Microbiome digest, August 21, 2014

Ground squirrels, scallops, hypersaline water, and dead bodies.

Postmortem human microbiome

* Microbial communities associated with human decomposition and their potential use as postmortem clocks – Sheree J. Finley – International Journal of Legal Medicine

“the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.”

* Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota – Timothy J Stevenson – Applied and Environmental Microbiology

“We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (Urocitellus parryii) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation).”

Invertebrate microbiome

* IMMR abstract: Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing – Aide Lasa – Frontiers in Microbiology

“In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. “

Soil microbiome

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons – Viviane D. Rodrigues – Antonie van Leeuwenhoek

“In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. “

* Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil – Yao Pan – FEMS Microbiology Ecology

“Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. “

Water microbiome

The Santa Pola saltern as a model for studying the microbiota of hypersaline environments – Antonio Ventosa – Extremophiles

“Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. “

Food microbiology

Book: Microorganisms and Fermentation of Traditional Foods – Ramesh C. Ray, Montet Didier – CRC Press

Fungi

Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR – Samart Dorn-In – FEMS Microbiology Letters

“A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. “

 

From Dandruff to Deep-Sea Vents: Malassezia-like Fungi Are Ecologically Hyper-diverse – Anthony Amend – PLOS Pathogens

“As the dominant component of the mycobiota on human skin —both healthy and diseased [2] —the genus Malassezia has received a fair amount of attention. “

Microbes in the news

The Birth of Pathogens: How Bacteria Become Deadly – Brian Stallard – Nature World News

“Two new studies have revealed two very different ways bothersome bacteria strains can suddenly become deadly, evolving into difficult-to-rid pathogens that can threaten entire populations.” – belongs to a PNAS paper on Salmonella enterica, and a Nature Communications paper on Group B Streptococcus.

Bacteria colonies removed from Savannah River Site using special vacuum – Meg Mirshak – The Augusta Chronicle

“Scientists studied samples and determined the white, stringy “cobwebs” were made up of a broad variety of bacteria and a few types of microbes.”

ASU experts follow gut reaction in autism treatment study – Arizona State University

“A new study approved by the U.S. Food and Drug Administration and led by Arizona State University will examine a novel treatment – called fecal microbiota transplant (FMT) – for GI problems in children with autism.”

Science and career

Ailing academia needs culture change – Viviane Callier, Nathan L. Vanderford – Science

“The research enterprise has become unsustainable in its current form. Research funding levels/mechanisms, the peer-review process, and the methods of training Ph.D.’s are flawed, and these issues are crippling the pipeline of future, successful academic researchers”

Science Media Beset with Gender Gaps – By Curtis Brainard – Scientific American

“One antidote, summit participants suggested, would be having more reporters abide by the seven-part Finkbeiner Test”

Bik’s Picks

* Why does asparagus make our urine smell? – Claudia Hammond – BBC Future

“After eating asparagus, some people can detect a strange smell, while others claim not to notice a thing. What’s going on?”

Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery – Danielle L. Dixson – Science

“We show that juveniles of both corals and fishes are repelled by chemical cues from fished, seaweed-dominated reefs but attracted to cues from coral-dominated areas where fishing is prohibited. “

Scientists discover how lizards regrow tails – John von Radowitz – The Independent

“Researchers have identified a genetic programme that triggers new tissue growth after a lizard sacrifices its tail to escape a predator.”

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Microbiome digest, August 20, 2014

Ocular microbiome, life under ice, and gut microbiome and behavior.

Human ocular microbiome

Assessment of ocular surface microbiota in keratoconus patients – a pilot study – M Gajecka – Acta Ophthalmologica

“Culture-based microbiology methods are used in the investigation to preliminary examine the OS microbiota. Simultaneously, microbial genetic material is extracted from the eye swabs for further qualitative and quantitative analyzes using molecular biology methods (real-time PCR, NGS).”

Microbial detection in clinical samples

Elevated Levels of Circulating DNA in Cardiovascular Disease Patients: Metagenomic Profiling of Microbiome in the Circulation – Vasudevan Dinakaran – PLOS ONE

“This work was aimed to study the circulating human microbiome in CVD patients and healthy subjects.”

Animal models of microbiome

A Possible Link between Food and Mood: Dietary Impact on Gut Microbiota and Behavior in BALB/c Mice – Bettina Pyndt Jørgensen – PLOS ONE

“Behavioral changes were accompanied by a significant change in GM composition of mice fed a high-fat diet” “Denaturation gradient gel electrophoresis (DGGE) was used to investigate differences in the composition of the GM.”

