Tag Archives: cute animals

General microbiology and science, July 14

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Rectal swabs instead of stool samples, faster way of finding orthologs, and intelligence in bacteria.

Bioinformatics

Screen shot 2014-07-14 at 06.24PM, Jul 14Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss? – Natalie Ward, Gabriel Moreno-Hagelsieb – PLOS ONE

“Since sequence comparison can be time consuming, we decided to compare the number and quality of RBHs detected using algorithms that run in a fraction of the time as BLAST. We tested BLAT, LAST and UBLAST.”

Sampling techniques

Screen shot 2014-07-14 at 06.24PM, Jul 14ectal Swabs for Analysis of the Intestinal Microbiota – Andries E. Budding – PLOS ONE

“In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota.”

Screen shot 2014-07-14 at 06.25PM, Jul 14Some Are More Equal – A Comparative Study on Swab Uptake and Release of Bacterial Suspensions – Philipp Warnke – PLOS ONE

“Highest amount of CFU release was detected for the MWE Dryswab in the unrestricted setting for both S. aureus and S. epidermidis with 1544 CFU and 553 CFU, respectively, lowest release for the Sarstedt neutral swab with 32 CFU and 17 CFU, respectively (p<0.001).”

Antibiotics, resistance, biofilms

Screen shot 2014-07-14 at 06.26PM, Jul 14Beta-Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism – Siva Wu – PLOS ONE

“When exposed to sub-inhibitory concentrations of beta-lactam antibiotics NTHi strains produced tightly packed biofilms with decreased numbers of culturable bacteria but increased biomass.”

General microbiology

Screen shot 2014-07-14 at 12.23PM, Jul 14Macromolecular networks and intelligence in microorganisms – Hans V. Westerhoff – Frontiers in Microbiology

“Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected.”

Screen shot 2014-07-14 at 06.26PM, Jul 14 1The syndemics of childhood diarrhoea: A biosocial perspective on efforts to combat global inequities in diarrhoea-related morbidity and mortality – Nicola Bulled – Global Public Health

“Drawing from available literature, this paper uses syndemic theory to explore the role of adverse biosocial interactions in increasing the total disease burden of enteric infections in low-resources populations and assesses the limitations of recent global calls to action.”

Bacteria in the news

Screen shot 2014-07-14 at 06.19PM, Jul 14We Are Our Bacteria – Jane E. Brody – New York Times (illustration by Ken Orvidas)

“We may think of ourselves as just human, but we’re really a mass of microorganisms housed in a human shell.”

Screen shot 2014-07-14 at 06.27PM, Jul 14#BacteriaHysteria : Gross! Lots of bacteria found on new swimsuits – Jane Weaver – Today Health

“The removable liner in women’s swimsuits that is meant to protect the fabric from our cooties isn’t really protective after all, according to a microbe researcher. “

Screen shot 2014-07-14 at 06.28PM, Jul 14Milford hospital enlists robots in war against infections – Mary MacDonald – Boston Globe

“The robots, made by Xenex Disinfection Services, use an intense flash of ultraviolet light to fight the bacteria, viruses, fungi, and other micro-organisms that traditional cleaning methods can miss, according to the hospital’s infection control staff.”

Screen shot 2014-07-14 at 06.29PM, Jul 14CDC Cracks Down on Labs After Anthrax, Bird Flu Scares – Jonel Aleccia – NBC News

“Dr. Tom Frieden, director of the Centers for Disease Control and Prevention, on Friday announced an immediate moratorium on all shipments of biological materials from CDC biosecurity level 3 and level 4 labs until problems are addressed.”

Marine Mammals

Screen shot 2014-07-14 at 06.29PM, Jul 14 1How Dolphins’ Genetics Could Help Find Answers Into Mysterious Animal Die-Off – Sascha Cordner – WFSU

“A discovery into dolphin genetics may have brought research scientists one step closer to finding out the source of a mysterious animal die-off last year in the troubled Indian River Lagoon.”

Science and publishing

Screen shot 2014-07-14 at 12.45PM, Jul 14Retractions are coming thick and fast: it’s time for publishers to act – Adam Marcus and Ivan Oransky – The Guardian

“Another encouraging development is the rise of post-publication peer review, which has been made possible in recent years by the availability of papers online. Contributors to PubPeer, for example, have found signs of flawed or falsified results, leading to papers being retracted.”

