Category Archives: Science – Career – Publishing

Microbiome digest, September 25, 2014

Posted on by

[hr]

Asbestos and microbiome, human gut microbiome during a long stay in the hospital, gut microbiome of 15 mammals, Wolbachia in insects, microbiome of plant roots, and eukaryotes in Norwegian waters.

Human respiratory microbiome

Airways microbiota: Hidden Trojan horses in asbestos exposed individuals? – Dimitrios E. Magouliotis – Medical Hypotheses

“Here, we propose and discuss that certain proteins secreted by airways symbiotic microbiota create membrane pores to the airway epithelial cells, through which asbestos fibers can penetrate the lung parenchyma and reach the sub-pleural areas.”

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

“We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients.”

Mammal microbiome

Convergence of gut microbiomes in myrmecophagous mammals – Frederic Delsuc – Molecular Ecology

“Here, we expand upon previous mammalian gut microbiome studies … to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples.

Insect microbiome

Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains – Julien Martinez – PLOS Pathogens

“We have investigated antiviral protection in 19 Wolbachia strains originating from 16 Drosophila species after transfer into the same genotype of Drosophila simulans. “

Plant microbiome

Niche and host-associated functional signatures of the root surface microbiome – Maya Ofek-Lalzar – Nature Communications

“Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. “

Water microbiome

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing – Elianne S. Egge – Journal of Eukaryotic Microbiology

“Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. “

Microbes in the news

Intensive Loss of Gut Bacteria Diversity – Molly Sharlach – The Scientist

In a study published today (September 23) in mBio, researchers also fed ICU patients’ “ultra-low-diversity” gut microbes to C. elegans roundworms.

How Termites Evolved to Decompose Plant Matter: Gut Bacteria and Fungus – Catherine Griffin – Science World Report

“In order to better understand this interaction, the researchers analyzed plant decomposition genes in the first genome sequencing of a fungus-farming termite and its fungal crop, and bacterial gut communities.”

Science and Career

Scientists Are Not Trusted By Americans – Here’s Why – Science 2.0

“A paper in PNAS finds that Americans seem wary of researchers because they get grant funding and do not trust scientists pushing political and cultural agendas. “

Read The Nasty Comments Women In Science Deal With Daily – Macrina Cooper-White – Huffington Post

“Every day you’re faced with some comment, some snide remark, some inability to get a name on a research paper. “

Bik’s Picks

Water on Earth is older than the sun, scientists say – Deborah Netburn – Los Angeles Times

“Some of the water molecules in your drinking glass were created more than 4.5 billion years ago, according to new research.”

Science Graphic of the Week: Three Ways to Visualize Our Melting Northern Ice Cap – Nick Stockton – Wired.com

“These three visualizations, by NASA’s Scientific Visualization Studio, illustrate this steadily unfolding situation, which has nightmarish implications..“

Healthy food might be bad for patients – here’s why – Amanda Squire – The Conversation

“The truth is that healthy food as we think of it may not be what patients really need.”

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

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever.”

[hr]

Microbiome digest, September 24, 2014

Posted on by

[hr]

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

Human microbiome general

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

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

Mammal microbiome

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

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

Soil microbiome

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

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

Metabolomics

Metabolomic profiles and childhood obesity – Wei Perng – Obesity

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

Microbes in the news

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

“The title pretty much sums this one up”

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

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

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

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

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

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

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

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

Science and publishing

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

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

Women in Science

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

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

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

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

Bik’s Picks

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

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

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

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

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

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

[hr]

Microbiome digest, September 23, 2014

Posted on by

I don’t have much time tonight, so I’ll keep it short.

