Non-human microbiome digest, October 14, 2014

Diatoms in aquatic animals, bacteria in agaves and soybeans, and bacteria in artificial soil.

Animal microbiome

Diatoms in cytologic specimens of aquatic animals – Part I, fecal samples – Nicole StacyDiatoms in cytologic specimens of aquatic animals – Part II, dermal, respiratory, and gastric samples – Nicole Stacy – Veterinary Clinical Pathology

“Diatoms are a common finding in cytologic samples of aquatic animals…and it is necessary to differentiate these microbiota from parasite ova or protozoa.”

Impacts of large-bodied crustaceans on the microbial loop – Krystyna Kalinowska – Hydrobiologia

“Three alien crustacean species (Daphnia pulex, Simocephalus vetulus and Macrocyclops albidus) were collected from the regional species pool and added to mesocosms that were filled with water from a eutrophic lake “

Bacterial Community Composition of Three Candidate Insect Vectors of Palm Phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing) –  Christopher M. Powell – Current Microbiology

“Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.”

Plant microbiome

Diazotrophic potential among bacterial communities associated with wild and cultivated agaves – Damaris Desgarennes – FEMS Microbiology Ecology

“Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA-DGGE fingerprinting and sequencing.”

Spatio temporal influence of isoflavonoids on bacterial diversity in the soybean rhizosphere – Laura J White – Molecular Plant-Microbe Interactions

“We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy root composite plants, and examined changes in rhizosphere bacteriome diversity.”

Soil microbiome

Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particles size fractions – Michael Hemkemeyer – FEMS Microbiology Ecology

“this study demonstrates that the mineral composition and the particle size fractions have specific and different selective effects on the three domains”

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding – S Terrat – Heredity

“Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. “

The role of stochasticity differs in the assembly of soil- and root-associated fungal communities – Sarah Beck – Soil Biology and Biochemistry

“The importance of spatial and environmental factors in shaping fungal beta diversity was determined over a 500 km transect.”

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Microbiome and general science digest, July 10

Hi all, just one post today, with everything combined. Bacterial vaginosis, daily rhythms  of marine bacteria, food microbiology, and The Picks.

Human vaginal microbiome

Role of Gardnerella vaginalis in the Pathogenesis of Bacterial Vaginosis: A Conceptual Model – Jane R. Schwebke – Journal of Infectious Diseases

“Our model suggests that BV is initiated by the sexual transmission of Gardnerella vaginalis, which has the appropriate virulence factors to adhere to host epithelium, create a biofilm community, and successfully compete with lactobacilli for dominance in the vaginal environment. “

Seawater microbiome

Multispecies dielMultispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages – Elizabeth A. Ottesen – Science, with an Editorial by E. Virginia Armbrust: “Taking the pulse of ocean microbes

“As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. “

Screen Shot 2014-07-10 at 11.53.04 PMReview: Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome – Ivone Vaz-Moreira – FEMS Microbiology Reviews

“In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. “

Food microbiology

Cassava beerLocal domestication of lactic acid bacteria via cassava beer fermentation – Alese M. Colehour – PeerJ

“Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. “

LobsterCharacterization of the dominant bacterial communities during storage of Norway lobster and Norway lobster tails (Nephrops norvegicus) based on 16S rDNA analysis by PCR-DGGE – Bekaert Karen – Food Microbiology

“To characterize as many bacterial species present as possible, we performed advanced molecular identification techniques (PCR-DGGE). The initial TVC of fresh Norway lobster meat was high (3.0 log cfu/g) as compared to fish.”

charquiEffect of autochthonous bacteriocin-producing Lactococcus lactis on bacterial population dynamics and growth of halotolerant bacteria in Brazilian charqui – Vanessa Biscola – Food Microbiology

“Charqui is a fermented, salted and sun-dried meat product, widely consumed in Brazil and exported to several countries. “

Microbes in the news

Using the gut microbiome to improve health – Mary MacVean – LA Times

“The “bistable” groups, the authors wrote, represent “tipping elements,” or components of the gut microbes that “exhibit alternative stable states linked to the overall ecosystem state and our physiology.” “

Science, Ethics and Publishing

Crack Down on Scientific Fraudsters – Adam Marcus and Ivan Oransky – New York Times

“Criminal charges against scientists who commit fraud are even more uncommon. In fact, according to a study published last year, “most investigators who engage in wrongdoing, even serious wrongdoing, continue to conduct research at their institutions.””