Mammalian microbiome

Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus – Jana Sachsenröder – Journal of General Virology

“Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids.”

Water microbiome

A microbial ecosystem beneath the West Antarctic ice sheet – Brent C. Christner – Nature

“Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. “

See also: Lakes under the ice: Antarctica’s secret garden – Douglas Fox – Nature

“Samples from a lake hidden under 800 metres of ice contain thousands of microbes and hint at vast ecosystems yet to be discovered.”

Bioinformatics

A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis – Liviu P. Dinu – PLOS ONE

“This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. “

Viruses and phages (see also the rat/rotavirus paper above)

Unveiling viral–host interactions within the ‘microbial dark matter’ – Manuel Martínez-García – Nature Communications

“Using this method, we pinpoint viruses infecting the ubiquitous hyperhalophilic Nanohaloarchaeota, included in the so-called ‘microbial dark matter’ (the uncultured fraction of the microbial world).”

Microbes in the news

Archiving: Don’t let microbial samples perish – Noah Fierer and Craig Cary – Nature

“Microbial ecologists must coordinate to archive sample collections and genetic material.”

Microbiology: Microbiome science needs a healthy dose of scepticism – William P. Hanage – Nature

“To guard against hype, those interpreting research on the body’s microscopic communities should ask five questions”

Science, publishing and career

Editorial: Finding the root – The NIH is right to investigate whether bias makes grant awards unfair – Nature

“The idea that scientists who volunteer time and energy to review NIH grants could be biased against qualified minority researchers is a tough pill to swallow. “

Today’s YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015 – Jonathan Eisen – The Tree of Life

Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg. “

 

Equally productive women are tenured less -Beryl Lieff Benderly – Science

“Women received tenure less often than men with equal productivity in three disciplines studied by Kate Weisshaar, a Ph.D. student in sociology at Stanford University.”

Bik’s Picks

Solar energy that doesn’t block the view – Science Daily

“Researchers have developed a new type of solar concentrator that when placed over a window creates solar energy while allowing people to actually see through the window. “

If Seals Hadn’t Introduced Tuberculosis To The New World, Europeans Would Have – Science 2.0

A new study documents that again, finding isolated Mycobacterium pinnipedii from skeletons found in Peru which are at least 1000 years old. The pathogen is a relative of the TB bacterium that affects seals, so it likely that seals carried the pathogens from Africa to the Peruvian coast.”

Which Hot New Lab Coat Should You Buy This Season? – Fake Science

“We’ve found the hottest coats from Paris, Milan, and Batavia, Illinois and put them into our patented quiz. Take it and find out which lab coat will have you steaming up the beakers!”

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Microbiome digest, August 15, 2014

Today we got donkey, goat, and camel milk, deodorants, kitten microbiomes, and coffee as a new mouth rinse.

Pregnancy and birth

Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study – Mohamed Ben Said – Early Human Development

“Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. “

Human oral microbiome

Antibacterial effect of coffee: calcium concentration in a culture containing teeth/biofilm exposed to Coffea Canephora aqueous extract – N. Meckelburg – Letters in Applied Microbiology

“This study revealed an inhibitory action of Coffea canephora against dental biofilm. This coffee species caused bacterial lysis and consequent release of calcium into the medium.”

Human gut microbiome

Review: Exploring gut microbes in Human health and disease: pushing the envelope
Jun Sun, Eugene B. Chang – Genes & Diseases

“In this review and commentary, we highlight recent progress in our understanding of the intestinal microbiome in the context of health and diseases, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.”

Review: Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology – Alexander Khoruts, Alexa R. Weingarden – Immunology Letters

“Mechanistic understanding will be required in development of next generation microbiota therapeutics, which may include FMT or defined microbial consortia.”

Gut Bacteria May Play a Role in Autism – Melinda Wenner Moyer – Scientific American

“One open question is whether these microbial differences drive the development of the condition or are instead a consequence of it. “

Skin microbiome

Deodorants and antiperspirants affect the axillary bacterial community – Chris Callewaert — Archives of Dermatological Research

“The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics.”

Goat and Ass Milk microbiome

Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity – Elizabeth A. McInnis – Food Microbiology

“Milk from transgenic goats containing lysozyme had a similar microbiota over time.”

