General microbiology and science, June 25

Arsenic profiling in rats, Bacillus in space, and antibiotic resistance in populations. And Dr. Bik’s Picks featuring butterflies, mummies and unfeelability cloaks.

Microbes in space

Screen Shot 2014-06-25 at 10.31.28 PMBacillus anthracis-Like Bacteria and Other B. cereus Group Members in a Microbial Community Within the International Space Station: A Challenge for Rapid and Easy Molecular Detection of Virulent B. anthracis – Sandra P. van Tongeren – PLOS ONE

“In this study we show the presence of B. anthracis-like bacteria and other members of the B. cereus group in a microbial community within the human environment of the International Space Station and their preliminary identification by using conventional culturing as well as molecular techniques including 16S rDNA sequencing, PCR and real-time PCR. “

Metagenomics

Screen Shot 2014-06-25 at 10.31.54 PMElucidation of Operon Structures across Closely Related Bacterial Genomes – Chuan Zhou – PLOS ONE

“Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes.”

Antibiotic resistance

Screen Shot 2014-06-25 at 10.32.23 PMOptimization of lag time underlies antibiotic tolerance in evolved bacterial populations – Ofer Fridman – Nature

“Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. “

Arsenic metabolism

Screen Shot 2014-06-25 at 10.32.54 PMThe metabolomic profiling of serum in rats exposed to arsenic using UPLC/Q-TOF MS – Cheng Wang – Toxicology Letters

“The aim of this study is to determine the impact of chronic arsenic exposure on the metabolism of organism, and find the metabolites changes by using metabolomic techniques. “

Screen Shot 2014-06-25 at 10.33.15 PMInvestigation of arsenic species stability by HPLC-ICP-MS in plants stored under different conditions for 12 months – Clarice D.B. Amaral – Microchemical Journal

“For the As species here studied it can be concluded that lyophilization and cryogenic grinding strategies were the most suitable sample pretreatments for As speciation in plant tissue.”

Science and careers

Screen Shot 2014-06-25 at 10.33.54 PMLove in the lab: Close collaborators – Kerri Smith – Nature

“Romance often sparks between colleagues, and scientists are no different. Nature profiles four super-couples who have combined love and the lab.”

Dr. Bik’s Picks

Screen Shot 2014-06-25 at 10.35.06 PMMetagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman – Frank Maixner – PLOS ONE

“Initially, the metagenomic data of the Iceman’s genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. “

Screen Shot 2014-06-25 at 10.35.42 PMA magnetic compass aids monarch butterfly migration – Patrick A Guerra – Nature Communications

“Here we use flight simulator studies to show that migrants indeed possess an inclination magnetic compass to help direct their flight equatorward in the fall. “

Screen Shot 2014-06-25 at 10.36.07 PMAn elasto-mechanical unfeelability cloak made of pentamode metamaterials
T. Bückmann – Nature Communications

“Here, inspired by invisible core-shell nanoparticles in optics, we design an approximate elasto-mechanical core-shell ‘unfeelability’ cloak based on pentamode metamaterials. “

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General microbiology and science, June 16

It’s late and I got lots for you, so no pictures today. Dengue, phages, ecology, techniques, and lots more.

Antibiotic resistance

Review: Microbiological effects of sublethal levels of antibiotics – Dan I. Andersson & Diarmaid Hughes – Nature Reviews Microbiology

“In this Review, we discuss the ecology of antibiotics and the ability of subinhibitory concentrations to select for bacterial resistance. “

A Bacterial Battle  – Lisa M. Jarvis – Chemical and Engineering News

“The regulatory path to approving new antibiotics has been cleared, but work still remains to rebuild a healthy drug pipeline”

Bacteria are everywhere
How safe is your kitchen? – Lyxan Toledanes – The Daily News Online

Despite a spacious kitchen, Parker sat on the counter next to Masters’ prep area, where she was chopping vegetables and chicken on separate cutting mats. 

Adventures in the microbiome (part 2) – Mike Edmund

“There’s an intriguing case report that was just published in Clinical Microbiology and Infection”

Stafford students find bacteria on tainted tablets – Amanda Oglesby

“Four sixth-graders huddled over a table inside All Saints Regional Catholic School as they took turns swabbing bacteria from the surfaces of an iPhone and iPad.”