Dr. Bik’s Picks

Screen shot 2014-07-14 at 06.34PM, Jul 14Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease – Britt-Sabina Petersen – BMC Genomics

“We present a thorough genetic characterization of the sequenced individuals but detected no consistent differences within the twin pairs. “

Screen shot 2014-07-14 at 06.32PM, Jul 14How much science is there in new Planet of the Apes film? – Paul Rincon – BBC Science

“The latest instalment in the Planet of the Apes film franchise opens in the US on Friday. The rubber masks of the 60s and 70s films have been discarded in favour of motion capture suits and CGI. But how much did science inform the new movie’s portrayal of our close relatives?”

Screen shot 2014-07-14 at 06.31PM, Jul 14Domestication syndrome: White patches, baby faces and tameness explained by mild neural crest deficits – Science Daily

“Compared to their wild ancestors, domestic species are more tame, and they also tend to display a suite of other characteristic features, including floppier ears, patches of white fur, and more juvenile faces with smaller jaws.”

 

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Non-human microbiome, July 2014

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Kittens! And squid, sponges, acid mine drainage in someone’s backyard, soils, and sediments.

Cat microbiome

KittensDeep Illumina-Based Shotgun Sequencing Reveals Dietary Effects on the Structure and Function of the Fecal Microbiome of Growing Kittens – Oliver Deusch – PLOS ONE

“The present study… applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.”

Squid microbiome

Squid albaGene-Swapping Mediates Host Specificity among Symbiotic Bacteria in a Beneficial Symbiosis – Alba A. Chavez-Dozal – PLOS ONE

“Our results demonstrate that multiple bacterial genetic elements can determine V. fischeri strain specificity between two closely related squid hosts, indicating how important genetic variation is for regulating conspecific beneficial interactions that are acquired from the environment.”

Sponge microbiome 

Review: Diversity and biotechnological potential of microorganisms associated with marine sponges – Fuerst JA – Applied Microbiol Biotechnol (Direct link not working)

“Here, we review recent progress in our understanding of this genetic diversity, its retrieval via culture and genomic approaches, and its implications for chemical diversity and other biotechnology applications of sponge microorganisms and their genes.”

Soils and sediments

StroudMetal(loid) bioaccessibility dictates microbial community composition in acid sulfate soil horizons and sulfidic drain sediments – Jackie Stroud – Environmental Science & Technology

“Microbial community compositions were determined for three soil horizons and drain sediments within an anthropogenically-disturbed coastal acid sulfate landscape using 16S rRNA gene tagged 454 pyrosequencing.”

Screen shot 2014-07-14 at 12.34PM, Jul 14Geochemical and microbiological response to oxidant introduction into reduced subsurface sediment from the Hanford 300 Area, WA – Elizabeth M Percak-Dennett and Eric E. Roden – Environmental Science & Technology

“Together these results indicate the potential for heterotrophic carbon metabolism in the reduced sediments, consistent with the proliferation of known heterotrophic taxa (e.g. Pseudomonadaceae, Burkholderiaceae, Clostridiaceae) inferred from 16S rRNA gene pyrosequencing.”

Brantner AMDResponse of Soil-Associated Microbial Communities to Intrusion of Coal Mine-Derived Acid Mine Drainage – Justin S. Brantner and John M. Senko – Environmental Science & Technology

“Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment.”

Screen shot 2014-07-14 at 12.36PM, Jul 14New carbohydrate-active enzymes identified by screening two metagenomic libraries derived from the soil of a winter wheat field – A. Stroobants – Journal of Applied Microbiology

“The aim of this work was to discover new β-glucosidases by constructing two metagenomic DNA libraries from soil samples collected in winter and spring from a field of winter wheat.”

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General microbiology and science, June 27

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Viruses in primate genomes, viruses altering shrimp metabolome, transposable elements and repeats, dengue, other infectious diseases in developing countries and Dr. Bik’s Picks.