Dr. Bik’s Picks

Microplastics in the seas – Kara Lavender Law, Richard C. Thompson – Science

“Microplastics are likely the most numerically abundant items of plastic debris in the ocean today, and quantities will inevitably increase, in part because large, single plastic items ultimately degrade into millions of microplastic pieces. “

Uncontacted tribe in Brazil emerges from isolation – Heather Pringle – Science

“The meeting was Brazil’s first official contact with an isolated Amazonian tribe in 20 years. Anthropologists remain deeply concerned about the tribe’s future as it encounters novel diseases and resource-hungry outsiders. “

Polar BearsPolar Bears from Space: Assessing Satellite Imagery as a Tool to Track Arctic Wildlife – Seth Stapleton – PLOS ONE

“We examined satellite images of a small island in Foxe Basin, Canada, occupied by a high density of bears during the summer ice-free season. Bears were distinguished from other light-colored spots by comparing images collected on different dates. “

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General microbiology and science, July 7

Metagenomics binning based on co-abundance, bias in Illumina sequencing, and lots of metabolomics.

Phages and viruses

Bacteriophage-based synthetic biology for the study of infectious diseases – Robert J Citorik – Current Opinion in Microbiology

“Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. “

Sequencing and Metagenomics

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes – H Bjørn Nielsen (and 142 other authors) – Nature Biotechnology

“Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.”

Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles – Katherine Kennedy – Applied and Environmental Microbiology

“In this study, we tested the effects of template concentration, pooling of PCR amplicons, and sample preparation/inter-lane sequencing on the reproducibility associated with paired-end Illumina sequencing of bacterial 16S rRNA genes.”

Next generation sequencing technology: Advances and applications – HPJ Buermans, JT den Dunnen – Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease

“In this chapter we review the technical background of the different commercially available NGS platforms with respect to template generation and the sequencing reaction and take a small step towards what the upcoming NGS technologies will bring.”

Systems biology as an approach for deciphering microbial interactions – Puneet Kumar Singh – Briefings in Functional Genomics

“Here, we endeavor to summarize, epigrammatic description of sophisticated techniques and software that provides an enhanced understanding of metagenomics data analysis. “

Metabolomics

Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations – Tommi Suvitaival – Bioinformatics

“We propose a hierarchical Bayesian model for inferring
differences between groups of samples more accurately in
metabolomic studies, where the observed compounds are collinear.”

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

“Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems.”

Metabolomics Analysis Identifies Intestinal Microbiota-Derived Biomarkers of Colonization Resistance in Clindamycin-Treated Mice – Robin L. P. Jump – PLOS ONE

“Clindamycin treatment caused marked changes in metabolites present in fecal specimens. Of 484 compounds analyzed, 146 (30%) exhibited a significant increase or decrease in concentration during clindamycin treatment followed by recovery to baseline that coincided with restoration of in vivo colonization resistance.”

Volatile Organic Compounds as Novel Markers for the Detection of Bacterial
Infections – Mohsen Sohrabi – Clinical Microbiology

“The possibility of using VOCs markers as one of the largest groups of bacterial metabolites would open a new frontier for developing more efficient techniques in the diagnosis of bacterial infections.”

The importance of sulfur-containing metabolites in discriminating fecal extracts between normal and type 2 diabetic mice – Alesia Walker – Journal of Proteome Research

“We demonstrate that a metabolic disorder such as T2DM affects the gastrointestinal tract environment thereby influencing different metabolic pathways and their respective metabolites in diabetic mice. “

Microarrrays

Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes (PDF) -Oleg Paliy and Vijay Shankar – Book chapter

“This chapter will focus on currently available phylogenetic microarrays for the inter- rogation of human-associated microbiota, the technologies used to construct the arrays, as well as several key features that distinguish them from other approaches. “

Arsenic metabolism

Infant toenails as a biomarker of in utero arsenic exposure – Matthew A Davis – Journal of Exposure Science and Environmental Epidemiology

“In a sample of 170 mother–infant pairs from New Hampshire, we determined infant exposure to in utero arsenic by evaluating infant toenails as a biomarker using inductively coupled plasma mass spectrometry. “

Chromosomal organization

Spatial confinement is a major determinant of the folding landscape of human chromosomes – Gamze Gürsoy – Nucleic Acids Research

“Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding. “

Bacteria in the news

The bacteria has been decimated: how much should we care what words used to mean? – By Tom Chivers – Telegraph

“Much amusement this morning on the Today programme, as John Humphrys shamefacedly confessed to having said “a bacteria” on the previous day’s episode.”

