Category Archives: More Microbes

Microbiome digest, October 16, 2014

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Lung microbiome and pneumonia, bacterial vaginosis, microbiome and jetlag, cardiovascular consequences of gut dysbiosis, bacteria in locust guts and cropland in China, and how to earn some $$$ with your poop.

Human respiratory microbiome

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia – Ian Toma – Journal of Clinical Microbiology

“The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia.”

Human vaginal microbiome

Recent progress in understanding the epidemiology of bacterial vaginosis – Kenyon, Chris R.; Osbak, Kara – Current Opinion in Obstetrics & Gynecology

“Bacterial vaginosis epidemiology has been transformed by new theoretical insights and methodologies, such as molecular sequencing. We summarize the progress made in these domains.”

Human gut microbiome

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis – Christoph A. Thaiss – Cell

“Consequently, jet-lag-induced dysbiosis in both mice and humans promotes glucose intolerance and obesity that are transferrable to germ-free mice upon fecal transplantation.”

Far from the Eyes, Close to the Heart: Dysbiosis of Gut Microbiota and Cardiovascular Consequences – Matteo Serino – Current Cardiology Reports

“Here, we report evidence from the literature, as well as a few controversial reports, regarding the putative role of gut microbiota dysbiosis-induced cardiovascular diseases”

Insect microbiome

Cellulolytic activity and structure of symbiotic bacteria in locust guts – L-J Su – Genetics and Molecular Research

“The diversity of gut symbiotic bacteria was studied using denaturing gradient gel electrophoresis (DGGE). “

Soil microbiome

* Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China – Zhen Zhen – PLOS ONE

“Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. “

Water microbiome

Substratum-Associated Microbiota – Furey, Paula C.; Liess, Antonia – Water Environment Research

“In this review of the 2013 literature, advances in laboratory, field, and assessment methods are highlighted as are updates in taxonomy and systematics.”

More microbiology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

“Donia et al. have carried out the first systematic screen of biosynthetic gene clusters (BGCs) in the healthy human microbiota and found that BGCs for the thiopeptide class of antibiotics are widely distributed.”

First aid kit for cholera – Andrea Du Toit – Nature Reviews Microbiology

“In a new study, Gordon and colleagues examined the role of the human gut microbiota in V. cholerae infection and showed that one of its members, Ruminococcus obeum, decreases the expression of V. cholerae virulence factors to limit colonization.”

Microbes in the news

* A Poop Bank in Massachusetts Will Pay You $40 Every Day – Chelsea Rice – Boston.com

“All you have to do is visit OpenBiome, launched in 2012 as the only independent nonprofit stool bank in the country.”

Study reveals rats in NYC carry variety of infectious bacteria – Larry McShane – New York Daily News

“The first-of-its-kind study showed the rodents carrying an average of two bacteria capable of causing gastrointestinal problems for humans and the Seoul hantavirus, which causes a potentially life-threatening fever and kidney failure.”

* New Genes = New Archaea? – Molly Sharlach – The Scientist

“The study, published today (October 15) in Nature, also suggests that genetic transfers from bacteria to archaea are at least five times more common than from archaea to bacteria.”

Bik’s Picks

“Epicenters” of resilience – Mary Lou Zoback – Science

“The 25th anniversary of the magnitude (M) 6.9 Loma Prieta earthquake that struck the San Francisco Bay Area on 17 October 1989 is a fitting time to examine what progress has been made in increasing community resilience to minimize seismic risk. “

Cells’ powerhouses were once energy parasites: Study upends current theories of how mitochondria began – Science Daily

“Parasitic bacteria were the first cousins of the mitochondria that power cells in animals and plants — and first acted as energy parasites in those cells before becoming beneficial, according to a new study”

How Did We Become a Society Suspicious of Science? – Keith M. Parsons – Huffington Post

“But something has been lost. Fifty years ago science was king. Science had respect; it was bigger than ideology. No longer. “

 

Biology Week: Bio-bodies Bake Off Public Vote – Physiological Society

“In the lead up to biology week we set you a challenge! We wanted you to celebrate the science of life by creating your own physiology bakes, and you didn’t let us down! ”

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Microbiome digest, October 15, 2014

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A seminar this Friday with Pat Schloss, but without HMP girl, aspartame and gut microbiome in a rat model, bacteria in arsenic contaminated soil, and inter-kingdom horizontal gene transfer.

Human oral microbiome

General Immune Status and Oral Microbiology in Patients with Different Forms of Periodontitis and Healthy Control Subjects – Jana Schmidt – PLOS ONE

“Subgingival plaque samples were taken from each individual and immediately cultivated for microbiological examination.”