Metagenomics / viruses

Screen Shot 2014-06-27 at 9.21.29 PMCute animal alert! A tarsier is a tiny primate with huge eyes.
The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses – Amr Aswad, Aris Katzourakis – PLOS Genetics

“We describe the first endogenous herpesvirus from the genome of the Philippine tarsier, belonging to the Roseolovirus genus, and characterize its highly defective genome that is integrated and flanked by unambiguous host DNA. From a draft assembly of the aye-aye genome, we use bioinformatic tools to reveal over 100,000 bp of a novel rhadinovirus that is the first lemur gammaherpesvirus, closely related to Kaposi’s sarcoma-associated virus.”

 Metabolomics

Screen Shot 2014-06-27 at 9.32.37 PMAn Invertebrate Warburg Effect: A Shrimp Virus Achieves Successful Replication by Altering the Host Metabolome via the PI3K-Akt-mTOR Pathway – Mei-An Su – PLOS Pathogens

“We show that the PI3K-Akt-mTOR pathway was of central importance in triggering this WSSV-induced Warburg effect. Although dsRNA silencing of the mTORC1 activator Rheb had only a relatively minor impact on WSSV replication, in vivo chemical inhibition of Akt, mTORC1 and mTORC2 suppressed the WSSV-induced Warburg effect and reduced both WSSV gene expression and viral genome replication.”

Biofilms

Screen Shot 2014-06-27 at 9.33.21 PMFilaments in curved streamlines: rapid formation of Staphylococcus aureus biofilm streamers – Minyoung Kevin Kim – New Journal of Physics

“We discovered that S. aureus rapidly forms flow-induced, filamentous biofilm streamers, and furthermore if surfaces are coated with human blood plasma, streamers appear within minutes and clog the channels more rapidly than if the channels are uncoated. “

Chromosomal organization

Screen Shot 2014-06-27 at 9.34.04 PMDigital Genotyping of Macrosatellites and Multicopy Genes Reveals Novel Biological Functions Associated with Copy Number Variation of Large Tandem Repeats – Manisha Brahmachary – PLOS Genetics

“Here, we demonstrate the utility of Nanostring technology as a targeted approach to perform accurate measurement of tandem repeats even at extremely high copy number, and apply this technology to genotype 165 HapMap samples from three different populations and five species of non-human primates. “

Screen Shot 2014-06-27 at 9.34.37 PMLarge-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes – Jaime Iranzo – PLOS Computational Biology

“In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. “

Microbial Ecology

Screen Shot 2014-06-27 at 9.35.00 PMEx Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community – Margie Kinnersley – PLOS Genetics

“We previously showed that a population of E. coli that originated from a single clone and was cultured in the presence of a single limiting resource, evolves into a stable, three-membered community, wherein one clone excretes metabolites that the others utilize as carbon sources. To discern the genetic factors at work in producing this outcome and to illuminate the community’s physiology, we sequenced the genomes of the ancestral and evolved clones.”

Infectious diseases in developing countries

Screen Shot 2014-06-27 at 9.35.43 PMExploring the Relationship between Access to Water, Sanitation and Hygiene and Soil-Transmitted Helminth Infection: A Demonstration of Two Recursive Partitioning Tools – Katherine Gass – PLOS Neglected Tropical Diseases

“Improvements to water, sanitation and hygiene (WASH) likely provide sustained benefit, but few rigorous studies have evaluated the specific WASH components most influential in reducing infection. “

Screen Shot 2014-06-27 at 9.36.14 PMSocial Sciences Research on Infectious Diseases of Poverty: Too Little and Too Late? – José Azoh Barry – PLOS Neglected Tropical Diseases

“Besides the vicious circle these diseases maintain with dire conditions of poverty, an increased microbial resistance to some therapeutic drugs adds to the complexity of health disparities and human suffering among the socially disadvantaged, marginalized, and prejudiced against.”

Dengue

Screen Shot 2014-06-27 at 9.36.37 PMVariability in Dengue Titer Estimates from Plaque Reduction Neutralization Tests Poses a Challenge to Epidemiological Studies and Vaccine Development – Henrik Salje – PLOS Neglected Tropical Diseases

“We used repeated assays on the same two pools of serum using five different viruses (2,319 assays) to characterize the variability in the technique under identical experimental conditions. We also assessed the performance of multiple statistical models to interpolate continuous values of neutralization titer from discrete measurements from serial dilutions.”

Science and career

PLOSTen Simple Rules for Approaching a New Job – Philip E. Bourne – PLOS Computational Biology

“Thinking both as a job applicant and a job interviewer about how I have approached job situations over the years before, during, and after the interview and how those situations have turned out, I can offer the following ten simple rules as you prepare.”