Yoghurt industry blamed for encouraging bacteria – The Daily Mash

“One day massive cow-sized bacteria will rule the world and they will kill everyone who doesn’t like special yoghurts.”

When Scientists Experiment on Themselves: H. pylori and Ulcers – By Hanno Charisius – Scientific American

“With his famous self-experiment, Marshall was able to demonstrate that Helicobacter pylori bacteria can cause acute gastritis which in turn may cause ulcers. He had asked neither an ethics commission nor his wife for permission to conduct this experiment. “

In rental cars, dangerous bacteria may come along for the ride – Jeff Rossen and Josh Davis, Today

“Armed with gloves and goggles, they swabbed every car from top to bottom: the steering wheels, gearshifts, door handles, even the GPS units.”

Bacteria that ‘eats’ odour could bring end to smelly toilets in China – Stephen Chen – South China Morning Post

“Mainland scientists have developed a “bioweapon” that can wipe out the notorious bad smell in public toilets. Up to 75 per cent of the odour can be removed, with the rest suppressed by a natural, pleasant fragrance, according to researchers with the Chinese Academy of Sciences.”

Marine Mammals

Some SeaWorld mammals survive longer in captivity – Mike Schneider – Associated Press

“Breakthroughs in training and medicine that allow the parks’ medical staffs to perform far fewer stressful or invasive procedures are partly responsible for those successes, SeaWorld officials said.”

Science and publishing

Highly cited Researchers 2014 – Thomson Reuters

“Over three thousand researchers earned the distinction by writing the greatest numbers of reports officially designated by Essential Science Indicators℠ as Highly Cited Papers—ranking among the top 1% most cited for their subject field and year of publication, earning them the mark of exceptional impact.”

Dr. Bik’s Picks

Rats use their whiskers in a similar way to how humans use their hands and fingers – Science Daily

“Rats deliberately change how they sense their environment using their facial whiskers depending on whether the environment is novel, if there is a risk of collision and whether or not they can see where they are going.”

Giraffe legs’ strong, skinny secret – Victoria Gill – BBC Science

“Scientists have worked out the anatomical secret to giraffes’ long and spindly – but strong – legs.”

Environmentalists Almost Killed My Friend – Josh Bloom – Science 2.0

“It is hysteria-producing nonsense like this that leads any non-scientist to conclude that we are systematically being poisoned every day. “

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Non-human microbiome digest, July 3

Parasites, effect of antibiotics in pigs, microbiome of birds, Drosophila, microbiome of plant crops, Hawai’i waters, and bacteria to preserve stone monuments.

Parasites and microbiome

Cooperation and conflict in host manipulation: interactions among macro-parasites and micro-organisms – Frank Cézilly – Frontiers in Microbiology

“Here, we review the empirical evidence in favor of the existence of synergistic or antagonistic interactions between co-occurring parasites, and highlight the neglected role of micro-organisms. “

holobiontHolobiont–Holobiont Interactions: Redefining Host–Parasite Interactions – Nolwenn Marie Dheilly – PLOS Pathogens

“It has been established in different model species that immune system maturation requires the presence of mutualistic bacteria”

Marine mammal microbiome

Screen shot 2014-07-03 at 04.24PM, Jul 03Intestinal helminth fauna of striped dolphins (Stenella coeruleoalba) in the western Mediterranean: No effects of host body length, age and sex – Paula Mateu – Marine Mammal Science

“The intestine of 52 (28 males and 24 females) striped dolphins (Stenella coeruleoalba) from western Mediterranean waters was examined for helminths. Animals were found stranded along the Spanish coasts during the morbillivirus epizootic in 1990.”