Pregnancy and birth

* The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

“Ascending bacterial infection is implicated in about 40–50% of preterm births. “

Animal models of microbiome research

* Low-Dose Aspartame Consumption Differentially Affects Gut Microbiota-Host Metabolic Interactions in the Diet-Induced Obese Rat – Marie S. A. Palmnäs – PLOS ONE

“Serum metabolomics analysis revealed aspartame to be rapidly metabolized and to be associated with elevations in the short chain fatty acid propionate, a bacterial end product and highly gluconeogenic substrate, potentially explaining its negative affects on insulin tolerance. “

Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep – T. Ma – Journal of Animal Physiology and Animal Nutrition

“Two experiments were conducted to evaluate the effect of resveratrol on methanogenesis and microbial flora in Dorper × thin-tailed Han cross-bred ewes. “

Soil microbiome

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate – Romain L Barnard – ISME Journal

“Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event”

Surface binding and intracellular uptake of arsenic in bacteria isolated from arsenic contaminated site – Neha Vishnoi, Sonal Dixit, D.P. Singh – Ecological Engineering

“The present study deals with the surface binding and uptake of arsenic (As) in two bacterial strains (Bacillus subtilis and Paenibacillus macerans) isolated from the As contaminated soil.”

Water microbiome

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden – Michael Forth – ISME Journal

“We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. “

Food microbiology

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity in 22 home-made yoghurt samples was analyzed by pyrosequencing. “

CRISPRs, phages, viruses

In Hopes Of Fixing Faulty Genes, One Scientist Starts With The Basics – Joe Palca – NPR Morning Edition

“That’s certainly true for Jennifer Doudna. She hasn’t won a Nobel Prize, but many are whispering that she’s in line to win one for her work on something called CRISPR/Cas9 — a tool for editing genes.”

Bioinformatics and metagenomics

* Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria – Alejandro Caro-Quintero and Konstantinos T Konstantinidis – ISME Journal

“Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. “

* Origins of major archaeal clades correspond to gene acquisitions from bacteria –
Shijulal Nelson-Sathi – Nature

“To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.”

Evidence of Carbon Fixation Pathway in a Bacterium from Candidate Phylum SBR1093 Revealed with Genomic Analysis – Zhiping Wang – PLOS ONE

“A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. “

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil – Jinming Luo – PLOS ONE

“Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb.”

More microbiology

* The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota! – Judge Starling

“The molecular revelation based on orthologous ribosomal RNA sequences that prokaryotes are separable into two basic taxa—archaebacteria and eubacteria, and that these two taxa are approximately equidistant from eukaryotes, prompted Woese et al. (1990) to come up with a tripartite taxonomy of all life forms.”

Adhesion as a weapon in microbial competition – Jonas Schluter – ISME Journal

“We test the predictions of our model using the enteric pathogen Vibrio cholerae, which produces an extracellular matrix important for biofilm formation. “

Microbes in the news:

* Google Hangout on Friday: MicroSeminar: A new way of doing conferences – Pat Schloss

“You will not see HMP Girl, no quotes of specious statistics, no mention of obscure disease, and no venturing into the weeds of bioinformatics. I will be describing unpublished experiments from the lab where we have taken various sources of microorganisms and used them to colonize mice that lack their own microbiota.”

‘Grapes of Wrath’: Stomping out grape disease one vineyard at a time – Phys.org

“A Rochester Institute of Technology scientist and an RIT alumnus are close to completing the genetic blueprint, or microbiome, of grape crown gall tumor disease—the bane of vineyards worldwide. ”

Redefining Human: The Microbiome Documentary Series – Root House Studio – Kickstarter

“We know science documentaries can be painfully boring, so Redefining Human will use a variety of new techniques to turn this complex science into an informative and entertaining documentary series.”

What’s in my microbiome? – Richard Sprague

“To find out what’s in my microbiome now, I bought a $400 kit from the San Francisco company uBiome. “

Science, publishing and career

* Rise of the Rest: The Growing Impact of Non-Elite Journals – Anurag Acharya – Google / Arxiv

“Our analysis indicates that the number of top-1000 papers published in non-elite journals for the representative subject category went from 149 in 1995 to 245 in 2013, a growth of 64%.”

Review rewards – Welcome efforts are being made to recognize academics who give up their time to peer review – Nature Editorial

“A welcome movement is under way to publicly register and recognize the hitherto invisible efforts of referees.”