A New Online Computational Biology Curriculum – David B. Searls – PLOS Computational Biology

“A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields. This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. “

Arsenic metabolism

Screen Shot 2014-06-27 at 10.00.06 PMAssociations between Arsenic Species in Exfoliated Urothelial Cells and Prevalence of Diabetes among Residents of Chihuahua, Mexico – Jenna M. Currier – Environ Health Perspect

“We measured concentrations of trivalent and pentavalent iAs, methyl-As (MAs), and dimethyl-As (DMAs) species in EUC from 374 residents of Chihuahua, Mexico, who were exposed to iAs in drinking water.”

Dr. Bik’s Picks

Screen Shot 2014-06-27 at 10.09.01 PMWith pictures and videos: Duration of urination does not change with body size – Patricia J. Yang – PNAS

“In this study, we report a mathematical model that clarifies misconceptions in urology and unifies the results from 41 independent urological and anatomical studies. The theoretical framework presented may be extended to study fluid ejection from animals, a universal phenomenon that has received little attention.”

Screen Shot 2014-06-27 at 10.01.44 PMFrom Gemstones to Arsenic: How the Development of Pigment Colored Art – Allison Meier

“A new exhibition at London’s National Gallery — Making Colour — looks at the development of color in art, from the Middle Ages to 1900. “

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Non-human microbiome, June 25

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Mongolian Gerbils, soil microbiome affects plant flowering time, soybeans, and seawater viruses.

Mammalian microbiome

Screen shot 2014-06-25 at 01.26PM, Jun 25Helicobacter pylori Induced Gastric Immunopathology Is Associated with Distinct Microbiota Changes in the Large Intestines of Long-Term Infected Mongolian Gerbils – Markus M. Heimesaat – PLOS ONE

“Comprehensive cultural analyses revealed that severe gastric diseases such as atrophic pangastritis and precancerous transformations were accompanied by elevated luminal loads of E. coli and enterococci in the caecum and together with Bacteroides/Prevotella spp. in the colon of H. pylori WT, but not MUT infected gerbils as compared to naïve animals. “

Plant microbiome

Screen shot 2014-06-25 at 01.27PM, Jun 25Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field – Akifumi Sugiyama – PLOS ONE

“Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. “

Screen shot 2014-06-25 at 06.41PM, Jun 25Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative – Maggie R. Wagner – Ecology Letters

“Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. “

Water microbiology

Screen shot 2014-06-25 at 01.27PM, Jun 25 1Anthropogenic Litter in Urban Freshwater Ecosystems: Distribution and Microbial Interactions – Timothy Hoellein – PLOS ONE

“To assess microbial interactions with AL, we incubated AL and natural substrates in 3 freshwater ecosystems, quantified biofilm metabolism as gross primary production (GPP) and community respiration (CR), and characterized biofilm bacterial community composition via high-throughput sequencing of 16S rRNA genes.”

Screen shot 2014-06-25 at 01.28PM, Jun 25Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea – Christian Winter – PLOS ONE

“The identifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accounting for 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. “

Screen shot 2014-06-25 at 01.28PM, Jun 25 1The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing – Patrick J. Keeling – PLOS Biology

“The MMETSP relies primarily on cultured organisms, and this introduces a different set of biases, most obviously, favoring organisms that are photosynthetic. “

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General microbiology and science, June 24

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Metabolomics, metagenomics, phages in the human gut, arsenic poisoning in China, and a big award for Dengue research.

Metabolomics

Metaproteomics: Extracting and Mining Proteome Information to Characterize Metabolic Activities in Microbial Communities – Paul E. Abraham – Current Protocols in Bioinformatics

“In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. “

Review: The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva – Anton Amann – Journal of Breath Research

“Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease.”

Metagenomics and DNA structure

Sequencing the Strange Communities: Taking on Metagenomics – Aaron Krol – Bio-IT World

““Communities are made up of organisms that interact,” says Jonathan Eisen, a professor at the School of Medicine and the College of Biological Sciences at the University of California, Davis. “They’re not made up of short reads of Illumina sequences. And we need to stitch those together into organisms in order to make useful predictions, and interpretation of experimental data.””