Pig microbiome

Screen shot 2014-07-03 at 03.17PM, Jul 03Carbadox has both temporary and lasting effects on the swine gut microbiota – Torey Looft – Frontiers in Microbiology

“Carbadox is an in-feed antibiotic that is widely used in swine production to prevent dysentery and to improve feed efficiency. The goal of this study was to characterize the effects of carbadox and its withdrawal on the swine gut microbiota. ”

Screen shot 2014-07-03 at 03.18PM, Jul 03Learning from agriculture: understanding low-dose antimicrobials as drivers of resistome expansion – Yaqi You – Frontiers in Microbiology

“Unconfined storage or land deposition of a large volume of animal waste causes its wide contact with the environment and drives the expansion of the environmental resistome through mobilome facilitated horizontal genet (sic, EB) transfer. “

Bird microbiome

Screen shot 2014-07-03 at 03.18PM, Jul 03Interspecific variations in the faecal microbiota of Procellariiform seabirds – Meagan L. Dewar – FEMS Microbiology Ecology

“Examining the faecal microbiota of three Procellariiform species (short-tailed shearwater, common diving petrel and fairy prion) provided a unique opportunity to not only characterise the gastrointestinal (GI) microbial composition of seabirds but to also examine the influence of stomach oils on the microbial community.”

Insect microbiome

Drosophila modelTransient adult microbiota, gut homeostasis and longevity: Novel insights from the Drosophila model – Berra Erkosar, Francois Leulier – FEBS Letters

“In the last decade, Drosophila has emerged as a useful model to study host–microbiota interactions, creating an active research field with prolific publications.”

Plant microbiome

Screen shot 2014-07-03 at 03.21PM, Jul 03Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance – Devin Coleman-Derr – Frontiers in Microbiology

“In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. “

Screen shot 2014-07-03 at 03.21PM, Jul 03Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants – Catherine A. Gehring – Frontiers in Microbiology

“We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa.”

Screen shot 2014-07-03 at 03.22PM, Jul 03Nitrogen-fixing Rhizobium-legume symbiosis: are polyploidy and host peptide-governed symbiont differentiation general principles of endosymbiosis? – Gergely Maróti- Frontiers in Microbiology

“This review focuses on symbiotic plant cell development and terminal bacteroid differentiation and demonstrates the crucial roles of symbiotic peptides”

Screen shot 2014-07-03 at 03.22PM, Jul 03Disparate origins of Bradyrhizobium symbionts for invasive populations of Cytisus scoparius (Leguminosae) in North America – Kevin Horn – FEMS Microbiology Ecology

“To identify the geographic origin of nodule bacteria associated with invasion of the European legume Cytisus scoparius in the United States, isolates from 15 sites in six states were compared to > 200 Bradyrhizobium strains from indigenous legumes in the U.S., Mexico, Europe (six countries), Morocco, and Australia. “

Food microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic – Marilynn R. Fairfax – Frontiers in Microbiology

“Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals.”

Stone microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03 1Application of calcifying bacteria for remediation of stones and cultural heritages – Navdeep Kaur Dhami – Frontiers in Microbiology

“The present review emphasizes about different causative agents leading to deterioration and application of microbially induced calcium carbonate precipitation as a novel and potential technology for dealing with these problems. “

Soil microbiology

Screen shot 2014-07-03 at 03.25PM, Jul 03Volatile-mediated interactions between phylogenetically different soil bacteria
Paolina Garbeva – Frontiers in Microbiology

“Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. “

Screen shot 2014-07-03 at 03.27PM, Jul 03Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil – Liliana Quiza – Frontiers in Microbiology

“The main objective of this study was to assess the impact of land-use and soil properties on coxL gene diversity and identify molecular indicators for the soil uptake of atmospheric CO.”

Screen shot 2014-07-03 at 03.26PM, Jul 03Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia
Yong-Liang Chen – FEMS Microbiology Ecology

“… we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. “

Water microbiology

Screen shot 2014-07-03 at 03.27PM, Jul 03Biogeography of planktonic and benthic cyanobacteria in coastal waters of the Big Island, Hawai’i – Samuel D. Chamberlain – FEMS Microbiology Ecology

“To understand the patterns of cyanobacterial biogeography in relation to coastal environmental factors, we examined the diversity of planktonic and benthic cyanobacteria at 12 sites along the west coast of Hawaii’s Big Island.”

