis – a new emerging periodontal pathogen – A. Wilson Aruni – Microbes and Infection

Human gut microbiome

The FASEB Journal Abstracts:

Autism spectrum disorders and intestinal microbiota – Maria De Angelis – Gut Microbes

Review: Impacts of Gut Bacteria on Human Health and Diseases – Yu-Jie Zhang – International Journal of Molecular Sciences

Animal models of microbiome research

The FASEB Journal Abstracts:

Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model – Shaoping Wu – Physiological Reports

Metabolomic Modeling To Monitor Host Responsiveness to Gut Microbiota Manipulation in the BTBRT+tf/j Mouse – Matthias S. Klein – Journal of Proteome Research

Animal microbiome

The FASEB Journal Abstract: The Extraordinary Evolution of the Great Ape Microbiome
Howard Ochman

Pigs: How host gender affects the bacterial community in pig feces and its correlation to skatole production – Zhenjin Zhou – Annals of Microbiology

Pigs: Analysis of swine fecal microbiota at various growth stages – Jungman Kim – Archives of Microbiology

Fish / Review: Disinfection of teleost eggs: a review – Evelien De Swaef – Reviews in Aquaculture

Ticks: Concordance of bacterial communities of two tick species and blood of their shared rodent host – Evelyn C. Rynkiewicz – Molecular Ecology

Soil microbiome

Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity – Yuting Liang – mBio

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field – Cai-Yun Li – International Journal of Molecular Sciences

Effects of Functionalized and Raw Multi-Walled Carbon Nanotubes on Soil Bacterial Community Composition – Dorsaf Kerfahi – PLOS ONE

Review: Effective role of indigenous microorganisms for sustainable environment – Baduru Lakshman Kumar and D. V. R. Sai Gopal – 3 Biotech

Water microbiome

Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone – M.T. Duret – FEMS Microbial Ecology

Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols – Camilla Fahlgren – Environmental Microbiology Reports

Book: Microbiology of the Everglades Ecosystem – CRC Press

Extremophile microbiome

Physiochemical control of bacterial and protist community composition and diversity in Antarctic sea ice – Anders Torstensson – Environmental Microbiology

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment – Jamile Queiroz Pereira – Genome Announcements

Food microbiome

Microbial Ecology of Watery Kimchi – Kyu Hang Kyung – Journal of Food Science

Bioreactor and biofilter microbiome

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

Metagenomics, Metabolomics, and Transcriptomics

The FASEB Journal Abstracts:

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities – Jacob Moran-Gilad – BMC Infectious Diseases

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis – Yuzhen Ye, Haixu Tang – ArXiv

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton – Jessica M Labonté – The ISME Journal

Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample – Koen Illeghems – Food Microbiology

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone – Sangita Ganesh – The ISME Journal

Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone – Molly Carolan and J Michael Beman – Frontiers in Microbiology

Review: Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism – Linda C Duffy – Journal of Nutrition

Microbial Ecology

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities – Ville-Petri Friman – Proceedings B

Local–global overlap in diversity informs mechanisms of bacterial biogeography – Joshua A Livermore – The ISME Journal

Techniques

Assessing the performance of the Oxford Nanopore Technologies MinION – T. Laver – Biomolecular Detection and Quantification

Next-generation sequencing data analysis on cloud computing – Taesoo Kwon – Genes & Genomics

Microbes in the news

It’s a microbe’s world…we’re just living and dying in it – Margaret Leigh Sinrod – SciTechNow

May deadline: 2015 MO BIO Microbiome Awards – MoBIO

After cancer diagnosis, MIT student 3-D prints tumor, has microbiome analyzed – Nidhi Subbaraman – BetaBoston

Most of the text appears stolen from an article by Lita Proctor:  Human Microbiome: Quiz – Target Health

Video: Why Your Beard Is Disgusting – Discovery News

Episode 4 of The Microbiome Podcast: What’s hot in the microbiome field with Kristina Campbell – American Microbiome Institute