Pregnancy and birth

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women – Yi-E Huang- Microbial Ecology

Impact of Feeding and Medical Practices on the Development of Necrotizing Enterocolitis – Brian L. Montenegro, Camilia R. Martin – Current Pediatrics Reports

Human respiratory microbiome

Expanding Our Understanding of Respiratory Microbiota in Cystic Fibrosis – John J. LiPuma – Annals of the American Thoracic Society

Microbiota in the throat and risk factors of laryngeal carcinoma – Hongli Gong – Applied and Environmental Microbiology

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

The Overarching Influence of the Gut Microbiome on End-Organ Function: The Role of Live Probiotic Cultures – Luis Vitetta – Pharmaceuticals

Excretion of host DNA in feces is associated with risk of Clostridium difficile infection –  Caroline Vincent – Journal of Immunology Research

Animal and in vitro studies of human microbiome

Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs – Hirotaka Igarashi – PLOS ONE

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Hannah Lees – PLOS ONE

A comparative evaluation of prebiotic oligosaccharides using in vitro cultures of infant fecal microbiome – J Stiverson – Applied and Environmental Microbiology

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs – Crystal L. Levesque – PLOS ONE

Mammal microbiome

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas), and binturongs (Arctictis binturong) – Erin A. McKenney – Integrative Zoology

Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey – Ibrahim Hamad – Scientific Reports

Insect microbiome

Routes of acquisition of the gut microbiota of Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

Sponge microbiome

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12427/abstract

Plant microbiome

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars – Márton Szoboszlay – Soil Biology and Biochemistry

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria – Pilar Martínez-Hidalgo – Scientific Reports

Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian – Ningfei Lei – PLOS ONE

Soil type dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

Soil microbiome

Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils – Keisuke Obase – FEMS Microbiology Ecology

Food microbiology

Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese – Bei Zhang – Dairy Science & Technology

Metabolomics / Functional metagenomics

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library – Fiona Fouhy – PLOS ONE

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

Aleksandr Milshteyn, Jessica S. Schneider, Sean F. Brady – Chemistry & Biology

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

Impact of dietary polydextrose fiber on the human gut metabolome – Santosh Lamichhane – Journal of Agricultural and Food Chemistry

Preserving the earth’s microbes for drug discovery in the future – Ranjith N. Kumavath and Satyanarayana S.V – Journal of Microbiology and Microbial Research

Microbial Ecology

PNAS has a special issue this week on Biogeography (with the Panama forest trees paper by Jessica Green): The emergence and promise of functional biogeography – Cyrille Violle – PNAS

Active invasion of bacteria into living fungal cells – Nadine Moebius – eLife

Microbes in the news

Microbiome: You are never alone – John A Goldman – Atlanta Medicine

Seeking the Sweet Spot, from Mouth to Microbiome – David Katz – Huffington Post

New evidence suggests long-term relationships with bacteria begins before we’re born – Norbert Berzog and David Niesel – Galveston County Daily News

MIT Developing Ship-Repairing Bacteria – World Maritime News

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science

[hr]

Microbiome digest, September 22, 2014

Posted on by

[hr]

Temporal stability of the microbiomes of 85 adults, bacteria in breast milk, vaginal microbiome during pregnancy, water microbiomes, and Bik’s Picks.

Human microbiome general

Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – PeerJ PrePrints

“Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.”

Pregnancy and birth

It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant – Lars Bode – Advances in Nutrition

“This article is a summary of the symposium “It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant” held 29 April 2014 at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA.”

Microorganisms in the Female Genital Tract during Pregnancy: Tolerance versus Pathogenesis – Bruna de Andrade Ramos – American Journal of Reproductive Immunology

“We review the state of knowledge of microbe–host interactions in gestational tissues and highlight mechanisms that promote tolerance or pathogenesis.”

Determinants and pattern of care seeking for preterm newborns in a rural Bangladeshi cohort – Rashed Shah – BMC Health Services Research

“Only one-fifth (19.7%) of preterm newborns were taken to seek either preventive or curative health care.”

Human oral microbiome

Microbial signature profiles of periodontally healthy and diseased patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

“Subgingival biofilm was obtained from patients with periodontal health (27), gingivitis (11), chronic periodontitis (35) and aggressive periodontitis (24), and analysed for the presence of >250 species/phylotypes using HOMIM.”