Fasscinating stuff: Cleopatra took daily baths in assmilk to keep her skin wrinklefree. Maybe lactic acid bacteria were her secret?  Biotyping of cultivable lactic acid bacteria isolated from donkey milk – D. Carminati – Letters in Applied Microbiology

“The large amounts of antimicrobial components and defence factors present in donkey’s milk provide protection from microbial infections and distinguish donkey’s milk from the milks of other mammals”

The Kitten Microbiome Project

“Keeping track of the cutest, fluffiest microbiome project around”

Insect microbiome

Microbial impacts on insect evolutionary diversification: From patterns to mechanisms
Fabrice Vavre, Natacha Kremer – Current Opinion in Insect Science

“Symbiosis can favor rapid shifts in host phenotypic traits, particularly through the contribution of symbionts to the host’s physiology.”

How resident microbes modulate ecologically-important traits of insects
Kerry M. Oliver, Adam J. Martinez – Current Opinion in Insect Science

“In addition to their better-known roles in nutrient provisioning and degrading plant polymers, there is emerging evidence that microorganisms also aid herbivores in countering plant defenses. “

Metabolomics

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking – Kalai Vanii Jayaseelan and Christoph Steinbeck – BMC Bioinformatics

“In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process.”

Phages and viruses

Bacteriophage as effective decolonising agent for elimination of MRSA from anterior nares of BALB/c mice – Sanjay Chhibber – BMC Microbiology

“Phage MR-10, given along with mupirocin showed an additive effect and the combination was able to effectively eradicate the colonising MRSA population from the nares of mice by day 5.”

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target – Sabin Mulepati, Annie Héroux, Scott Bailey – Science

“The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. “

Bik’s Picks – weekend edition

15 Real-Life Scientists Share Their Favorite Science Fiction Books, Movies – Jacqueline Howard – Huffington Post

“There’s a big difference between science and science fiction, but there’s abundant evidence to suggest that sci-fi books and movies can spark a lifelong interest in science.”

After donkey and goat milk, this one was only appropriate: A Nice Tall Glass of Camel’s Milk – Olga Khazan – The Atlantic

“An oasis in the dromedary-dairy desert?”

Male Mathematicians Agree That Fields Medal Gender Balance Is Now OK – The Allium

“Now that a woman has won the fields medal, there is true and genuine equality and there is no need to worry any more about it.”

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General microbiology and science, August 14

A metabolic map of Faecalibacterium prausnitzii, bacteria injections to cure cancer, a researcher smuggling live bacteria in a lunchbox,  and a scientist in trouble for posting a PhD thesis.

Metabolomics

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe – Almut Heinken – Journal of Bacteriology

“In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms.”

Transcriptomics

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes – Joseph T. Wade & David C. Grainger – Nature Reviews Microbiology

“In this Opinion article, we discuss our current understanding of pervasive transcription, its genetic origin and its regulation. “

More microbiology

Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses
Nicholas J. Roberts – Science Translational Medicine

“On the basis of these encouraging results, we treated a human patient who had an advanced leiomyosarcoma with an intratumoral injection of C. novyi-NT spores. This treatment reduced the tumor within and surrounding the bone. “

Canadian ex-researcher pleads guilty in attempted bacteria-smuggling case – Lee-Anne Goodman

“With his wife in the passenger seat, they discovered in his suitcase 17 vials of live Brucella — contained in a block of ice and swathed in bubble wrap in a children’s lunch bag — and a substantial quantity of goat’s blood.”

Techniques

Preprint: Swabs to Genomes: A Comprehensive Workflow – David A Coil – PeerJ

“The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome”

Accuracy of Next Generation Sequencing Platforms – Edward J Fox – Next Generation: Sequencing & Applications

“The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates”

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences — Pablo Yarza – Nature Reviews Microbiology

“Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.”

Science, Publishing, Career

Financial costs and personal consequences of research misconduct resulting in retracted publications – Andrew M Stern, Arturo Casadevall, R Grant Steen, Ferric C Fang – eLife

“We found that papers retracted due to misconduct accounted for approximately $58 million in direct funding by the NIH between 1992 and 2012, less than 1% of the NIH budget over this period. ”

Student may be jailed for posting scientist’s thesis on web – David Reay – Nature News Blog

“Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network. Diego Gómez Hoyos posted the 2006 work, about amphibian taxonomy, on Scribd in 2011.

Study: Uncivil work environment pushing women out of the engineering field – Brigid Schulte – Washington Post

“a new National Science Foundation report released on Saturday about why so few women go into engineering, or stay in the field, highlights a key reason: a workplace culture of incivility toward women.”