Gene positioning and genome function – Nidhi Vishnoi, Jie Yao – Frontiers in Biology

” In this review, we discuss some recent findings as well as experimental tools to investigate subnuclear gene positioning and to explore its implications in genome functions.”

Phages and viruses

Classification and quantification of bacteriophage taxa in human gut metagenomes – Alison S Waller – ISME Journal 

“Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. “

Techniques

Enzymatic Treatment of Specimens before DNA Extraction Directly Influences Molecular Detection of Infectious Agents – Pablo Goldschmidt – PLOS ONE

“The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.”

Dengue

Sustainable Sciences Institute (SSI) Awarded $1 Million to Battle Growing Threat to Global Public Health: Mosquito-borne Dengue Virus – PR Web

“SSI, a San Francisco nonprofit founded by Eva Harris, UC Berkeley Professor of Infectious Disease and Vaccinology and former MacArthur “Genius” award winner, has worked to minimize the threat of potentially fatal Dengue disease for 15 years. With the latest award of $1 million dollars, Harris and other SSI investigators will be able to extend their reach and speed up their efforts.”

Infection and host response

Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection – Laxmi Yeruva – mBio

“To determine if chemokine and cytokine production within 24 h of infection is associated with the outcome of pathology, levels of 15 chemokines and cytokines were measured. “

Immunity to gastrointestinal nematodes: mechanisms and myths – Richard K. Grencis – Immunological Reviews

“This review aims to discuss the recent discoveries in both host protection and immunoregulation against gastrointestinal nematodes, placing the data in context of the specific life cycles imposed by the different parasites studied and the future challenges of considering the mucosal/immune axis to encompass host, parasite, and microbiome in its widest sense.”

Tailored immunity at mucosae – Yasmine Belkaid – Immunological Reviews

“This issue of Immunological Reviews presents articles from investigators involved in the exploration of the mechanisms by which mucosal barrier sites induce and control innate and adaptive immune responses.”

Detection of bacteria in blood and other sites

Rapid Detection of Enterobacteriaceae Producing Extended Spectrum Beta-Lactamases Directly From Positive Blood Cultures by Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) – Marina Oviaño – Clinical Microbiology and Infection

“In the assay, 141 blood cultures were tested, 13 out of them were real bacteremias and 128 corresponded to blood culture bottles seeded with bacterial clinical isolates. Bacteremias were analyzed by MALDI-TOF after a positive growth result and the 128 remaining blood cultures 24 hours after the bacterial seeding. “

General microbiology and ecology

The quest for a unified view of bacterial land colonization – Hao Wu – ISME Journal

“Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. “

Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes – Akinori Yabuki – ISME Journal

“Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate.”

Arsenic metabolism

Arsenic Pollution Sows Despair in Chinese Cancer Village (slideshow)- Yahoo News

“Xiong Demin could not have foreseen that the mine he worked at for 32 years would leave his home village poisoned and hundreds of residents, including himself and his wife, stricken with cancer.”

Dr. Bik’s Picks – Evolution Edition

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials – Kieren J. Mitchell – Molecular Biology and Evolution

“We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species”

Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals – Zhen Liu – Molecular Biology and Evolution

“By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency bat, Stoliczka’s trident bat (Aselliscus stoliczkanus). “

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape – Yasunori Ichihashi – PNAS

“Utilizing the natural variation in leaf morphology between tomato and two related wild species, we identified a gene network module that leads to a dynamic rewiring of interactions in the whole leaf developmental gene regulatory network. “

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Non-human microbiome, June 23

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What happens with all that triclosan we flush down the drain? Also, baby squirrels, tse-tse flies, pot, and Chinese liquor.

Animal microbiome general 

Two very different papers from the same group, but both are finding that Blautia species are host specific.

Screen Shot 2014-06-23 at 10.57.57 PM

A single genus in the gut microbiome reflects host preference and specificity – A Murat Eren – The ISME Journal

“In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping.” (Humans, cows, swine, deer, chickens)

Screen Shot 2014-06-23 at 11.26.18 PMBlautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters – Amber M. Koskey – Environmental Microbiology Reports

“We used oligotyping to identify Prevotella and Blautia sequences that can distinguish human fecal contamination. Thirty-five of 61 Blautia oligotypes and 13 of 108 Prevotella oligotypes in humans were specific to or highly abundant (i.e. host-preferred) compared to pig, dog, horse, and cow sources.”