Human gut microbiome

Review: Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties – Céline Druart – Advances in Nutrition

“In this review, we describe how changes in the composition and/or activity of the gut microbiota by administration of nutrients with probiotic or prebiotic properties can modulate host gene expression and metabolism and thereby positively influence host adipose tissue development and related metabolic disorders.”

Mammal microbiome

Resistance to Antibiotics of Clinical Relevance in the Fecal Microbiota of Mexican Wildlife – Jurgi Cristóbal-Azkarate – PLOS ONE

“Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys, spider monkeys, tapirs and felids living freely in two regions of the Mexican state of Veracruz under different degrees of human influence.“

Bird microbiome

Do feather-degrading bacteria actually degrade feather colour? No significant effects of plumage microbiome modifications on feather colouration in wild great tits – Staffan Jacob – Naturwissenschaften

“Here, we tested whether (i) keratinolytic microorganisms can degrade feathers in vivo and thus modify the colour of feathers during the nesting period and (ii) whether feather microorganisms have a long-term effect on the investment in colouration of newly moulted feathers.”

Plant microbiome

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize – David Johnston-Monje – BMC Plant Biology

“The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping.“

Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems – Leszek Lenc – Journal of Phytopathology

“The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. “

Soil microbiome

Bacterial and Archaeal Communities in Bleached Mottles of Tropical Podzols –
K. J. Silva, P. Vidal-Torrado, M. R. Lambais – Microbial Ecology

“In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling.”

Water microbiome

Microplastic is an abundant and distinct microbial habitat in an urban river – Amanda McCormick – Environmental Science & Technology

“Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter.”

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity – Masanori Fujimoto – PLOS ONE

“The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry.”

Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes – Avinash Sharma – Annals of Microbiology

“Bacterial diversity of the Soldhar hot spring, located in the Chamoli district of Uttarakhand, India, was investigated using a clone library, denaturing gradient gel electrophoresis (DGGE) and functional genes.”

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbial Ecology

“Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. “

A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing – Thangavelu Boopathi – Polar Biology

“In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing.”

Built Environment

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities? – Gary M. King – Journal of Microbiology

“I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems”

Phages and viruses

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution – Elyse Stachler and Kyle Bibby – Environmental Science & Technology

“Here, 86 publically available metagenomes were surveyed to determine the presence and abundance of crAssphage in various environments, and to identify its utility for source tracking of human fecal pollution.”

Microbes in the news

Understanding the Microbiome and Its Impact on Human Health – Kristine Nally – HCPLive

“Instant polling at an educational session of the 2014 American Academy of Pain Management annual clinical meeting in Phoenix, AZ, revealed that only 40 percent of the approximately 350-person audience was “familiar” with the concept of a microbiome.”

Mining the microbiome for medicines – Set a thief… – The Economist

“Antibiotics are not the only things Dr Donia’s technique might turn up, for the bugs in the human microbiome spit out all sorts of other chemicals that could potentially be put to use as drugs.”

Techniques

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr and Elhanan Borenstein – MicroBEnet

“We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample.”

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science Insider

“The power of anonymous comments—and the liability of those who make them—is at the heart of a possible legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review.”

Time to Raise the Profile of Women and Minorities in Science – Brian Welle and Megan Smith – Scientific American

“Along these lines, over the past few years, we discovered some pretty ugly news about our beloved Google Doodles. “

Bik’s Picks

Immune system of newborn babies stronger than previously thought – Science Daily

“Contrary to what was previously thought, newborn immune T cells may have the ability to trigger an inflammatory response to bacteria, according to a new study.”

The Preservation Of Lonesome George – Sarah Fecht – PopSci.com

“Decades after the last giant tortoise was thought to have disappeared from the island of Pinta in the Galapagos, Lonesome George turned up in 1971 and became a conservation icon.”

 Great white sharks partly to blame for otter recovery stall – Peter Fimrite – SF Gate

“Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.”