Bioslime: new sensor to detect harmful bacteria on food industry surfaces – BarfBlog

“The Biolisme project is using research from the University to develop a sensor capable of collecting and detecting Listeria monocytogenes on food industry surfaces, thereby preventing contaminated products from entering the market.”

Viruses and phages

Functional long-range RNA–RNA interactions in positive-strand RNA viruses – Beth L. Nicholson & K. Andrew White – Nature Reviews Microbiology

“In this Review, we discuss recent insights into the structure and function of these intriguing genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.”

Unravelling the structural and mechanistic basis of CRISPR–Cas systems – John van der Oost – Nature Reviews Microbiology

“In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR–Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.”

The elemental composition of virus particles: implications for marine biogeochemical cycles – Luis F. Jover – Nature Reviews Microbiology

“In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. “

Phage therapies for plants and people – Michael Gross – Current Biology

Dengue

NEA to explore biological control methods to tackle dengue

“One of the techniques involves the use of Aedes aegypti mosquitoes, which are infected with a certain bacteria, to control their population.”

Techniques general

Storage of Human Biospecimens: Selection of the Optimal Storage Temperature – Allison Hubel – Biopreservation and Biobanking

“The overall objective of this article is to describe the scientific basis for selecting a storage temperature for a biospecimen based on current scientific understanding. To that end, this article reviews some physical basics of the temperature, nucleation, and ice crystal growth present in biological samples stored at low temperatures (−20°C to −196°C), and our current understanding of the role of temperature on the activity of degradative molecules present in biospecimens.”

DNA polymerase hybrids derived from the family-B enzymes of Pyrococcus furiosus and Thermococcus kodakarensis: improving performance in the polymerase chain reaction – Ashraf M. Elshawadfy – Frontiers Microbiology

“The significance of this work is the observation that improvements in PCR performance are easily attainable by blending elements from closely related archaeal polymerases, an approach that may, in future, be extended by using more polymerases from these organisms.”

Metabolomics, Proteomics, Mass spectrometry

Bruker Announces Powerful New Mass Spectrometry Systems and Solutions for Life-Science Research, Clinical Research, Biopharma and Applied Markets – Wall Street Journal

“At the 62(nd) ASMS Conference on Mass Spectrometry and Allied Topics today, Bruker Corporation (NASDAQ:BRKR) today announced mass spectrometry-based product introductions for life-science research and proteomics, for clinical research, for pharma/biopharma/CRO customers, as well as for applied and industrial markets. “

Medically, Proteomics Advances Will Rival the Genetics Advances of the Last Ten Years – Genetic Engineering and Biotechnology News

“..in explaining why proteomics is likely to have such a major impact, Dr. Anderson starts with a major difference between the genetic testing common today, and the proteomic testing that is fast coming on the scene. “

Metagenomics and informatics

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation – Yvonne L. Chan – Molecular Biology and Evolution

“Here we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage.”

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit – Jesse D. Bloom – Molecular Biology and Evolution

“Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing.”

Ecology

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning – Sascha Krause – Frontiers in Microbiology

“We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. “

The importance of the viable but non-culturable state in human bacterial pathogens – Laam Li – Frontiers in Microbiology

“The conditions that trigger the induction of the VBNC state and resuscitation from it are summarized and the mechanisms underlying these two processes are discussed. “

Deciphering microbial interactions and detecting keystone species with co-occurrence networks – David Berry – Frontiers in Microbiology

“Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation.”

Scientific writing and publishing

Sources of error in the retracted scientific literature – Arturo Casadevall, R. Grant Steen and Ferric C. Fang – The FASEB Journal

“Analysis of the retraction notices for 423 articles indexed in PubMed revealed that the most common causes of error-related retraction are laboratory errors, analytical errors, and irreproducible results.”

Dr. Bik’s Picks

Magnets: Artificial Magnetic Bacteria: Living Magnets at Room Temperature – Miguel Martín – Adv. Funct. Mater

After grafting the magnetic nanoparticles, the artificial magnetic bacteria remain alive. In fact they are converted into living magnets at room temperature.”

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Human microbiome, June 10

Today we’ll cover the lung microbiome, salivary gland function, NEC, and sequencing of cosmid clones.
Oral microbiome

AutophagyAutophagy Correlates with Maintenance of Salivary Gland Function Following Radiation – Maria Morgan-Bathke – Nature Scientific Reports

“Thus, autophagy appears to play a beneficial role in salivary glands following radiation”

UbiquitousUbiquitous Sialometabolism Present among Oral Fusobacteria – Saori Yoneda – PLOS ONE

“Using microarray analysis, we examined the transcriptional response of F. nucleatum subspecies nucleatum to whole blood in order to identify some of the genetic responses that might occur during the transition from health to disease.”