Screen shot 2014-07-03 at 03.29PM, Jul 03Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments – François Thomas – Frontiers in Microbiology

“We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays.”

Screen shot 2014-07-03 at 03.28PM, Jul 03Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities – Luisa Delgado-Serrano – FEMS Microbiology Ecology

“In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea – Nicole J. Bale – FEMS Microbiology Ecology

“The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03 1Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools – Tanja Shabarova – FEMS Microbiology Ecology

“Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes.”

Screen shot 2014-07-03 at 03.30PM, Jul 03Abundance, diversity and seasonal dynamics of predatory bacteria in aquaculture zero discharge systems – Prem P. Kandel – FEMS Microbiology Ecology

“The dynamics of populations belonging to the obligate predators Bdellovibrio and like organisms (BALOs) were analyzed in freshwater and saline ZDS over a 7-month period using QPCR targeting the Bdellovibrionaceae, and the Bacteriovorax and Bacteriolyticum genera in the Bacteriovoracaeae”

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General microbiology and science, June 26

Detection of bacteria in blood cultures, detection of fungi with mass spectrometry, metagenomics, and humans influencing microbes. And the Picks.

Detection of bacteria in clinical sites

Pediatric Multicenter Evaluation of the Verigene Gram-Negative Blood Culture Test for Rapid Detection of Inpatient Bacteremia Involving Gram-Negative Organisms, Extended-Spectrum Beta-Lactamases, and Carbapenemases – K. V. Sullivan – Journal of Clinical Microbiology

“We evaluated the investigational use only (IUO) version of the rapid Verigene Gram-negative blood culture test (BC-GN), a microarray that detects 9 genus/species targets “

Evaluation of Three Rapid Diagnostic Methods for Direct Identification of Microorganisms in Positive Blood Cultures – Raquel M. Martinez – Journal of Clinical Microbiology

“A total of 159 blood cultures (VersaTREK Trek Diagnostic Systems, Cleveland, OH) positive for Gram-positive and Gram-negative bacteria as well as yeast were analyzed with QuickFISH and MALDI-TOF MS. In all, 102 blood cultures were analyzed using the BC-GP assay.”

Fungal detection

Screen Shot 2014-06-26 at 10.12.46 PMAccuracy of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Clinical Pathogenic Fungi: a Meta-Analysis – Huazhi Ling – Journal of Clinical Microbiology

Metagenomics

Screen Shot 2014-06-26 at 10.13.18 PMPredicting microbial growth – Jonathan Monk, Bernhard O. Palsson – Science

“This detailed biochemical information can be converted into a computational model—a genome-scale model, or GEM (1)—that allows phenotypic functions to be predicted. Both environmental and genetic parameters are explicitly accounted for in GEMs, enabling increasingly accurate predictions of the genotype-phenotype relationship in a given environment.”

Screen Shot 2014-06-26 at 10.11.58 PMBeyond the Chromosome: The Prevalence of Unique Extra-Chromosomal Bacteriophages with Integrated Virulence Genes in Pathogenic Staphylococcus aureus – Bryan Utter – PLOS ONE

“We selectively enriched and sequenced extra-chromosomal DNA from S. aureus isolates using Roche-454 technology and uncovered evidence for the widespread distribution of multiple extra-chromosomal prophages (ExPΦs) throughout both antibiotic-sensitive and -resistant strains. “

Antibiotic resistance

Screen Shot 2014-06-26 at 10.14.32 PMNext-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli – J. Veenemans – Journal of Clinical Microbiology

“We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands.”

General microbiology

Screen Shot 2014-06-26 at 10.15.15 PMAspergillomarasmine A overcomes metallo-β-lactamase antibiotic resistance – Andrew M. King – Nature

“Here we have identified a fungal natural product, aspergillomarasmine A (AMA), that is a rapid and potent inhibitor of the NDM-1 enzyme and another clinically relevant MBL, VIM-2. AMA also fully restored the activity of meropenem against Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. possessing either VIM or NDM-type alleles.”