[hr]

Microbiome digest, September 19, 2014

Posted on by

[hr]

An update from the Cochrane Review Journal on probiotics to prevent necrotizing enterocolitis, oral microbiome in apical periodontitis or polycystic ovary syndrome, vaginal and gut microbiome, and bacteria in shrimp, soil, and water.
Pregnancy and birth

Probiotics for prevention of necrotizing enterocolitis in preterm infants – Khalid AlFaleh, and Jasim Anabrees – Evidence-Based Child Health: A Cochrane Review Journal

“For this update, searches were made of MEDLINE (1966 to October 2013), EMBASE (1980 to October 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library (2013, Issue 10), and abstracts of annual meetings of the Society for Pediatric Research (1995 to 2013).”

Anne Geddes Unveils New Image Of A Baby Born Too Soon – March of Dimes

“Mrs. Geddes donated the image of Alfred, who was born 8 weeks too soon, weighing just two pounds, six ounces, to the March of Dimes, which made the photo the center of its 2014 World Prematurity Day campaign.”

Human oral microbiome

Highly Diverse Microbiota in Dental Root Canals in Cases of Apical Periodontitis (Data of Illumina Sequencing) – Veiko Vengerfeldt – Journal of Endodontics

“Samples were collected under strict aseptic conditions from 12 teeth … and characterized by profiling the microbial community on the basis of the V6 hypervariable region of the 16S ribosomal RNA gene by using Illumina HiSeq2000 sequencing combinatorial sequence-tagged polymerase chain reaction products.”

Association between Polycystic Ovary Syndrome, Oral Microbiota and Systemic Antibody Responses – Aliye Akcalı – PLOS ONE

“Salivary levels of seven putative periodontal pathogens were analyzed by quantitative real-time polymerase chain reaction and serum antibody levels were analyzed by ELISA. “

Human genital microbiome

The Changing Landscape of the Vaginal Microbiome – Bernice Huang – Clinics in Laboratory Medicine

“The vaginal microbiome is a dynamic ecosystem in which the microbiota play a major role in regulating parameters such as pH and in limiting the growth of potentially harmful organisms”

Human gut microbiome

Review: Diet, gut microbes, and genetics in immune function: can we leverage our current knowledge to achieve better outcomes in inflammatory bowel diseases? – Vanessa A Leone – Current Opinion in Immunology

“This review summarizes our current understanding of dietary-induced changes in gut microbiota on autoimmunity in the context of IBD.”

The evolving role of the gut microbiome in human disease – Lloyd H. Kasper – FEBS Letters

“We are delighted to introduce this Special Issue, which summarizes the current understanding of the complex relationship between the gut microbiome and the host.”

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B Burns – bioRxiv Preprints

“We characterized the microbiome in 44 primary tumor and 44 patient-matched normal colon tissues. We find that tumors harbor distinct microbial communities compared to nearby healthy tissue.”

Gut Microbiota: A Natural Adjuvant for Vaccination – Oliver Pabst, Mathias Hornef – Immunity

“In this issue of Immunity, Oh et al. (2014) reveal an unappreciated facet of how the microbiota influences immune responses. Immunity to nonadjuvanted vaccines depends on Toll-like-receptor-5-mediated sensing of the microbiota.”

Animal and bioreactor models

TLR5-Mediated Sensing of Gut Microbiota Is Necessary for Antibody Responses to Seasonal Influenza Vaccination – Jason Z. Oh – Immunity

“Vaccination of Trl5−/− mice resulted in reduced antibody titers and lower frequencies of plasma cells, demonstrating a role for TLR5 in immunity to TIV. This was due to a failure to sense host microbiota. “

In vivo degradation of alginate in the presence and in the absence of resistant starch – Melliana Jonathan – Food Chemistry

“This study evaluated the intestinal degradability of alginate during 74 days intake in pigs as models for humans. “

Effect of prebiotics on the fecal microbiota of elderly volunteers after dietary supplementation of Bacillus coagulans GBI-30, 6086 – Edna P. Nyangale – Anaerobe

“Single stage batch culture anaerobic fermenters were used and inoculated with fecal microbiota obtained from volunteers after taking a 28 day treatment of Bacillus coagulans GBI-30, 6086 (GanedenBC30 (BC30)) or a placebo.”