NYU and UCSF researchers develop a framework for monitoring oral cancer – ScienceCodex

“”We know that other cancers, including gallbladder, colon, lung and prostate, have been associated with particular bacterial infections, so we hypothesized that shifts in the composition of the normal oral cavity microbiome could be promoters or causes of oral cancer,” said Dr. Albertson.”

Respiratory microbiome

Screen Shot 2014-06-10 at 9.32.19 PMBreathing Life into Lung Microbiome Research – Rina Shaikh-Lesko – The Scientist

“Although it’s far less populated than the mouth community that helps feed it, researchers increasingly appreciate the role of the lung microbiome in respiratory health.”

Impact off extImpact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“To better understand how these bacteria change in relation to pneumococcal colonization, we used species-specific quantitative PCR to examine bacterial densities in 52 subjects 7 days before, and 2, 7, and 14 days after controlled inoculation of healthy human adults with S. pneumoniae serotype 6B.”

Pregnancy and Birth

BrainModerate and Late Preterm Birth: Effect on Brain Size and Maturation at Term-Equivalent Age – Jennifer M. Walsh – Radiology

“MLPT birth is associated with smaller brain size, less-developed myelination of the posterior limb of the internal capsule, and more immature gyral folding than those associated with full-term birth. “

Preemie Research Highlights Concerns With Human Experimentation – Frederick Reese – Mintpress

“Parents weren’t fully aware of the risks associated with a medical research trial they allowed their babies to participate in.”

Screen Shot 2014-06-10 at 9.30.20 PMSmall Intestinal Intraepithelial TCRγδ+ T Lymphocytes Are Present in the Premature Intestine but Selectively Reduced in Surgical Necrotizing Enterocolitis – Jörn-Hendrik Weitkamp – PLOS ONE

“In human preterm infants, the proportion of IEL was reduced by 66% in 11 NEC ileum resections compared to 30 non-NEC controls (p<0.001). While γδ IEL dominated over conventional αβ IEL early in gestation in mice and in humans, γδ IEL were preferential decreased in the ileum of surgical NEC patients compared to non-NEC controls (50% reduction, p<0.05).”

Antibiotics and microbiome

Synthetic Biologics and Enterome Bioscience Collaborate on Microbiome Research to Support Synthetic Biologics’ C. difficile Program – MarketWatch

“Synthetic Biologics, Inc. (nyse mkt:SYN), a developer of novel anti-infective biologic and drug candidates targeting specific pathogens that cause serious infections and diseases, and Enterome Bioscience SA, a pioneer in the development of innovative disease management solutions based on a deep understanding of the gut microbiome, today announced that they have entered into an agreement to conduct metagenomic research on the effects of beta-lactam antibiotics on the gastrointestinal microflora (microbiome) of human patients”

Animal models of human disease

Screen Shot 2014-06-10 at 9.38.10 PMSaccharomyces boulardii Administration Changes Gut Microbiota and Reduces Hepatic Steatosis, Low-Grade Inflammation, and Fat Mass in Obese and Type 2 Diabetic db/db Mice – Amandine Everard – mBio

“Here we found that type 2 diabetic and obese mice (db/db) treated with Saccharomyces boulardii exhibited reduced body weight, fat mass, hepatic steatosis, and inflammatory tone. “

Metagenomics and sequencing

Evaluation of a pooledEvaluation of a Pooled Strategy for High-Throughput Sequencing of Cosmid Clones from Metagenomic Libraries – Kathy N. Lam – PLOS ONE

“We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. “

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Human microbiomes, June 5

Today we have some commentaries on recent papers about microbiotas in malnutrition or on placentas, and new papers about oral bacteria in the bloodstream, helminths, and coincidental killers.