Overqualified or underqualified? – Carrie Arnold – Science

“As unemployment stretched from weeks into months, Milstein decided that her Ph.D. was working against her. “

 

Satire: Facebook Offers To Freeze Female Employee’s Newborn Children – The Onion

“Women deserve to have the option to postpone motherhood until they feel fully prepared, which is why Facebook will also cover the cryonic facility’s annual maintenance costs for as many years as our employees feel they need. “

Bik’s Picks

360-Degree View of the Tomato – Anna Azvolinsky – The Scientist

“Researchers have sequenced 360 varieties of the tomato plant to create a comprehensive map of the evolution of the fruit from its wild form to the modern varieties. “

Extinct giant kangaroos didn’t hop, they walked – Andy Coghlan – New Scientist

“They had faces like rabbits and some were 2 metres tall. But now it seems that an extinct giant kangaroo didn’t hop – it walked.“

 

Chimpanzees have favorite ‘tool set’ for hunting staple food of army ants – Science Daily

“New research shows that chimpanzees search for the right tools from a key plant species when preparing to ‘ant dip’ — a crafty technique enabling them to feast on army ants without getting bitten. “

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General microbiology and science, October 14, 2014

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A living review of multivariate techniques, spatial organizations of bacterial genomes, and metabolomics of wetlands, pigs, marine bacteria and free-living humans.

Bioinformatics

* A Guide to Statistical Analysis in Microbial Ecology: a community-focused, living review of multivariate data analyses – Pier Luigi Buttigieg – FEMS Microbiology Ecology

“we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists”

Techniques

New approaches to understanding the spatial organization of bacterial genomes – Tung BK Le, Michael T Laub – Current Opinion in Microbiology

“Here, we review the current arsenal of techniques used to query chromosome structure”

Development of Clamping Probe for Rare DNA Detection using Universal Primers – Meyong il Kim – E-FAS Journal

“In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis”

Metabolomics

Microbial community metabolic function in subsurface flow constructed wetlands of different designs – Mark Button – Ecological Engineering

“Microbial community function followed a clear gradient along the flow direction. Metabolic profiles were system specific (horizontal, vertical, and aerated).”

A high fat, high choleststerol diet leads to changes in metabolite patterns in pigs – a metabolomic study – Jianghao Sun – Food Chemistry

“Extracts of plasma, fecal and urine samples from pigs fed high fat or basal regular diets for 11 weeks were analyzed using ultra-high performance liquid chromatography with high-resolution mass spectrometry “

Free-living individuals – as in “not in prison”?
An NMR metabolomics approach reveals a combined-biomarkers model in a wine interventional trial with validation in free-living individuals of the PREDIMED study – Rosa Vázquez-Fresno – Metabolomics

A High-Resolution LC-MS-Based Secondary Metabolite Fingerprint Database of Marine Bacteria – Liang Lu – Nature Scientific Reports

“Till now, 1,430 bacterial strains spanning 168 known species collected from different marine environments were cultured and profiled. “

Viruses and phages

Ribonucleotide reductases reveal novel viral diversity and predict biological and ecological features of unknown marine viruses – Eric G. Sakowski – PNAS USA

“We identify ribonucleotide reductase (RNR) genes as superior markers of viral diversity. RNR genes are distributed over a broad range of viruses”

More microbiology

Strength in Diversity – Daniel J. Wolter, Lucas R. Hoffman – Cell Host & Microbe

“In this issue of Cell Host & Microbe, Hammer et al. (2014) show that distinct, slow-growing bacteria have better in vitro and in vivo growth and virulence when cocultured than in isolation. “

The Journal of Infectious Diseases has a special Issue on Polio: The Final Phase of Polio Eradication and Endgame Strategies for the Post-Eradication Era – Journal of Infectious Diseases

Science, publishing, career

Correcting the scientific record: An introduction to retractions – Bonnie Swoger – Scientific American

“Although the system is far from perfect, the retraction process is one of the ways in which the scientific literature corrects itself over time.”

 

Bik’s Picks

When Racism Was a Science – ‘Haunted Files: The Eugenics Record Office’ Recreates a Dark Time in a Laboratory’s Past – Joshua A. Krisch – New York Times

“In its heyday, the office was the premier scientific enterprise at Cold Spring Harbor. There, bigoted scientists applied rudimentary genetics to singling out supposedly superior races and degrading minorities. “

Paul Ryan: Science doesn’t get climate change – Jane C. Timm – MSNBC

“A full 97% of researchers taking a stance on climate change say it’s man-made, as do 97-98% of the most frequently-published climate scientists. But according to Wisconsin Rep. Paul Ryan, they’re all wrong.”

Get fish fry with a side of science at ‘Science of the Supper Club’ this Friday – Lindsay Christians – The Capital Times

“Science is everywhere, even at a Friday night fish fry. That’s the message of a new event this Friday called “Science of Supper Clubs,” part of the four-day Wisconsin Science Festival held at various venues around the state.”

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Microbiome digest, October 13, 2014

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Preterm infant gut microbiome, fecal transplants, microbes in space, and microbiome of 8 different fish species.

Pregnancy and birth

* Development of the preterm infant gut microbiome: a research priority – Maureen W Groer (Jack Gilbert lab) – Microbiome

“This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant.”

Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis – D. Schmiedel – Clinical Microbiology and Infection

“Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. “

The Role of Mycoplasma and Ureaplasma in Adverse Pregnancy Outcomes – Amy P. Murtha – Obstetrics and Gynecology Clinics of North America

* Impact Of Lifestyle On The Gut Microbiota Of Healthy Infants And Their Mothers – The Aladdin Birth Cohort – Helena Marell Hesla – FEMS Microbiology Ecology

“Samples collected from infants at ages six days, three weeks, two months and six months and from their mothers before and after delivery, respectively, were analyzed using 454-pyrosequencing.”

Human gut microbiome

* Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection – Ilan Youngster – JAMA

“Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5  for overall health and 4.5  for gastrointestinal-specific health on the day prior to FMT to 8 after FMT administration for both overall and gastrointestinal health (P = .001).”

* Impact of Experimental Hookworm Infection on the Human Gut Microbiota – Cinzia Cantacessi – Journal of Infectious Diseases

“We used 16S rRNA gene amplification and pyrosequencing to characterize, for the first time to our knowledge, the differences in composition and relative abundance of fecal microbial communities in human subjects prior to and following experimental infection with the blood-feeding intestinal hookworm, Necator americanus. “

Genomics of schizophrenia: time to consider the gut microbiome? – T G Dinan – Molecular Psychiatry

“To date, this vast quantity of DNA has been largely ignored in schizophrenia research.”

Animal microbiome

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits – Jinjin Li – Journal of Applied Microbiology

“The V1 to V3 regions of 16S rRNA gene were analyzed by highthroughput sequencing (454 platform) to compare the gut microbiota of different fish species. “

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured – Richard O’Rorke – Environmental Microbiology

“we collected 102 snail fecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. “

Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus) – Amber R Paulson – BMC Microbiology

“We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees.“

Bioreactor microbiome

Biofouling and Microbial Communities in Membrane Distillation and Reverse Osmosis – Katherine R. Zodrow – Environmental Science & Technology

“Phylogenetic analysis using next-generation sequencing of 16S ribosomal DNA showed significant shifts in the microbial communities. “

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture – Amy A Boaro – FEMS Microbiology Ecology

“16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment.”

Environmental microbiome

Effects of Bioavailable Heavy Metal Species, Arsenic, and Acid Drainage from Mine Tailings on a Microbial Community Sampled Along a Pollution Gradient in a Freshwater Ecosystem – Togwell A. Jackson – Geomicrobiology Journal

“Ribosomal ribonucleic acid, fatty acid, and phospholipid analyses, along with assays of CO2 production, denitrification, and enzyme activities, were performed to characterise the microflora; and environmental conditions were defined by various physicochemical analyses, including determination of bioavailable metal species. “

The role of macrobiota in structuring microbial communities along rocky shores – Catherine A Pfister​, Jack A Gilbert, Sean M Gibbons – PeerJ

“At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton.”

Microbes in (simulated) space

The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1 – Yi Sun – 40th COSPAR Scientific Assembly

“In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment.”

The viability of native microbial communities in martian environment (model) – Vorobyova, Elena – 40th COSPAR Scientific Assembly

“It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ.”

Food microbiology

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine – Joanita Sulaiman – Frontiers in Microbiology

“Whole genome shotgun (WGS) method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida.”

Transcriptomics/metagenomics

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities – Leyden Fernandez – BMC Genomics

“We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. “

Other microbiology

Inverse Correlation Between Helicobacter pylori Colonization and Obesity in a Cohort of Inner City Children – Hanh D. Vo – Helicobacter

“Our findings in a North American cohort are in agreement with studies from Asia and Europe suggesting that H. pylori infection decreases the prevalence of obesity in children.”

Microbes in the news

* Podcast: Your Home, Your Bacteria – Science Friday

“Jack Gilbert… is trying to develop a better understanding of the way people, bacteria, and the environment around them interact, from the kitchen floor to the greater Chicago area.”

Landmark Crohn’s Microbiome Study Yields Important Findings – David Wild – GastroEndoNews

“The association suggests that there is a potential link between the presence of these microbes and the serologic biomarkers, but that needs to be determined in future studies,” said Dr. Xavier, who presented the study at Digestive Disease Week 2014”

Is that how the capsules will look like? Good news: You can take your fecal transplants orally – Rachel Feltman – Washington Post

“In a study published Saturday in the Journal of the American Medical Association, researchers report that the same success rate can be reached by processing the healthy excrement into capsules and administering the pills by mouth.“

Probiotics on the brain: A growing number of scientists now believe that gut bacteria can influence mental health – Elizabeth Gehrman – Boston Globe

“Whenever someone says there’s an impossibility in medicine,” says Williams, “they end up being corrected in a few years.”