Intestinal anastomotic injury alters spatially defined microbiome composition and function – Benjamin D Shogan – Microbiome journal

“Using 16S rRNA amplicon sequencing of samples collected on the day of surgery … and the 6th day following surgery …, we analyzed the changes in luminal versus tissue-associated microbiota at anastomotic sites created in the colon of rats.”

General human microbiome

Microbiome in Human Immunodeficiency Virus Infection – January T. Salas, Theresa L. Chang – Clinics in Laboratory Medicine

“Individuals infected with the human immunodeficiency virus (HIV) have altered microbiome associated with immune activation that impacts the consquence of disease progression”

Shrimp microbiome

Characterization of the intestinal microbiota in Pacific white shrimp, Litopenaeus vannamei, fed diets with different lipid sources – Meiling Zhang – Aquaculture

“an Illumina-based sequencing method was used to examine the intestinal bacterial composition of L. vannamei following six diets with different lipid sources.”

Soil microbiome

Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil –
S. Lladó – Journal of Hazardous Materials

“Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided”

Water microbiome

High-throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters – Joe D. Taylor and Michael Cunliffe – Journal of Phycology

“Here, we use high-throughput 18S rRNA gene sequencing to characterize protist and fungal diversity in the SML at a coastal time-series station and compare with underlying plankton assemblages. “

Microbes in the news

Sex in the Sink: Gene-Swapping Bacteria Are Making New Superbugs – Maggie Fox – NBC News

“Over the past decade, there has been a steady and alarming increase in antibiotic-resistant bacteria, a trend that poses a serious threat to the U.S. medical system,” Segre and colleagues wrote in their report.

Science, publishing, and career

To Get More Out of Science, Show the Rejected Research – Brendan Nyhan – New York Times

“In a new white paper, I propose that the American Political Science Association offer options for articles in a Registered Reports-style format. “

Pushing Women and People of Color Out of Science Before We Go In – Jennifer Selvidge – Huffington Post

“The misogyny and racism I experienced and saw at MIT became more and more concerning, between professors making “get back in the kitchen jokes” and hearing about what seemed to be legions of male PhD student sexually harassing woman undergraduates.”

Bik’s Picks

I want one! These adorable giant African rats detect land mines and TB for a living – Bec Crew – Scientific American

“So yesterday, I adopted an unborn land-mine-detecting African giant pouched rat (Cricetomys gambianus) from Tanzania. “

No sedative necessary: Scientists discover new ‘sleep node’ in the brain – Science Daily

“A sleep-promoting circuit located deep in the primitive brainstem has revealed how we fall into deep sleep. “

Experts: Science Class Can Dazzle With Less Danger – Dan Elliott – ABC News

“On Sept. 3, 13 people, mostly children, were burned by a methanol-fueled flash fire during a science demonstration at the Terry Lee Wells Nevada Discovery Museum in Reno.”

(Satire) Bono Showcases New Genome Sequencers, The i-LUMINA 6 and i-LUMINA 6 plus – the Allium

“Lead singer with the rock band U2, Bono, revealed the latest in genome sequencing technology at a gala event in the Moscone Center in San Francisco, yesterday.”

[hr]

Microbiome digest, September 18, 2014

Posted on by

It’s an exciting day at MicrobiomeDigest, with an Ig Nobel Prize awarded to the baby poop sausages paper, the Breaking Bad of gut microbiota, the microbiome of salami, and how bacteria can help in agriculture. Here we go:

Respiratory microbiome

Persistence of livestock-associated antibiotic-resistant Staphylococcus aureus among industrial hog operation workers in North Carolina over 14 days – Maya Nadimpalli – Occupational & Environmental Medicine (see also below)

“Nasal carriage of livestock-associated S. aureus, multidrug-resistant S. aureus and methicillin-resistant S. aureus can persist among industrial hog operation workers over a 14-day period, which included up to 96 h away from work.”