Solving the complex problem of recurrent C. diff with a simple solution: 
Physician scientists are using fecal transplants to break the deadly cycle of a killer infection – Bryan Goodchild and Ellie Castano – University of Massachusetts Medical School

Gut Bacteria May Influence Parkinson’s Risk, Phenotype – Pauline Anderson – Medscape

Summing up: Bassis et al.’s take on the influence of the URT on other human-associated biogeographies – Fiona Whelan – Human Microbiome Journal Club:

Under the microscope, strong-swimming swamp bacteria spontaneously organize into crystals – Phys.org

Science, publishing, and career

Female peers in small work groups enhance women’s motivation, verbal participation, and career aspirations in engineering – Nilanjana Dasgupta – PNAS USA

Bik’s Picks

How California can survive the drought — State is not in complete control – Danielle Venton – Nature

The Brontosaurus Is Back, Baby – Rich Juzwiak – Gawker

Endangered Tortoises Feasting on Invasive Plants – Richard Farrell – Discovery
[hr]

April 6, 2015

Posted on by

Not all human breast milk sold online is 100% human, microbiome of veggies, and a book by Rob Knight.

Pregnancy and birth

Cow’s Milk Contamination of Human Milk Purchased via the Internet – Sarah A. Keim – Pediatrics

Review: Milk Bioactives May Manipulate Microbes to Mediate Parent-Offspring Conflict – Cary R. Allen-Blevins – Evolution, Medicine, and Public Health

Food microbiology

Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables – Colin R. Jackson – Agriculture

Metabolomics

Link did not work as of now – might work later? The colibactin warhead crosslinks DNA – Crawford – Nature Chemistry

Microbes in the news

Beyond Probiotics: Can You ‘Hack’ Your Microbiome? – Beth Skwarecki – LifeHacker Australia

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature – Jonathan Eisen – The Tree of Life

Book by Rob Knight – Follow Your Gut – The Enormous Impact of Tiny Microbes – TED books

Ice Worm Guts Tell a Story of Partnership – Manon Verchot – Glacier Hub

An Amazonian Tribe May Hold The Secret To Better Gut Health – Anna Almendrala – Huffington Post

Microbes scared to death by virus presence – ScienceDaily

Spotting a molecular warhead for disease in the human gut – Jim Shelton – Yale News

Microbes are partly to blame for Arctic’s melting permafrost – Mary Beth Griggs – Popular Science

That Vagina Yogurt Probably Wasn’t Really Vagina Yogurt, Says Expert – Ben Richmond – Motherboard

MRSA Bacteria Thrives In Cigarette Smoke Environment – Paola Celedonio – Diabetes Insider

Raising money to go the ASM conference: E. coli and Ebola already sold out: Microbiology students sell giant plush microbes – KCCI

Glowing GE bacteria produced from kits ‘illegally’ in New Zealand – Tom Hunt – The Dominion Post

Bik’s Picks

Breast Milk Sold Online May Not Be 100% Human Milk – Cari Nierenberg – LiveScience

Please learn the difference between tortoises and sea turtles, say Florida wildlife officials – Rowena Lindsay – CS Monitor

What Americans Think About Climate Change in Seven Maps – Eric Roston – Bloomberg
[hr]

April 4, 2015

Posted on by

In this weekend edition, I found papers on iron supplements, phage and TM6 genomics, millipedes, ground squirrels, and coffee consumption. 

Human oral microbiome

Salivary Microbiota Reflects Changes in Gut Microbiota in Cirrhosis with Hepatic Encephalopathy – Jasmohan S Bajaj – Hepatology

The Peri-Implant and Periodontal Microbiota in Patients with and without Clinical Signs of Inflammation – Meike Luise Jakobi – Dental Journal

Almost completely plagiarized Review: Interspecies communication in oral biofilm: An ocean of information – Amit Parashar – Oral Science International

Human respiratory microbiome

Possible role of anaerobes in the pathogenesis of nontuberculous mycobacterial infection – Kei Yamasaki – Respirology

Human gut microbiome

Isn’t that Ironic: Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants – Tanja Jaeggi – Gut