Oral microbiome

Screen Shot 2014-06-05 at 7.59.36 PMDissemination of Periodontal Pathogens in the Bloodstream after Periodontal Procedures: A Systematic Review – Anna Carolina Ratto Tempestini Horliana – PLOS ONE

“MEDLINE, EMBASE and LILACS databases were searched in duplicate through August, 2013 without language restriction. Observational studies were included if blood samples were collected before, during or after periodontal procedures of patients with periodontitis”

Screen Shot 2014-06-05 at 7.56.12 PMThe Emerging Landscape of Salivary Diagnostics – Yong Zhang- OHDM – Omics Online

“Here we review recent developments in salivary diagnostics that have been accomplished using salivaomics, the mechanisms of saliva diagnostics, as well as the translational and clinical application of saliva biomarkers”

Gut microbiome

Screen Shot 2014-06-05 at 7.57.14 PMInfection and Co-infection with Helminths and Plasmodium among School Children in Côte d’Ivoire: Results from a National Cross-Sectional Survey – Richard B. Yapi – PLOS Neglected Tropical Diseases

“We carried out the first national survey on parasitic worm and Plasmodium infection among children in 92 schools all over Côte d’Ivoire. Questionnaires were administered to determine the children’s socioeconomic status and infection-related risk factors. We found an overall prevalence of Plasmodium infection of 63.3%.”

ColonSome Antibiotics May Slightly Increase Colon Cancer Risk – Bahar Gholipour – LiveScience

“The researchers compared the amount of antibiotics the patients had taken at least six months before being diagnosed with cancer, to the amount of antibiotics taken by a group of about 86,000 healthy people.”

Screen Shot 2014-06-05 at 10.07.58 AMWhy Can’t Once-Malnourished Children “Catch Up”? Answer May Lie in Gut – Karen Weintraub – National Geographic

“There’s something lacking in our current approach to treatment,” said Gordon, who suspects the children may need to eat therapeutic foods for longer and/or get supplements of probiotics, or beneficial microorganisms, to catch up. “We need to think of food as interacting with this microbial organ.”

Screen Shot 2014-06-05 at 8.03.26 PMSevere hunger can have lasting effects for gut health, study finds – MedicalXPress

“Nutrition therapy has saved the lives of millions of malnourished infants, but may not restore an imbalance in gut bacteria that is key to long-term health and vitality, researchers said Wednesday.”

Pregnancy and birth

Screen Shot 2014-06-05 at 8.05.15 PMGearing up for a closer look at the human placenta – Jocelyn Kaiser – Science

“A placenta sustained you and every person ever born for 9 months, serving as your lungs and kidneys and pumping out hormones while you developed in the womb. Problems with this disk-shaped mass of tissue can contribute to everything from preterm births to diseases of middle age. Yet when a baby is born, hospitals usually throw the placenta away.”

Screen Shot 2014-06-05 at 9.57.32 AMMicrobirth: Why ‘Seeding Baby’s Microbiome’ Needs to Be on Every Birth Plan – Toni Harman – HuffingtonPost

“The latest scientific research is now starting to indicate that if the baby is not properly seeded with the mother’s own bacteria at birth, then the baby’s microbiome, in the words of Rodney R Dietert, Professor of Immunotoxicology at Cornell University, is left “incomplete”.”

General human microbiome

Screen Shot 2014-06-05 at 8.07.51 PMCoincidental killers – We assume that microbes evolved to attack humans when actually we are just civilian casualties in a much older war – Ed Yong – Aeon Magazine

“And some supposedly pathogenic bacteria were often common parts of the environment. ‘These organisms become accidental pathogens,’ says the microbiologist Arturo Casadevall from Yeshiva University in New York. ‘They’ll still be there even if you remove all the animals from the planet. And yet, evolution selected for just the right combination of traits to cause disease in humans.’”

Screen Shot 2014-06-05 at 8.12.08 PMSilicon Valley’s Top Ten Tech Trends – Jacqueline Vanacek – Forbes
Trend #7: Data-driven healthcare (from your gut).

The combination of personal health and fitness data, genomics, and even microbiomics will drive healthcare choices from real outcomes and individual probabilities. And since the bacteria in our digestive tracks has greater influence on our health than previously known, we really are what we eat!

Microbiome and Bioinformatics

Screen Shot 2014-06-05 at 8.11.20 PMBOTUX: Bayesian–like operational taxonomic unit examiner – Vishal N. Koparde – International Journal of Computational Biology and Drug Design

“Bayesian–like operational taxonomic unit examiner (BOTUX) is a new tool for the classification of 16S rRNA gene sequences into operational taxonomic units (OTUs) that addresses the problem of overestimation caused by errors introduced during PCR amplification and DNA sequencing steps”

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Animal, plant, environmental microbiome digest, June 3, 2014

Microbiomes of wild mice, antibiotic treated cattle, catfish, insects, soil, and water. And some good old plagiarism.