Human gut microbiome

Breaking Bad – the two sides of gut microbiota in portal hypertension – Gautam Mehta and Rajeshwar P Mookerjee – Liver International

“In this issue of Liver International, Rincon and colleagues bring these threads together by exploring the effects of modulating gut flora on portal hypertension in the context of decompensated cirrhosis.”

Pregnancy and birth

Winners of the 2014 Ig Nobel Prize in Nutrition – ABC News

2014 IgNobel Prize in Nutrition: “Raquel Rubio, Anna Jofra, Belen Martin, Teresa Aymerich and Margarita Garriga, for their study of using infant fecal bacteria as potential probiotic starter cultures for fermented sausages.”

Plant microbiome

Why Tiny Microbes Mean Big Things for Farming – Peter Andrey Smith – National Geographic

“The soil-dwelling bacteria that we walk on every day are working their way into technologies that could help feed the world.”

Plant interactions with other organisms: molecules, ecology and evolution – Amy T. Austin and Carlos L. Ballaré – New Phytologist

“There are still many open questions regarding how plant interactions with other organisms are shaped by evolutionary forces over time. “

Food microbiology

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons – Justyna Połka – Food Microbiology

“Salame Piacentino PDO was analysed by HTS (Illumina) of 16S rRNA amplicons.”

Techniques

1-day bowel preparation with polyethylene glycol 3350 is as effective and safe as a 3-day preparation for colonoscopy in children – Serge A Sorser – BMC Research Notes

“There were no differences between the groups in efficacy of bowel preparation based on colonoscopic grading or the safety of the preparation.”

Viruses and phages

Metagenomic Analysis of Double-stranded DNA viruses in Healthy Adults – Kristine M. Wylie – BMC Biology

“We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediates of single-stranded DNA viruses, in metagenomic sequence data generated by the HMP. “

see also: Your own personal virome – Biome – BioMedCentral

“If life gives you lemons, you make lemonade. And if your bacterial DNA datasets give you viral DNA contaminants, you use them to study the virome. “

Bioinformatics

Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLAT – Gabriel Moreno-Hagelsieb and Brigitte Hudy-Yuffa – BMC Research Notes

“Despite faster programs miss sequence matches otherwise found by NCBI?s BLAST, the overannotation estimates are very similar and thus these programs can be used with confidence for this task.”

Antibiotic and resistance

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae – Sean Conlan – Science Translational Medicine

“we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. “

U.S. Lays Out Strategy to Combat Crisis of Antibiotic Resistance – Sabrina Tavernise – NY Times

“The Obama administration on Thursday announced measures to tackle the growing threat of antibiotic resistance”

Factory-Farm Workers Found to Carry High Levels of Antibiotic-Resistant Bacteria – Willy Blackmore – TakePart (see also above)

“While only one worker was found to be carrying MRSA after nostril swabs were tested, 86 percent carried staph bacteria associated with livestock—far higher than the general population. “

Microbes in the News

Microbirth: The Extra Question Every Expectant Mother Needs To Ask – Toni Harman – Huffington Post

“The doctor or midwife looks at the expectant mother blankly. “I’m sorry. I have never heard of the microbiome. And I’ve never heard of Microbirth.”

Science, publishing, and career

Rhubarb pie and science – Sandy Becker – Science Working Life

“When I am asked how I became a developmental biologist, I say, “Jim hired me for my rhubarb pie and my Phi Beta Kappa key, and the rest is history.””

Can Post-Publication Peer-Reviews Increase Research Transparency? – Liz Allen – Berkeley Bitts

“When Peer Review is done in the open by named individuals, we believe it should be more constructive and issues will surface more quickly.”

 

Bik’s Picks

Winners of the 2014 Ig Nobel Awards – ABC News

“The 2014 Ig Nobel winners, awarded Thursday at Harvard University by the Annals of Improbable Research magazine”

Europeans drawn from three ancient ‘tribes’ – Paul Rincon – BBC News

“The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature journal reports.”