Review: The gut microbiome in cardio-metabolic health – Tue H Hansen – Genome Medicine

Review: The role of the commensal microbiota in the regulation of tolerance to dietary allergens – Berni Canani – Current Opinion in Allergy and Clinical Immunology

Review: The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems – Marilia Carabotti – Annals of Gastroenterology

Human urine microbiome

Review: “Sterile Urine” and the Presence of Bacteria – Alan J. Wolfe and Linda Brubaker – European Urology

Animal and other models of microbiome research

Lacking vitamin D receptor leads to intestinal dysbiosis – Dapeng Jin – The FASEB Journal

Evidence for a link between Gut Microbiota and Hypertension in the Dahl rat model – Blair Mell – Physiological Genomics

In vitro colonic metabolism of coffee and chlorogenic acid results in selective changes in human faecal microbiota growth – Charlotte E. Mills – British Journal of Nutrition

Ingestion of coffee polyphenols increases postprandial release of the active glucagon-like peptide-1 (GLP-1(7–36)) amide in C57BL/6J mice – Yoshie Fujii – British Journal of Nutrition

 

Animal microbiome

Squirrels: Functional Analysis of Seasonally-Changing Gut Microbiotas in Hibernating Ground Squirrels – Hannah Carey – The FASEB Journal

Fish: Community assembly of a euryhaline fish microbiome during salinity acclimation –
Victor T. Schmidt – Molecular Ecology

Aphids: Shifts in Buchnera aphidicola density in soybean aphids (Aphis glycines) feeding on virus-infected soybean – Bryan J. Cassone – Insect Molecular Biology

Millipedes: Litter-type specific microbial responses to the transformation of leaf litter into millipede feces – François-Xavier Joly – Soil Biology and Biochemistry

Plant root and soil microbiome

Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes – Tanya E. Cheeke – Molecular Ecology

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination – Yi Liang – Applied Microbiology and Biotechnology

A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes– Carolina Senés-Guerrero and Arthur Schüßler – Fungal Diversity

Built environment microbiome

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children – Karen C. Dannemiller – Indoor Air

Bioreactor microbiome

Characterisation of the complex microbial community associated with the ASTER™ thiocyanate biodegradation system – Robert J. Huddy – Minerals Engineering

A comprehensive study on algal-bacterial communities shift during thiocyanate degradation in a microalga-mediated process – Byung-Gon Ryu – Bioresource Technology

Metagenomics, genomes

TM6: Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae – Isabelle Pagnier – Biology Direct

Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage – Tung Gia Phan – Virology

Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment – Jessica M. Labonté – Frontiers in Microbiology

Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses – Lance R. Parsons – mBio

Techniques

Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community – Eva Theres Gensberger – PeerJ

Microbes in the news

World’s largest microbiome conference held in Luxembourg – University Du Luxembourg

Wash U. Study Finds Bacteria More Antibiotic Resistant – OzarksFirst

What did the bacteria say to the cigarette? “Don’t make me get aggressive” — study finds that smoke strengthens bad bugs – Dave Rice – SanDiegoReader

Urine Isn’t Free of Bacteria – HealthDay

Bad bacteria in your beer? Problem Solvers put taps to the test – Shellie Bailey-Shah – KATU.com

Is it time to bid farewell to your Beats? Your pricey designer headphones could be causing bacteria build-up, acne and even nasty skin infections – Erica Tempesta – Daily Mail UK

Science, publishing, and career

Gender pay inequality at UK Universities: It’s not just bad, it’s wrong – John Gill – Times Higher Education

Bik’s Picks

Yes, Mice Can Sing. And You Won’t Believe How Much They Sound Like Songbirds – Macrina Cooper-White – Huffington Post

Mars rover Curiosity spots strange, 2-tone veins on planet’s surface – Amina Khan – LA Times

Archaeologists uncover 330 year old “war camel” skeleton – David Demar – The American Register

April 3, 2015

Posted on by

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

[hr]

April 2, 2015

Posted on by

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

[hr]

April 1, 2015

Posted on by

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

[hr]