Unravelling the link between gut bacteria and horse health – University of Surrey

“Researchers at the University of Surrey, in collaboration with colleagues from Reading and Liverpool universities, have been awarded £100,000 funding by Petplan Charitable Trust… to create a laboratory model of the horse’s hindgut.”

The Second Brain: Gut Bacteria Control Human Behavior to Get the Best Nutrients – David Gutierrez – Epoch Times

“Bacteria within the gut are manipulative,” researcher Carlo Maley, PhD, said. “There is a diversity of interests represented in the microbiome, some aligned with our own dietary goals, and others not.”

Science, publishing, career

Sometimes My Job Seems Like a Secret – Amy Davidson – Speaking Of Research

“You are going to hell.” “You are a horrible person.” “We cannot be friends anymore.”

Sell yourself: Adding substance to your personal statement – Brian Rybarczyk – Science Careers at Science Magazine

“Obtaining feedback on your personal statement (or any piece of writing) can be intimidating, but feedback is essential for creating a polished and readable document.”

Bik’s Picks

Why Orange Juice Tastes Disgusting After You Brush Your Teeth: Finally, an answer – Sarah Fecht – Popular Science

“In a handy video, the American Chemical Society has explained why orange juice (and food in general) tastes like soap after you brush your teeth. “

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Microbiome Digest, October 9, 2014

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Human microbiome general

Advancing the Microbiome Research Community – Curtis Huttenhower – Cell

“We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. “

Human oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – K.J. Cross – Molecular Oral Microbiology

“The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins.”

Human skin microbiome

Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin – Elizabeth C. Murphy – Molecular Microbiology

“This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. “

Human gut microbiome

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders – N Tennoune – Translational Psychiatry

“Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH.”

Animal models of microbiome research

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs – Zhikai Zeng – Animal Science Journal

Soil microbiome

Poster presentation: Starting study of microbial genetics diversity in soils of mangrove preserved in sergipe – Karla Cristina Santos Freire – BMC Proceedings

“This paper proposes the characterization and evaluation of structures and diversity of microbial communities in the soil of mangroves in three conservation areas located in Sergipe.“

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession – Cheng Gao – New Phytologist

“We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing”

Metagenomics / Bioinformatics

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam – Juanjuan Chai – BMC Evolutionary Biology

“A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. “

More Microbiology

Halting harmful helminths – Karl F. Hoffmann, Paul J. Brindley, Matthew Berriman – Science

“More than 300 million people are infected each year with parasitic flatworms such as hydatid tapeworms and blood fluke schistosomes. “

Chromosome position effects on gene expression in Escherichia coli K-12 – Jack A. Bryant – Nucleic Acids Research

“Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. “

Microbes in the news

‘Good Poop’ Diet Is the Next Big Thing – Daniela Drake – The Daily Beast

“Now a new book, The Skinny Gut Diet, by nutritionist Brenda Watson, tracks the progress of people who follow a diet specifically designed to alter the gut microbiome. “

Another probiotic advantage: Bacteria protects against heavy metal poisoning – Jim Algar – Tech Times

“Probiotic bacteria found in yogurt can protect people from the effects of exposure to heavy metals, particularly in pregnant women and children, a Canadian study suggests.”

Science, publishing, career

The scientists who get credit for peer review – Richard Van Noorden – Nature

“Publons rewards researchers for putting their peer-review activity online. Nature spoke to the startup’s co-founder and two super-users.”

Meet the New Underclass: People With Ph.D.s in Science – Mark Strauss – iO9

“Once upon a time, newly-minted science Ph.D.s would get research jobs at a senior scientist’s laboratory, to train and hone the ideas they would explore at their own labs. But now the supply of post-doctoral students is outpacing demand, creating a new, hyper-educated underclass.”

Glut of postdoc researchers stirs quiet crisis in science –  Carolyn Y. Johnson – Boston Globe

Japan’s Missing Female Scientists – Jack Grove – Times Higher Education

“Too many female scientists are leaving Japan because they do not feel they can get ahead in its “male-dominated” society, a senior university leader has said.”

Bik’s Picks

Cave paintings change ideas about the origin of art – Pallab Ghosh – BBC

“Researchers tell the journal Nature that the Indonesian discovery transforms ideas about how humans first developed the ability to produce art.”

A timeline of a baby’s first hour – Laura Sanders – Science News

Fired science teacher did not have state license – 9 News

“The teacher fired after his science experiment injured four students, one seriously, did not have a valid Colorado teacher’s license.”

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Microbiome digest, October 8, 2014

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Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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General microbiology and science digest, October 7, 2014

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Transmission of Staph aureus in the hospital, a new assembler tool, metabolomics of the human gut microbiome, and a polio virus spill in Belgium.