Bowl Half Empty: Dogs Can Be Pessimists – Richard Farrell – Discovery

“New PhD research out of the University of Sydney by Dr. Melissa Starling, from the school’s Faculty of Veterinary Science, sought to find out if dogs had underlying personalities that tended toward either optimism of pessimism.”

[hr]

Microbiome digest, September 17, 2014

Posted on by

[hr]

Human gut microbiome and artificial sweeteners, cholera recovery, or ancient coprolites, protbiotics and the brain, coastal soil, diversity and science, metabolomics, and Bik’s Picks.
Human gut microbiome

Artificial sweeteners induce glucose intolerance by altering the gut microbiota – Jotham Suez – Nature

“We identify NAS-altered microbial metabolic pathways that are linked to host susceptibility to metabolic disease, and demonstrate similar NAS-induced dysbiosis and glucose intolerance in healthy human subjects.”

Members of the human gut microbiota involved in recovery from Vibrio cholerae infection – Ansel Hsiao – Nature

“We find that recovery is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of assembly/maturation of the gut microbiota in healthy Bangladeshi children”

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures – Raul J. Cano – PLOS ONE

“We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico.”

Animal models of microbiome research

Modulation of Intestinal Microbiota by the Probiotic VSL#3 Resets Brain Gene Expression and Ameliorates the Age-Related Deficit in LTP – Eleonora Distrutti – PLOS ONE

“Here, we report that treatment of aged rats with VSL#3 induced a robust change in the composition of intestinal microbiota with an increase in the abundance of Actinobacteria and Bacterioidetes, which was reduced in control-treated aged rats.”

Soil microbiome

Unravelling the Carbon and Sulphur Metabolism in Coastal Soil Ecosystems Using Comparative Cultivation-Independent Genome-Level Characterisation of Microbial Communities – Basit Yousuf – PLOS ONE

“Distinct compositional differences were observed among the clone libraries, which revealed a dominance of phylotypes associated with carbon and sulphur cycling”

Techniques

Partition Enrichment of Nucleotide Sequences (PINS) – A Generally Applicable, Sequence Based Method for Enrichment of Complex DNA Samples – Thomas Kvist, Line Sondt-Marcussen, Marie Just Mikkelsen – PLOS ONE

“The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. “

Metabolomics

Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species – Edoardo Saccenti – PLOS ONE

“we show that despite the standardization of diet as the most relevant extrinsic factor, a clear individual and discriminative metabolic fingerprint also exists for monkeys.”

Science and Career

Diversity: Pride in science – M Mitchell Waldrop – Nature

“The sciences can be a sanctuary for gay, lesbian, bisexual and transgender individuals, but biases may still discourage many from coming out.”

Bik’s Picks

Only 4 of them are women…. – The top 50 science stars of Twitter – Jia You – Science

“Though Hall says he meant his K-index lightheartedly, his article in Genome Biology sparked a Twitter storm of criticism. So just who are the Kardashians of science, and is Hall’s criticism justified?”

Breast milk reveals a correlation between dietary fats and academic success – Science Daily

“You are what you eat, the saying goes, and now a study conducted by researchers at UC Santa Barbara and the University of Pittsburgh suggests that the oft-repeated adage applies not just to physical health but to brain power as well.”

Forensic science solves mystery of Richard III’s death (the parking-lot king) –  Agata Blaszczak-Boxe – CBS News

“More than 500 years after Richard III became the last king of England to die in battle, researchers using modern forensic science have figured out which injuries likely caused his death.”

[hr]

General microbiology and science digest, September 16, 2014

Posted on by

Detection of microbes in tissues, a magnet to pull out bacteria from blood, temperature stability of samples, enriching for rare microbial community members, bioinformatics tools for microbiome research, and Bik’s Picks.
Microbial detection

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues – Don A. Baldwin – mBio

“the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. “

More microbes

Review: Physical stress and bacterial colonization – Michael Otto – FEMS Microbiology Reviews

“This review will give an overview over the mechanisms human bacterial colonizers have to withstand physical stresses with a focus on bacterial adhesion.”

Techniques

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles – Jun Hang – Microbiome

“Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis.”