Science of inclusion – Holly McDede – SFBG.com

“As Big Tech struggles with diversity, women find support and fellowship in the biotech industry.”

Bik’s Picks

Pour on the Salt? New Research Suggests More Is OK – Judy Silverman and Lisa Tolin – NBC News

“New research suggests that healthy people can eat about twice the amount of salt that’s currently recommended — or about as much as most people consume anyway. “

At Harvard, tiny robots ‘swarm’ into shape – Carolyn Y. Johnson – Boston Globe

When Harvard scientist Michael Rubenstein walks into the laboratory in the morning, he is greeted with a scene somewhere between a disco and the opening of a science fiction movie about a robot apocalypse. A constellation of LED lights blinks in the darkness — the electronic heartbeat of his 1,024-robot horde. They are ready to do his bidding.”

Newborns’ genetic code sends infection distress signal – Science Daily

“Babies suffering from life-threatening bacterial infections such as sepsis could benefit from improved treatment, thanks to a ground-breaking study. “

[hr]

General microbiology and science, August 12, 2014

Prokaryotic Essential Genes, 10 years of next-generation sequencing, a short podcast on the Hadza microbiome, and Ebola.

 

Metagenomics

Protein Localization Analysis of Essential Genes in Prokaryotes – Chong Peng & Feng Gao – Nature Scientific Reports

“Here, a comprehensive protein localization analysis of essential genes in 27 prokaryotes including 24 bacteria, 2 mycoplasmas and 1 archaeon has been performed. “

Techniques

Review: Ten years of next-generation sequencing technology – Erwin L. van Dijk – Trends in Genetics

“Here we provide an overview of the evolution of NGS and discuss the most significant improvements in sequencing technologies and library preparation protocols.”

More Microbiology

CISAC experts tackle public health & policy questions on Ebola – Beth Duff-Brown – Stanford University

“We ask CISAC biosecurity experts to answer several questions about Ebola and the public health concerns and policy implications. “

Rapid and reagentless detection of microbial contamination within meat utilizing a smartphone-based biosensor – Pei-Shih Liang – Nature Scientific Reports

“An 880 nm near infrared LED was irradiated perpendicular to the surface of ground beef, and the scatter signals at various angles were evaluated utilizing the gyro sensor and the digital camera of a smartphone.”

Academic Minute Podcast: Microbiota of the Hadza Tribe – Alyssa Crittenden, UNLV

“My colleagues and I have, for the first time, characterized the hunter-gatherer gut microbiome– working with a population of foragers in East Africa, the Hadza of Tanzania.”

Women in Science

Why are the media so obsessed with female scientists’ appearance? –  Alice Bell – The Guardian

“Yet another profile of Susan Greenfield feels the need to dwell on her ‘long, youthfully blond hair’. Why are the media so rubbish at covering women in science?”

Bik’s Picks

Under- and over-water halves of Gyrinidae beetle eyes harbor different corneal nanocoatings providing adaptation to the water and air environments – Artem Blagodatski – Nature Scientific Reports

“In this study we analyze the micro- and nanostructure of the split eyes of two Gyrinidae beetles genera, Gyrinus and Orectochilus. “

Antarctic midge’s genome is smallest in insects to date: Bare-bones genome is adaptation to deep freeze – Science Daily

“Scientists who sequenced the genome of the Antarctic midge suspect the genome’s small size — the smallest in insects described to date — can probably be explained by the midge’s adaptation to its extreme living environment.”

[hr]

General microbiology and science, August 11, 2014

Single cell genomics, metagenomics and bioinformatics, primers for protozoa detection, and Bik’s Picks.
Microbial detection

Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data – Allyson L Byrd – BMC Bioinformatics

“Clinical PathoScope is the only pathogen identification method currently available that can identify multiple pathogens from mixed samples and distinguish between very closely related species and strains in samples with very few reads per pathogen. “

Metagenomics

Recent advances in genomic DNA sequencing of microbial species from single cells – Roger S. Lasken & Jeffrey S. McLean – Nature Review Genetics

“With the advent of single-cell sequencing, genomes of uncultivated species are rapidly filling in unsequenced branches of the microbial phylogenetic tree.”

Employing whole genome mapping for optimal de novo assembly of bacterial genomes
Basil Britto Xavier – BMC Research Notes

“Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. “

Protozoal components of microbiome

Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa – Suzanne L. Ishaq and André-Denis G. Wright – Applied and Environmental Microbiology

“PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29.”