Screen Shot 2014-06-26 at 10.13.55 PMMicrobiology of the Anthropocene – Michael R. Gillings, Ian T. Paulsen – Anthropocene

“Recent advances in microbial genomics and ecology show that human perturbations to microbial populations correspond closely to the proposed phases of the Anthropocene: the ‘paleoanthropocene’ which began with the rise of agriculture; the industrial revolution, from the late 1700’s; and the ‘great acceleration’ from the 1950’s to the present day. “

Marine mammals

Retrospective Study of Etiologic Agents Associated with Nonsuppurative Meningoencephalitis in Stranded Cetaceans in the Canary Islands – Eva Sierra – Journal of Clinical Microbiology

” Six animals (5 striped dolphins and 1 common dolphin) showed IHC and/or molecular evidence of morbilliviral antigens and/or genomes, mainly in brain tissue. Conventional nested PCR detected herpesviral DNA in brain tissue samples from two striped dolphins”

Free Willy? Dolphin drama riles aquaria – David Grimm – Science

“This week, the Dolphin Research Center in Grassy Key, Florida, sent a letter to the National Aquarium stating that removing these animals from their current facilities would be bad for both science and public engagement. “

Dr. Bik’s Picks

Screen Shot 2014-06-26 at 10.33.00 PMFlower discrimination by pollinators in a dynamic chemical environment – Jeffrey A. Riffell – Science

“Here, we measured the plume from Datura wrightii flowers, a nectar resource for Manduca sexta moths, and show that the scent was dynamic and rapidly embedded among background odors.”

Screen Shot 2014-06-26 at 10.32.13 PMBig Data Is Complex, Cluster Analysis Can Make It A Little Simpler – Science 2.0

“Imagine having to identify all the cities in the world, without having access to a map. A huge task”, says Rodriguez. “We therefore identified a heuristic, that is, a simple rule or a sort of shortcut to achieve the result”.”

Goosebump sensor developed by Korean research team – Leo Kelion – BBC News

“It works by recording a drop in the sensor’s capacitance – its ability to store an electrical charge – caused by it being deformed by the buckling of the skin’s surface.”

Screen Shot 2014-06-26 at 10.33.56 PMChimps like listening to music with a different beat – Science Daily

“While preferring silence to music from the West, chimpanzees apparently like to listen to the different rhythms of music from Africa and India, according to new research published by the American Psychological Association.”

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General microbiology and science, June 24

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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General microbiology and science, June 12

A whale with graffiti and morbillivirus, polio eradication, it’s fun to be a grad student, and Dr. Bik’s Picks.

Marine Mammals

grafwhaleGraffiti tagged A.C. whale died of dolphin-killer morbillivirus – Amy S. Rosenberg – The Inquirer

“Schoelkopf said the virus last summer was primarily found in bottle-nosed dolphins but that there was some inter-species crossover, including two humpback whales, a pygmy sperm whale and striped dolphins.”

austsealionPinnipednesday – Neophoca cinerea Edition – Mythbri – ObservationDeck

“It’s believed that the feces of Australian Sea Lions provide valuable nutrients to the local ecosystem. The bacteria found in the feces is very efficient in breaking down the waste into forms that are easily absorbed by coastal ecosystems.”

Phages and viruses

SciencePolio eradicators struggle to prevent the next outbreak – Leslie Roberts – Science

“But in 2013, the virus jumped borders and set off outbreaks in eight countries that had already eliminated it, sending cases soaring to 407. Now, by creating a “Red List,” the Global Polio Eradication Initiative is trying to predict where future outbreaks will occur—and prevent them.”

Science careers

fungradThe fun of science – Cathy Walker – Science

“Recently, I was reminded that my job as a graduate student in a science lab is actually “really cool.” I was in need of a reminder. “

Dr. Bik’s Picks

dinosEvidence for mesothermy in dinosaurs – John M. Grady – Science

“Moreover, when the effects of size and temperature are considered, dinosaur metabolic rates were intermediate to those of endotherms and ectotherms and closest to those of extant mesotherms. Our results suggest that the modern dichotomy of endothermic versus ectothermic is overly simplistic.”

bromineChemical element bromine is essential to life in humans and other animals, researchers discover – ScienceDaily

“The researchers, led by co-first authors Scott McCall, Christopher Cummings, Ph.D., and Gautam (Jay) Bhave, M.D., Ph.D., showed that fruit flies died when bromine was removed from their diet but survived when bromine was restored.”

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