Squirrel microbiome

Screen Shot 2014-06-23 at 11.35.26 PMTemporal Dynamics of the Cecal Gut Microbiota of Juvenile Arctic Ground Squirrels: a Strong Litter Effect across the First Active Season – Timothy J. Stevenson – Applied and Environmental Microbiology  (image courtesy of ego-alterego.com)

“We characterized trends in diversity (454 pyrosequencing), density (flow cytometry), viability (flow cytometry), and metabolism (short-chain fatty acid analysis) of the gut microbial community of juvenile arctic ground squirrels across their first active season at weaning and at 4, 6, 8, and 10 weeks postweaning.”

Insect microbiome

Screen Shot 2014-06-23 at 11.20.33 PMAnalysis of Multiple Tsetse Fly Populations in Uganda Reveals Limited Diversity and Species-Specific Gut Microbiota – Emre Aksoy – Applied and Environmental Microbiology

“We used multiple approaches, including deep sequencing of the V4 hypervariable region of the 16S rRNA gene, 16S rRNA gene clone libraries, and bacterium-specific quantitative PCR (qPCR), to investigate the levels and patterns of gut microbial diversity from a total of 151 individuals.”

Screen Shot 2014-06-23 at 11.22.49 PMMicrobial Population Dynamics in the Hemolymph of Manduca sexta Infected with Xenorhabdus nematophila and the Entomopathogenic Nematode Steinernema carpocapsae – Swati Singh – Applied and Environmental Microbiology

“We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine.”

Screen Shot 2014-06-23 at 11.23.22 PMPurine Biosynthesis, Biofilm Formation, and Persistence of an Insect-Microbe Gut Symbiosis – Jiyeun Kate Kim – Applied and Environmental Microbiology

“When we disrupted purN and purT in the Burkholderia symbiont, the ΔpurN and ΔpurT mutants grew normally, and only the ΔpurT mutant failed to form biofilms. “

Plant microbiome

Plant metabolomics for plant chemical responses to belowground community change by climate change – Sangkyu Park – Journal of Plant Biology

“In this review, we will first summarize recent progress in plant metabolomics methodology and subsequently review recent studies of interactions between plants and soil organisms in relation to climate change issues.”

Bioreactor and sewage microbiology

TriclosanThe Impacts of Triclosan on Anaerobic Community Structures, Function, and Antimicrobial Resistance – Patrick J McNamara – Environmental Science & Technology

“Triclosan amendment caused all of the Bacteria and Archaea communities to structurally diverge from that of the control cultures (based on ARISA).”

Screen Shot 2014-06-23 at 11.24.07 PMShifts in the Microbial Community, Nitrifiers and Denitrifiers in the Biofilm in a Full-scale Rotating Biological Contactor – Xingxing Peng – Environmental Science & Technology

“The objective of this study was to investigate the Microbial community shifts of bacteria, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath”

Soil microbiology

Screen Shot 2014-06-23 at 11.32.29 PMIdentifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment – Catriona A Macdonald – Environmental Microbiology

“All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits.”

Screen Shot 2014-06-23 at 11.25.34 PMExtensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi – Robert Riley – PNAS

“To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. “

Food and other consumables microbiology

Screen Shot 2014-06-23 at 11.33.28 PMIf the pot doesn’t worry you, the bacteria might: Food safety a new frontier for legal pot – Kristen Wyatt – The Republic

“In Washington state, where retail sales are expected to begin the week of July 7, regulations call for samples of all marijuana sold for consumption to clear a “microbiological screening,” whether it’s in edible, smokeable or concentrate form.”

Screen Shot 2014-06-23 at 11.34.50 PMStarter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation – Qun Wu – Applied and Environmental Microbiology

“To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor.”

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More Microbiology and Science, June 5

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Today we’ll learn why koalas hug trees, how to grow plants taller using blood and bacteria, and how to (not) get sick in a veterinary hospital.