Microbes in the news

What Causes Antibiotic Resistance? Video Answers This In Awesome Animation – Kevin Wu – Inquisitr.com

“Kevin Wu details the evolution of this problem that present a big challenge for the future of medicine in this amazing animated video uploaded on YouTube.”

Women in Science

Harassment in Science, Replicated – Christie Aschwanden – The New York Times

“The findings are depressingly similar to the data some colleagues and I collected this year from an online questionnaire sent to science writers. “

Bik’s Picks

Comparative population genomics reveals the domestication history of the peach (Prunus persica) and human influences on perennial fruit crops – Ke Cao – Genome Biology

“We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach.”

Grizzly bears master healthy obesity – Meghan Rosen – Science News

“Though the animals beef up before hibernating, they may avoid diabetes by tweaking signals in fat cells, researchers report in the Aug. 5 Cell Metabolism.”

Natural light in office boosts health – Science Daily

“Office workers with more natural light exposure at the office had longer sleep duration, better sleep quality, more physical activity and better quality of life compared to office workers with less light exposure in the workplace, a study shows.”

[hr]

General microbiology and science, July 21

Pyrosequencing reproducibility, Microbes in the News, plague, tatoos, and Dr. Bik’s Picks.

Techniques

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities – Aibin Zhan – Methods in Ecology and Evolution

“Here we evaluated reproducibility by analyzing 454 pyrosequenced biological replicates of two complex plankton communities collected from one freshwater port and one marine port. We also tested whether reproducibility potentially influences biodiversity estimates, notably α- and β-diversity.”

Microbial Ecology / Bioinformatics

Synthetic microbial consortia: from systematic analysis to construction and applications
Hao Song – Chem Soc Rev

“Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell–cell interactions in synthetic microbial consortia. “

Microbes in the News

Be nice to your germs, they keep you alive – Nicky Phillips – Sydney Morning Herald

“Without a well-balanced community of these microscopic critters we would not survive, says Holmes. ‘‘We shouldn’t view them as a separate thing, we should view them as a part of us,’’ he says.”

Desert Rat Relies on Microbes To Detoxify Its Deadly Meals – Ed Yong – National Geographic

“When Kevin Kohl learned about the woodrat, he wondered if bacteria in the rodent’s gut might help it to tolerate its otherwise lethal diet… The idea made sense. Kohl just needed to test it.”

Four Cases of Life-Threatening Plague Found in Colorado –  Sonali Basak and Jennifer Oldham – Bloomberg.com

“Three more plague cases were found in Colorado, a week after the first infection of the deadliest form of the disease was reported in the state in a decade.”

Tattoo Inks, Needles Recalled Due To Bacterial Contamination
Kristen McConnaughey – SiouxLandMatters.com

“”Extreme risks. I mean we’re talking death. There’s things out there that can kill you,” says Scott Alphawolf Davis, a tattoo artist.”

Science and career

Happy Thoughts May Help Postdocs Handle Stress – Rachel Bernstein – Science Careers

“It could be something as simple as watching a funny TV show or going out for a walk or jog. These little things really add up.”

Women in Science

Why is STEM Still a 4-Letter Word for Women? 7 Leaders Weigh In – Ravishly

“Women receive fewer invitations to professional meetings, and research paper acceptance, pay scales and promotion to tenure favor males over females.“

Dr. Bik’s Picks

Sixth-Grader’s Science Fair Finding Shocks Ecologists – NPR All Things Considered

“When 12-year-old Lauren Arrington heard about her sixth-grade science project, she knew she wanted to study lionfish. Growing up in Jupiter, Fla., she saw them in the ocean while snorkeling and fishing with her dad.”

Editorial: Science speaking up – Pensacola News Journal

“The letter read: “We note you have been asked several times about how, as Governor, you will handle the issue of climate change. You responded that you are ‘not a scientist.’ We are scientists and we would like the opportunity to explain what is at stake for our state.””

Book Review: Raising a Glass to Chemistry: ‘Proof’ Drinks in the Science of Alcohol – Alessandra Montalto – The New York Times

“How important is yeast? In 1996, it became the first living organism to have its DNA sequenced. As one modern alehouse puts it in a dubious ad: “Yeast — not just for infections anymore.””

New Allele Hopeful of Making The Big Time – The Allium – Science News You Won’t Read Nowhere Else

“Right now, I am at a low frequency and nobody really knows about me. Tomorrow I could be gone. It is that tough!”

[hr]

General microbiology and science, July 18

Talking to bacteria to make them feel more comfortable (Bacteria whisperers!), probiotics, viruses vs. helminths, and women in Science.