More Microbes

Absence of Patient-to-Patient Intrahospital Transmission of Staphylococcus aureus as Determined by Whole-Genome Sequencing – S. Wesley Long – mBio

“To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. “

Bioinformatics

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs – Matthew Scholz, Chien-Chi Lo & Patrick S. G. Chain – Nature Scientific Reports

“MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. “

Inferring phylogenies of evolving sequences without multiple sequence alignment – Cheong Xin Chan – Nature Scientific Reports

“Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. “

Gut Check: Exploring Your Microbiome – Coursera / University of Colorado Boulder

“Join us on a guided tour of the human gut and its microscopic inhabitants.”

Metabolomics

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Microbes in the news

* Petri Dish: The third branch of life – David Woodland – Summit Daily

“In addition to being an interesting branch on the tree of life, archaebacteria have turned out to be an incredibly valuable source of new products for science and industry. “

Pharmaceutical Giant GlaxoSmithKline “Accidentally” Released 45 Liters of Concentrated Live Polio Virus in the Environment – Global Research

“As reported to ECDC by Belgian authorities, on 2 September 2014, following a human error, 45 litres of concentrated live polio virus solution were released into the environment by the pharmaceutical company, GlaxoSmithKline (GSK), in Rixensart city, Belgium.”

Science, publishing and career

* Science is innate! (behind a paywall, even at Stanford) – Jack A Gilbert – Genome Biology

“….when I am asked, as I often am, about how my research findings have influenced my day-to-day activities, I like to take a step back and think about what it means to be a scientist.”

Why I have taken a leave of absence from Science: to protest the abrupt firing of 4 colleagues – Michael Balter – Letter to Science

“Thus it is particularly painful and sad for me to tell you that I will be taking a three-month leave of absence in protest of recent events at Science and within its publishing organization, the American Association for the Advancement of Science (AAAS).
“

Bik’s Picks

Killer whales learn to communicate like dolphins – Science Daily

“…killer whales can engage in cross-species vocal learning: when socialized with bottlenose dolphins, they shifted the sounds they made to more closely match their social partners.”

NASA selects astrobiologists to study life origins and extraterrestrial possibilities – Jim Algar – Tech Times

“NASA announced 5-year grants adding up to nearly $50 million for seven research groups across the U .S. to study life in the universe and its origins, distribution, evolution and future.”

The most passive aggressive acknowledgement ever – BioDataGanache – SciEasterEggs

“The authors in this paper put some serious time in on this sucker, and they wanted to make a statement about it.”

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General microbiology and science digest, October 6, 2014

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Phages to reduce biofilms or monitor virus outbreaks, binning metagenomic reads, lots of microbes in the news. In Bik’s Picks, we have the 2014 Nobel Prize for Medicine and a giant ant nest.

 

More Microbes

Combined Use of Bacteriophage K and a Novel Bacteriophage To Reduce Staphylococcus aureus Biofilm Formation – D. R. Alves – Applied and Environmental Microbiology

“DRA88 was mixed with phage K to produce a high-titer mixture that showed strong lytic activity against a wide range of S. aureus isolates, including representatives of the major international MRSA clones and coagulase-negative Staphylococcus. “

Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks – Maria Hellmér – Applied and Environmental Microbiology

“ In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. “

Bioinformatics

New software aims to improve sorting the microbiome – The Cherry Creek News

“MaxBin automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads,” says Singer, a chemist who also holds an appointment with Berkeley Lab’s Earth Sciences Division. “

Microbes in the news

* King’s launches British Gut – King’s College London

“British Gut – the UK’s largest open-source science project to understand the microbial diversity of the human gut – has been launched today by the Department of Twin Research at King’s College London, in collaboration with American Gut.”

Pay attention to your gut bacteria – Charles Wallace – Financial Times

“A number of organisations, such as Mr Leach’s own American Gut project and the commercial venture uBiome, offer an analysis of the bacteria in your gut for about $100. “

Home sweet microbiome – By Scott LaFee – UT San Diego

“The University of Chicago recently published findings from its Home Microbiome Project, which surveyed the domiciles of seven families: 18 people, three dogs and one cat.”

Medical superbugs: Antibiotic-resistant bacteria carried by more than a third of nursing home residents, study – ABC Australia

“Scientists from Monash University swabbed more than a 100 residents from four high-care facilities across the city.”

Special bacteria, 13000 cleaners to clean Dhaka – Rezaul Hoque – BDNews

“This special kind of microorganism will be sprayed on waste dumps. The spray has been developed in Thailand. We have introduced it here in Bangladesh with the aid of a Malaysian company.””

Yogurt bacteria could replace colonoscopies for cancer detection – Billy Steele – EnGadget

“MIT professor Sangeeta Bhatia is working on engineered bacteria that detects colorectal cancer. After the nanoparticles pass through the digestive system, a urine sample shows results on a reactive paper — similar to that of a pregnancy test.”