Mammalian microbiome

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice – Jun Wang – PNAS

“By performing stable isotope analysis of environmental samples, monitoring communities during dietary shifts, and collecting functional metagenomic sequence data, we provide novel insight into the origins and dynamics of enterotype-like community clustering in wild house mice.”

Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome – Neena Kanwar – Nature Scientific Reports

“The study objective was to determine the effects of two treatment regimens on quantities of ceftiofur and tetracycline resistance genes in feedlot cattle. “

Fish microbiome

An Asian Origin of Virulent Aeromonas hydrophila Responsible for Disease Epidemics in United States-Farmed Catfish – Mohammad J. Hossain – mBio

“Our phylogenomic analyses suggest that U.S. catfish isolates emerged from A. hydrophila populations of Asian origin.”

Insect microbiome

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics – Joel Gibson – PNAS

“We show that next-generation sequencing (NGS) of cytochrome c oxidase subunit I (COI) DNA barcodes can accurately detect 83.5% of individually sequenced species (corresponding to 91% of individuals) in a bulk sample of terrestrial arthropods from a Costa Rican species-rich site.”

GroEL from the endosymbiont Buchnera aphidicola betrays the aphid by triggering plant defense – Ritu Chaudhary – PNAS

“By means of mass spectrometry, we identified 105 proteins in the saliva of the potato aphid Macrosiphum euphorbiae. Among these proteins were some originating from the proteobacterium Buchnera aphidicola, which lives endosymbiotically within bacteriocytes in the hemocoel of the aphid. “

Soil and rock microbiome

Deep 16S rRNA Pyrosequencing Reveals a Bacterial Community Associated with Banana Fusarium Wilt Disease Suppression Induced by Bio-Organic Fertilizer Application – Zongzhuan Shen – PLOS ONE

“Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance”

Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere – Malin Bomberg – Open Journal of Ecology

“our results show that the inferred diversity and composition of microbial communities in deep fracture fluids is highly dependent on analytical technique and that the method should be carefully selected with this in mind.”

Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle – L. H. Orellana – mBio

“we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt”

Water microbiome

Survival secrets of Deep Lake – Graeme O’Neill – LifeScientist.com

“Deep Lake, in Antarctica’s Vestfold Hills, harbours a unique flora of salt-loving Archaea that survive at temperatures way below freezing. Professor Rick Cavicchioli’s team at UNSW has been plumbing the lake’s mysteries”

Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus – Patrick Martin – PNAS

” We show here that phytoplankton in the ultra–low-phosphorus Sargasso Sea are enriched in polyphosphate (polyP)”

Commonness and rarity in the marine biosphere – Sean R. Connolly – PNAS

“By identifying common features of different neutral models, we conduct a uniquely robust test of neutral theory across a global dataset of marine assemblages.”

Temporal Changes in Microbial Ecology and Geochemistry in Produced Water from Hydraulically Fractured Marcellus Shale Gas Wells – Maryam A. Cluff – Environmental Science & Technology

“This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period.”

General Ecology

Effects of differential habitat warming on complex communities – Tyler D. Tunney – PNAS

“To demonstrate differential warming effects on food webs, we use boreal lakes to show that the energy pathways leading to an apex predator shift, according to thermal preference, and the vertical pathway lengthened in warmer climate.”

Microbes in Space

Protein patterns of black fungi under simulated Mars-like conditions – Kristina Zakharova – Nature Scientific Reports

“In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis.”

Data mining and Bioinformatics

Detecting a Weak Association by Testing its Multiple Perturbations: a Data Mining Approach – Min-Tzu Lo & Wen-Chung Lee – Nature Scientific Reports

“Here, we propose a novel method which hinges on increasing sample size in a different direction–the total number of variables”

This paper contains plagiarized text, but I will toss it in anyway:
An Integrated Strategy for Functional Analysis of Microbial Communities Based on Gene Ontology and 16S rRNA Gene – Su-Ping Deng, De-Shuang Huang – SciencePaperOnline

“We analyzed the similarity between two microbial communities on functional state. In the experimental results, it shows that the semantic similarity can quantify the difference between two compared species on function level. “

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