Phages, viruses, helminths

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation – Lisa C. Osborne – Science

“Helminth coinfection resulted in impaired antiviral immunity and was associated with changes in the microbiota and STAT6-dependent helminth-induced alternative activation of macrophages.”

Probiotics

Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells – Prapaporn Boonma – BMC Microbiology

“We screened Lactobacillus conditioned media from 34 infant fecal isolates for the ability to suppress C. difficile-induced IL-8 production from HT-29 cells. Factors produced by two vancomycin-resistant lactobacilli, L. rhamnosus L34 (LR-L34) and L.casei L39 (LC-L39), suppressed the secretion and transcription of IL-8 without inhibiting C. difficile viability or toxin production. “

Cross-talk between probiotic lactobacilli and host immune system – T.S. Kemgang – Journal of Applied Microbiology

“This review summarizes the interplay existing between the host immune system and probiotic lactobacilli, that is, with emphasis on lactobacilli as a prototype probiotic genus.”

General microbiology

Talking to bacteria? Towards light-mediated sensing of bacterial comfort – G. Zafrilla – Letters in Applied Microbiology

“The framework is to convert the human voice into electric pulses, these into light pulses exciting bacterial fluorescent proteins, and convert light-emission back into electric pulses, which will be finally transformed into synthetic voice messages.”

Bacteria in the news

More Forgotten Virus, Bacteria Vials Found at Federal Lab – Newsplex.com

“Food and Drug Administration officials said Wednesday the undocumented collection contained 327 carefully packaged vials, listing pathogens like dengue, influenza and rickettsia.”

1 weird tip to not die of smallpox – Beth Skwarecki – PLOS Blogs

Jenner then attempted to infect the child with smallpox twenty more times in his life. Fortunately for the kid, the vaccine had worked.”

Women in Science

Science Has a Gender Problem. Science Just Made It Worse – Katy Waldman – Slate

“Transgender sex workers should not be expected to thank Science for “raising awareness” of them as erotic objects, jokes, or disease vectors. “

Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault – Kathryn B. H. Clancy – PLOS ONE

“Little is known about the climate of the scientific fieldwork setting as it relates to gendered experiences, sexual harassment, and sexual assault. We conducted an internet-based survey of field scientists (N = 666) to characterize these experiences. “

Dr. Bik’s Picks

Long read: One of a kind: What do you do if your child has a condition that is new to science? – Seth Mnookin – The New Yorker

“At first, they said, he seemed to represent a challenging problem for each new specialist to solve. But, as one conjecture after another was proved wrong, the specialists lost interest; many then insisted that the cause of Bertrand’s illness lay in someone else’s area of expertise. “

Introduction to special issue: Slicing the wheat genome – Kellye Eversole – Science

“Together, these Research Articles explore multiple dimensions of the 17-gigabase wheat genome and pave the way toward achieving a full reference sequence to underpin wheat research and breeding”

 

Earth-like soils on Mars? Ancient fossilized soils potentially found deep inside impact crater suggest microbial life – Science Daily

“Soil deep in a crater dating to some 3.7 billion years ago contains evidence that Mars was once much warmer and wetter, says a geologist based on images and data captured by the rover Curiosity.”

How Colors Smell – Julie Beck – The Atlantic

“But what color is the smell of, say, soap? A new study published in PLOS One finds that some people say white, some say yellow, some say blue. “

Suspects in science museum’s dinosaur heist turn themselves in – Andrew Kenney – Charlotte Observer

“A man and woman, both 21, turned themselves over to N.C. State Capitol Police on Thursday in the case of the missing model dinosaur.”

 

[hr]

General microbiome and science, July 8

Metabolic networks, CRISPR induced immunity, and influence of extraction methods and primers on microbiome analysis. Plus some smallpox in the Lost&Found, and a big citation scandal in SAGE journals.

Microbial ecology / metabolomics

Screen Shot 2014-07-08 at 10.07.56 PMIdentifying All Moiety Conservation Laws in Genome-Scale Metabolic Networks – Andrea De Martino – PLOS ONE

“ Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism.”

Emergent

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“We specifically focus on detecting emergent biosynthetic capacity – instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. “

DIET ArchaeaDirect Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri – Amelia-Elena Rotaru – Applied and Environmental Microbiology

“M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. “

Optimal defenseOptimal Defense Strategies in an Idealized Microbial Food Web under Trade-Off between Competition and Defense – Selina Våge – PLOS ONE

“ Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist.”