Science and Publishing

Adjudicating “misbehavior”: how can scientists respond when they don’t get fair credit? –  Janet D. Stemwedel – Scientific American

“Denying someone of fair credit for the contribution they made to a piece of research is not a good thing. But who can you turn to if someone does it to you? “

Twitter’s science stars, the sequel – John Travis – Science

“We listed. You tweeted (often in outrage). We listened (mostly). And now we’re doubling down on our recent list of Twitter’s 50 most popular researchers with a revision that names 100 of the most followed scientists on the social media platform. “

Bik’s Picks

2014 Nobel Prize in Physiology or Medicine: Cells that constitute a positioning system in the brain – Science Daily

“The 2014 Nobel Prize in Physiology or Medicine has been awarded to John O´Keefe, May-Britt Moser and Edvard I. Moser for their discoveries of cells that constitute a positioning system in the brain.”

Concrete Cast of Ant Nest Reveals Huge Underground Metropolis – Lisa Winter – IFL Science

“Through a process that took a few months, researchers made a cast of an anthill by pumping it full of concrete, allowing it to cure and dry, then excavating it out to explore the intricacies of the ant civilization. “

Tall tale: scientists unravel the genetics of human height – Will Dunham – Daily Mail

“Researchers on Sunday unveiled what they called the biggest such study to date, analyzing genome data from more than a quarter million people to identify nearly 700 genetic variants and more than 400 genome regions relating to height.”

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Microbiome Digest, October 3, 2014

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Antibiotics in the first 24 months of life associated with obesity, Giant Pandas are no cul-de-sac, and microbiome and inflammatory disease. And lots of weekend reads!

Pregnancy and birth

Association of Antibiotics in Infancy With Early Childhood Obesity – L. Charles Bailey – JAMA Pediatrics

“Cumulative exposure to antibiotics was associated with later obesity …; this effect was stronger for broad-spectrum antibiotics”

Human gut microbiome

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome – Jonna Jalanka-Tuovinen – Gut

“Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups”

Animal models of microbiome research

Dietary modulation of the microbiome affects autoinflammatory disease – John R. Lukens – Nature

“Here we show that the intestinal microbiota of diseased Pstpip2cmo mice was characterized by an outgrowth of Prevotella. “

Mammal microbiome

Giant pandas are not an evolutionary cul-de-sac: Evidence from multidisciplinary research
Fuwen Wei – Molecular Biology and Evolution

“The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological and genetic adaptations and co-adaptation of gut microbiota.”

Plant microbiome

Multi-symbiotic systems: functional implications of the coexistence of grass–endophyte and legume–rhizobia symbioses – Pablo A. García Parisi – Oikos

“After five months, we quantified the number of nodules in Trifolium roots, shoot biomass of both plant species, and the contribution of atmospheric nitrogen fixation vs. soil nitrogen uptake to above ground nitrogen in each plant species. “

Microbes in the news

Young companies, big ideas – The 2014 edition of the CNN 10: Startups – CNN

“Her doubts were assuaged when supporters donated $350,000 to help launch her startup, uBiome. Now, two years later, uBiome is exploring an emerging field of human biology while giving users a glimpse into how their bodies work.”

No women, unfortunately! And they did not accept my application to be a judge either. MO BIO Laboratories, Inc. announces Microbiome Awards winners – PR NewsWire

“MO BIO Laboratories, Inc. is proud to announce the winners of the MO BIO Microbiome Awards, which provide young, extraordinary scientists with funding and recognition to carry out scientific work in the field of microbiome research.”

Super-bacteria are growing in space … and we’re the ones breeding them – Meera Senthilingam – CNN

“You might think of space as a germ-free environment, but microbes can be carried to space inside human gut flora as well as in food and water and once up there, can be expelled by humans in their breath.”

There’s a simple way to stop the spread of antibiotic-resistant bacteria – Melinda Mary Pettigrew – Washington Post

“The issue boils down to this: we use too many antibiotics. Studies show that up to half of all antibiotics are prescribed unnecessarily.”

Across Indian zoos, rat pee spreading bacteria, killing big cats: Scientists – Priyangi Agarwal – The Times of India

“The leptospirosis bacteria, found in rodent urine, makes its way into blood samples of zoo animals and causes higher morbidity and mortality, scientists at the Indian Veterinary Research Institute (IVRI) in Bareilly have found. “

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever. The hope is they will multiply, breed and become the majority of mosquitoes, thus reducing cases of the disease.“

Science, Publishing, and Career

Young, Brilliant and Underfunded – Andy Harris – New York Times

“The bulk of that money goes to researchers who are in many cases esteemed in their fields — but also, in many cases, beyond the age when most scientists make their most important contributions to their fields.”

Why women leave tech: It’s the culture, not because ‘math is hard’ – Kieran Snyder – Fortune

“Stories from 716 women who left tech show that the industry’s culture is the primary culprit, not any issues related to science education.”