Infection, host response, sepsis

Screen Shot 2014-06-05 at 8.35.13 PMGene Expression Profiles of Human Dendritic Cells Interacting with Aspergillus fumigatus in a Bilayer Model of the Alveolar Epithelium/Endothelium Interface – Charles Oliver Morton – PLOS ONE

“Two distinct sub-groups of dendritic cells (DC), monocyte-derived DC (moDC) and myeloid DC (mDC), were included in the model to examine immune responses to fungal infection at the alveolar surface”

Screen Shot 2014-06-05 at 8.52.36 PMDusp3 and Psme3 Are Associated with Murine Susceptibility to Staphylococcus aureus Infection and Human Sepsis – Qin Yan – PLOS Pathogens

“One QTL region on chromosome 11 containing 422 genes was found to be significantly associated with susceptibility to S. aureus infection. “

Screen Shot 2014-06-05 at 8.36.06 PMAn Individual-Based Model of Transmission of Resistant Bacteria in a Veterinary Teaching Hospital – Neeraj Suthar – PLOS ONE

“The model suggested that transmission resulting from contact with healthcare workers was common, and that certain transmission points (housing wards, diagnostics room, and the intensive care unit) presented higher risk for transmission than others (lobby and surgery). “

Dengue

Screen Shot 2014-06-05 at 8.36.42 PMInduction of Neutralizing Antibody Response against Four Dengue Viruses in Mice by Intramuscular Electroporation of Tetravalent DNA Vaccines – Eakachai Prompetchara – PLOS ONE

“This study evaluated neutralizing antibody (NAb) induction of a dengue tetravalent DNA (TDNA) vaccine candidate administered by intramuscular-electroporation (IM-EP) and the benefit of homologous TDNA boosting in mice.”

Circulating Levels of Soluble MICB in Infants with Symptomatic Primary Dengue Virus Infections – Daniel H. Libraty – PLOS ONE

“We found that serum levels of sMICB increased between pre-infection and acute illness among infants with symptomatic primary dengue virus infections”

Screen Shot 2014-06-05 at 8.37.27 PMImmature Dengue Virus Is Infectious in Human Immature Dendritic Cells via Interaction with the Receptor Molecule DC-SIGN – Mareike K. S. Richter – PLOS ONE

“We show that immature DENV is infectious in cells expressing DC-SIGN. Furthermore, we demonstrate that immature dendritic cells, in contrast to macrophage-like cells, do not support antibody-dependent enhancement of immature DENV.”

Viruses and Phages

Screen Shot 2014-06-05 at 8.39.02 PMThe distribution and impact of viral lineages in domains of life – Arshan Nasir

“the distribution of viral lineages follows an ancient, highly dynamic and ongoing process that impacts the evolution of organisms. New viral lineages often arise from existing ones and may cross species barriers to infect new hosts”

Alternative invention for shrimp bacterial pathogens wins patent – Times of India

“Dr Indrani Karunasagar, director, UNESCO Centre for marine Biotechnology and Associate Director of Research, has received the patent for “the process of preparing a consortium of bacteriophages for controlling luminous bacterial disease in shrimp larvae.” Like a virus, a lytic bacteriophage is a virus that infects and replicates within the bacteria and kills it. “

Microbial Ecology

Screen Shot 2014-06-05 at 8.53.35 PMThe microbial contribution to macroecology – Albert Barberán – Frontiers in Microbiology

“We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales.”

More microbiology

Screen Shot 2014-06-05 at 8.40.05 PMInteractions between Bacillus anthracis and Plants May Promote Anthrax Transmission
Holly H. Ganz – PLOS Neglected Tropical Diseases

“We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls.”

Screen Shot 2014-06-05 at 8.54.21 PMTo be or not to be associated: power study of four statistical modeling approaches to identify parasite associations in cross-sectional studies – Elise Vaumourin – Frontiers in Cellular and Infection Microbiology

“We applied these four approaches to detect associations within two populations of multi-infected hosts: (1) rodents infected with Bartonella sp., Babesia microti and Anaplasma phagocytophilum and (2) bovine population infected with Theileria sp. and Babesia sp”

Screen Shot 2014-06-05 at 8.47.24 PMPCR performance of a thermostable heterodimeric archaeal DNA polymerase – Tom Killelea – Frontiers in Microbiology, Evolutionary and Genomic Microbiology

“Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. “

Arsenic metabolism

Screen Shot 2014-06-05 at 8.50.18 PMArsenic and old toenails – University of British Columbia

“We successfully recruited 35,000 Atlantic Canadians whose health will be tracked over the next 25 years, and the project will be a major resource for cancer prevention research. More than 22,000 participants provided blood and toenail clippings, which ended up being an official Guinness World Record.”