Microbial detection

Screen Shot 2014-07-08 at 10.13.13 PMHuman Herpes Viruses Are Associated with Classic Fever of Unknown Origin (FUO) in Beijing Patients – Weimin Zhou – PLOS ONE

“HHVs are associated with Chinese patients (especially for children) with classic FUO. Our study adds perspective to the aetiological and clinical characteristics of classic FUO in beijing patients.”

Phages and viruses

Screen Shot 2014-07-08 at 10.13.31 PMCRISPR-Induced Distributed Immunity in Microbial Populations – Lauren M. Childs – PLOS ONE

“We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities.”

Techniques

Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems – Perrine Cruaud – Applied and Environmental Microbiology

“Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples.”

Dengue

Sanofi’s dengue vaccine first to complete phase 3 – Gunjan Sinha – Nature Biotechnology

“Banking on approval, Sanofi has already started production, a move some have described as a “huge gamble” in light of the vaccine’s disappointing results from earlier studies, says Mark Clark, a pharmaceuticals analyst at Deutsche Bank in London.”

Microbes in the News

Found: Forgotten Vials of Smallpox – Maryn McKenna – Wired.com (also see CDC Media Statement)

“Workers clearing out an old storage room on the Bethesda, Md. campus of the National Institutes of Health have found a forgotten box of vials that contain smallpox.”

The Bacteria That Got Spread Throughout The US By Military Testing – Esther Inglis-Arkell – IO9

“Have you ever heard of serratia marcescens bacteria? Today they are a cause of hospital infections. In the 1960s, they were secretly sprayed across Washington, San Francisco, and New York.”

Manage Your Microbes – Laura Stec – Palo Alto Online

“I’ve been researching this wonderful advance in science for Manage Your Microbes, a cook class at Belmont Library on July 29th. “

Science, Publishing, and Career

SAGE Publications busts “peer review and citation ring,” 60 papers retracted – Retraction Watch

SAGE announces the retraction of 60 articles implicated in a peer review and citation ring at the Journal of Vibration and Control (JVC). “

13 Subtle Ways Women Are Treated Differently At Work – Jenna Goudreau – Business Insider

“Both men and women hold these views but often don’t even realize it. “It’s hard to fight this,” says Rivers, but awareness is key.

Dr. Bik’s Picks

Combining colour and temperature: A blue object is more likely to be judged as warm than a red object – Hsin-Ni Ho – Nature Scientific Reports

“It is commonly believed that reddish colour induces warm feelings while bluish colour induces cold feelings. We, however, demonstrate an opposite effect when the temperature information is acquired by direct touch.”

MandarinSequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication – G Albert Wu – Nature Biotechnology

“Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. “

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General digest, July 3

CRISPRs, the yearly NAR Web Server issue, dengue, arsenic, and The Picks.

CRISPRs

Screen shot 2014-07-03 at 03.59PM, Jul 03 1Detection and characterization of spacer integration intermediates in type I-E CRISPR–Cas system – Zihni Arslan – Nucleic Acids Research

“We identified and characterized in Escherichia coli intermediate states of spacer integration and mapped the integration site at the chromosomal CRISPR array in vivo. “

Bioinformatics

Screen shot 2014-07-03 at 03.59PM, Jul 03Nucleic Acids Research published their yearly Web Server issue. The names of some tools alone are very entertaining (CHOPCHOP, Coffee, COGNAC, just to lists some C’s), but here are some resources that sound interesting:

Alignment-Annotator web server: rendering and annotating sequence alignments
Christoph Gille

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches – Sebastian Horwege

EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles – W. James Dittmar

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra – Felicity Allen

PIQMIe: a web server for semi-quantitative proteomics data management and analysis – Arnold Kuzniar

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data – Daogang Guan

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data – Manuel Garcia-Albornoz

deepTools: a flexible platform for exploring deep-sequencing data – Fidel Ramírez

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling – Cyrille Pauthenier

PubServer: literature searches by homology – Lukasz Jaroszewski

Arsenic metabolism

Arsenic color toolSediment color tool for targeting arsenic-safe aquifers for the installation of shallow drinking water tubewells – Mohammed Hossain – Science of the Total Environment

“Laboratory analysis of 521 groundwater samples collected from 144 wells during 2009 to 2011 indicate that As concentrations in groundwater were generally higher in the black colored sediments with an average of 239 μg/L.”