Satire: Tips For Working With A Lab Partner – FakeScience

Bik’s Picks

Is this the end of autumn as we know it? – Stephanie Pappas – BBC Earth

“The study of the basic triggers of autumnal leaf changes, never mind the impact of climate change on these, is still in its infancy in part because scientists have traditionally focused their attentions on the seasonal changes in March and April than those later in the year.”

The Incredible Rubber Glove – Olga Khazan – The Atlantic

“Basic protective gear was revolutionary for 19th-century medicine, and health workers trying to stop Ebola are recognizing its importance all over again.”

This Is Why Your Voice Sounds So Frickin’ Weird To You – Macrina Cooper-White – The Huffington Post

“Have you ever listened to a recording of your own voice and thought, “Whoa. Do I really sound like that?” Well, it’s time to face the music. You really do.”

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Microbiome digest, September 24, 2014

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Today we will learn how to feed shit to flies, the gut microbes of Mexican monkeys, and soil microbes and climate change.

Human microbiome general

Microbes Central to Human Reproduction – Gregor Reid – American Journal of Reproductive Immunology

“A meeting of the International Scientific Association for Probiotics and Prebiotics held in Aberdeen, Scotland (June 2014), presented new views and challenged established concepts on the role of microbes in reproduction and health of the mother and infant. “

Mammal microbiome

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild, black howler monkeys (Alouatta pigra) – Katherine R. Amato – American Journal of Physical Anthropology

“..we examined differences in activity budget, diet, and the gut microbial community among adult male .., adult female .., and juvenile .. wild black howler monkeys (Alouatta pigra) across a ten-month period in Palenque National Park, Mexico “

Soil microbiome

Incorporating Soil Microbes in Climate Change Models – Joe Turner – The Scientist

“Without a solid understanding of how the soil microbiome contributes to atmospheric carbon, researchers are struggling to determine whether dirt-dwelling bacteria could impact—and be impacted by—climate change.”

Metabolomics

Metabolomic profiles and childhood obesity – Wei Perng – Obesity

“Principal components analysis was used to consolidate 345 metabolites into 18 factors and identified two that differed between obese .. and lean children “

Microbes in the news

A beginners guide to feeding shit to flies – Edan Foley – Frontiers blog

“The title pretty much sums this one up”

Meet my Microbiome – An Introduction to the bacterial zoo hidden in my colon – Edan Foley – Frontiers blog

“As detailed in the previous blog post, I fed a solution of my feces to axenic flies this summer.“

Giving Chickens Bacteria … To Keep Them Antibiotic-Free – Dan Charles – NPR The Salt

“Poultry companies are turning to probiotics as an alternative to antibiotics, which have become increasingly controversial.”

 Three Girls Won The Google Science Fair With A Bacteria-Based Plan To Solve The Food Crisis – Jessica Orwig – Business Insider

“Three young girls won the Google science fair on September 22 with their innovative way to feed the world: treat plants with bacteria to help farmers grow more food, faster”

Honeybees healing bacteria: The antimicrobial properties of honey – Jeremiah Yarmie – The Manitoban

“A research group from Lund University in Sweden has been investigating bacteria found in the honey-producing stomach of bees. “

Science and publishing

The Top Eleven Ways to Tell that a Journal is Fake – Shaili Jain – PLOS Blogs

“If you have ever published a scholarly paper, your email inbox is probably peppered with invitations to submit papers to new journals with plausible-sounding names. “

Women in Science

When words fail: women, science, and women-in-science – Jacquelyn Gill – The Contemplative Mammoth

“I don’t want to write about women in science today. I want to write about glaciers, or passenger pigeons, or the way the tilt of the earth is making the squirrels outside my window stash acorns”

Gender balance among University Research Fellows – Paul Nurse – UK Royal Society

“It was a great day for the 43 scientists who were awarded grants but I, like many Fellows, was personally very disappointed to see that only two of them were women.”

Bik’s Picks

Fossil Dolphin Otekaikea marplesi (Latest Oligocene, New Zealand) Expands the Morphological and Taxonomic Diversity of Oligocene Cetaceans – Yoshihiro Tanaka – PLOS ONE

“The New Zealand fossil dolphin “Prosqualodon” marplesi (latest Oligocene, ≥23.9 Ma) is here identified as a crown odontocete that represents a new genus, Otekaikea”

Review: The design and function of birds’ nests – Mark C. Mainwaring – Ecology and Evolution

“the design of birds’ nests is far more sophisticated than previously realized and that nests are multifunctional structures that have important fitness consequences for the builder/s.”

False memories could be a side-effect of human ability to learn rules – Science Daily

“New research suggests that individuals who are particularly good at learning rules and classifying objects by common properties are also particularly prone to false memory illusions.”

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