Marine Mammals (and turtles)

Screen Shot 2014-06-05 at 8.51.14 PMSatellite Tracking of Sympatric Marine Megafauna Can Inform the Biological Basis for Species Co-Management – Christian Gredzens – PLOS ONE

“Fast-acquisition satellite telemetry was used to track eleven dugongs and ten green turtles at two geographically distinct foraging locations in Queensland, Australia to evaluate the inter- and intra-species spatial relationships and assess the efficacy of existing protection zones. “

Dr. Bik’s Picks

Screen Shot 2014-06-05 at 8.48.40 PMThe sheep genome illuminates biology of the rumen and lipid metabolism – Yu Jiang- Science

“We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution.”

Screen Shot 2014-06-05 at 8.55.17 PMMapping the Global Distribution of Livestock – Timothy P. Robinson – PLOS ONE

“This paper describes the current approach in detail and presents new global distribution maps at 1 km resolution for cattle, pigs and chickens, and a partial distribution map for ducks. These digital layers are made publically available via the Livestock Geo-Wiki (http://www.livestock.geo-wiki.org), as will be the maps of other livestock types as they are produced.”

Screen Shot 2014-06-05 at 9.02.51 PMCatfish ‘See’ Their Next Meal with Acid-Sensing Whiskers – Charles Q. Choi – LiveScience

“Catfish have evolved sensors on their whiskers that can help the animals hunt in the dark by detecting slight changes in water acidity, the first time such sensors have been seen in fish, researchers say.”

Screen Shot 2014-06-05 at 8.56.34 PMWhy Koalas Hug Trees – Tia Ghose – LiveScience

“Now, scientists have figured out why the iconic Australian marsupials hug trees: The trunks help the koala bears keep cool, according to a new study.”

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Environmental microbiome digest, May 29 2014

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Today, we will learn about microbial communities in Petroleum “muck” and blue jeans.

Environmental microbiomes

  • Metagenomic Approach for Understanding Microbial Population from Petroleum Muck – M. N. Joshi – Genome Announcements –  “the first report which describes a next generation sequencing based study of microbial diversity from petroleum pipelines”
  • Opening session ASM 2014 (2h video): Microbes in Symbiosis, Signaling and at Sea – Michael Laub, Lora Hooper, Ove Hoegh-Guldberg
  • Screen Shot 2014-05-29 at 4.53.06 PMCan You Really Clean Your Jeans By Freezing Them? – Sam Brock and Kinsey Kiriakos – NBC Bay Area – “We traveled to an environment that is filled with bacteria, the zoo, and showcased a brand new pair of Levi’s jeans while we fed the lemurs, handled worms, grazed with the goats and transplanted saliva from the local zebu (a species of cattle) onto the pants. Next, we took the jeans to the Stanford lab for analysis. Perez swabbed the jeans for bacteria, both inside and out, before we froze them overnight and after.”

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Digest May 27, 2014

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Today’s Picks feature thousand cultured GI tract species, host-microbiome interactions during pregnancy, metagenome assemblies using Hi-C, and the microbiomes of snow leopards and possums.

Human microbiome general

Human Gut Microbiome

Pregnancy and birth microbiome

Respiratory tract microbiome

Mammalian microbiome

Amphibian microbiome

Insect microbiome

Fish microbiome

Animal and bioreactor models of gut microbiome

Environmental microbiome

Microbiome and Metabolomics

Phages and viruses

  • Beyond Antibiotics – “Today there is renewed interest in phages as warnings intensify that a “post-antibiotic” era looms” – Roger Highfield – Newsweek

Infection, sepsis, and host response

Microbial Ecology papers

Arsenic metabolism

Chromosome organization

General lab techniques papers

Dr. Bik’s Picks

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Digest May 22, 2014

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Today’s digest features armpits, helminths and fish probiotics.

Skin microbiome papers

Gut microbiome papers

Pregnancy and birth microbiome papers

Animal microbiome papers

General microbiome papers

Dengue papers

Arsenic metabolism papers

Science, Ethics and Misconduct

Dr. Bik’s Picks

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