Screen shot 2014-07-03 at 03.55PM, Jul 03Arsenite stimulates glutathione export and glycolytic flux in viable primary rat brain astrocytes – Nimesha Tadepalle – Neurochemistry International

“The strong stimulation of GSH export by arsenite was prevented by MK571, an inhibitor of the multidrug resistance protein 1, suggesting that this transporter mediates the accelerated GSH export.”

Screen shot 2014-07-03 at 03.55PM, Jul 03 1Trichoderma spp. alleviate phytotoxicity in lettuce plants (Lactuca sativa L.) irrigated with arsenic-contaminated water – Antonio G. Caporale – Journal of Plant Physiology

“Plant Growth-Promoting Fungi (PGPF) of both Trichoderma species alleviated, at least in part, the phytotoxicity of As, essentially by decreasing its accumulation in the tissues and enhancing plant growth, P status and net photosynthesis rate.”

Dengue

Kwissa DengueDengue Virus Infection Induces Expansion of a CD14+CD16+ Monocyte Population that Stimulates Plasmablast Differentiation – Marcin Kwissa – Cell Host & Microbe

“Transcriptomic analysis of whole blood revealed that genes encoding proinflammatory mediators and type I interferon-related proteins were associated with high DENV levels during initial symptomatic disease. “

dengue bidetG3BP1, G3BP2 and CAPRIN1 Are Required for Translation of Interferon Stimulated mRNAs and Are Targeted by a Dengue Virus Non-coding RNA – Katell Bidet – PLOS Pathogens

“We examined three conserved host RNA-binding proteins (RBPs) G3BP1, G3BP2 and CAPRIN1 in dengue virus (DENV-2) infection and found them to be novel regulators of the interferon (IFN) response against DENV-2. “

Dengue Virus Persists in Stored Platelets and Red Blood Cells – Michael R. Sutherland – Transfusion Medicine Reviews

“…we investigated the persistence of DENV (serotypes 1-4) in stored platelet (PC) and red blood cell concentrates (RCC) under standard blood bank conditions. “

2013: Rise of the deadly dengue fever in Pakistan – Anum Wasim – Journal of Infection and Public Health

“Last year saw more than 17000 dengue cases being reported from all over the country, the highest number ever in the country’s history.”

Women in Science 

Gender: Perception differences – Nature

“Female leaders underrate how their bosses and colleagues perceive their performance, find US researchers”

Screen shot 2014-07-03 at 03.57PM, Jul 03Leader self-awareness: An examination and implications of women’s under-prediction –
Rachel E. Sturm – Journal of Organizational Behavior

“…women under-predict their bosses’ ratings of their leadership compared with men, even though they self-rate the same and are rated by their bosses similarly to men”

 

10 Words Every Girl Should Learn – Soraya Chemaly – Huffington Post

Yes! This! “A woman, speaking clearly and out loud, can say something that no one appears to hear, only to have a man repeat it minutes, maybe seconds later, to accolades and group discussion.”

Science, Publishing, and Ethics

Science Editorial: Raising the bar – Marcia McNutt – Science

“For that reason, with much help from the American Statistical Association, Science has established, effective 1 July 2014, a Statistical Board of Reviewing Editors (SBoRE), consisting of experts in various aspects of statistics and data analysis, to provide better oversight of the interpretation of observational data.”

Science ethics: Young scientists speak – Shelly Benjaminy – Science

“What is the most challenging ethical question facing young investigators in your field? How should it be addressed? In April, we asked young scientists to tell us their thoughts.“

Science and Art

Screen shot 2014-07-03 at 03.57PM, Jul 03 1Can You Guess What These Cute Pink Tiles Are Made Of? – Francie Diep – Popular Science

“These images are from research into new techniques for medical diagnoses and biometrics.”

Dr. Bik’s Picks

Screen shot 2014-07-03 at 03.51PM, Jul 03Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes – Iakes Ezkurdia – Human Molecular Genetics

“Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. “

Screen shot 2014-07-03 at 03.50PM, Jul 03With Help From Extinct Humans, Tibetans Adapted To High Altitude – Rae Ellen Bichell – NPR

“According to Nielsen and a bunch of geneticists writing in the journal Nature, the Tibetans appear to have benefited from a genetic gift from the Denisovans, an extinct human ancestor known primarily from a little girl’s tooth and pinkie bone.”

Screen shot 2014-07-03 at 03.49PM, Jul 03NSF to decide all future grant proposals by penalty shoot-out – The Allium

“We feel that this will be a much less random way of giving out funding”, said Dr. France Cordóva, Director of the NSF.”

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