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalisation methods – Dragana Gagic – Molecular Ecology Resources

“The synthetic metagenome was fractionated and thermally re-natured, allowing the most abundant sequences to hybridise. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease (DSN).”

Bioinformatics

A better sequence-read simulator program for metagenomics – Stephen Johnson – BMC Bioinformatics

“We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions.”

Gene finding in metatranscriptomic sequences – Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang – BMC Bioinformatics

“In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences.”

Data analysis for 16S microbial profiling from different benchtop sequencing platforms
Victor S. Pylro – Journal of Microbiological Methods

“Satisfactory results were obtained in those pipelines that applied a chimera-filtering step.”

Metagenome fragment classification based on multiple motif-occurrence profiles – Naoki Matsushita – PeerJ

“we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence.”

Revolutionizing prokaryotic systematics through next-generation sequencing – Vartul Sangal – Methods in Microbiology

“In this chapter, we have provided a brief summary of recent advances in sequencing technologies and easy to use bioinformatic tools to analyse sequence data, with a focus on prokaryotic biology. “

Microbes in the news

A Lesson in Language – McAlarnen, Lindsey A. – Academic Medicine

“while I expected a challenge working with human microbiome expert Dr. Rob Knight, I never expected to be as lost as I was that first morning.”

An extracorporeal blood-cleansing device for sepsis therapy – Joo H Kang – Nature Medicine

“Magnets pull the opsonin-bound pathogens and toxins from the blood; the cleansed blood is then returned back to the individual. “

Science and career

Too Few University Jobs For America’s Young Scientists – Richard Harris – NPR Morning Edition

“Imagine a job where about half of all the work is being done by people who are in training. That’s, in fact, what happens in the world of biological and medical research.”

Diversity in Science: Where Are the Data? – Fred Guterl – Scientific American

“Global figures on diversity in the science and engineering workforce are hard to come by, but what we know is not flattering”

 

Bik’s Picks

Jack the Ripper, more poison at NIH, Rosetta & the comet – Tabitha M. Powledge – PLOS Blogs

“Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.”

Human faces are so variable because we evolved to look unique – ScienceDaily

“The amazing variety of human faces — far greater than that of most other animals — is the result of evolutionary pressure to make each of us unique and easily recognizable”

Joanne Chang Brings the Sweet Science of Sugar to Harvard – Leah Blumenthal – Eater.com

“Harvard University’s annual Science & Cooking public lecture series brings chefs from around the world to lecture on the intersection of science and cooking.”

[hr]

 

General microbiology and science, September 15, 2014

Posted on by

Biodiversity and evolution in microbial communities, metabolomics, swabbing, DNA extraction, ITS approaches, marine viruses, and Bik’s Picks.

Microbial Ecology

The cryptic role of biodiversity in the emergence of host–microbial mutualisms – Pradeep Pillai – Ecology Letters

“Using a metacommunity model, we show that competition between multiple cheaters within the host’s microbiome, when combined with the spatial structure of host–microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host.”

Microbial communities evolve faster in extreme environments – Sheng-Jin Li – Nature Scientific Reports

“Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. “

Metabolomics

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome – Ohad Manor, Roie Levy, Elhanan Borenstein – Cell Metabolism

“Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. “

Techniques

Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice – Janina Ferrand – Journal of Microbiological Methods

“DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR….For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.”

Swab Sample Transfer for Point-Of-Care Diagnostics: Characterization of Swab Types and Manual Agitation Methods – Nuttada Panpradist – PLOS ONE

“In this study, we compared bacterial release efficiency of seven swab types using manual-agitation methods typical of POC devices.”

Improved resolution of bacteria by high throughput sequence analysis of the rRNA internal transcribed spacer – Paul M. Ruegger – Journal of Microbiological Methods

“Comparisons of the ITS region and two SSU regions using annotated bacterial genomes in GenBank showed much greater resolving power is possible with the ITS region. “

Pyroprinting: A rapid and flexible genotypic fingerprinting method for typing bacterial strains – Michael W. Black – Journal of Microbiological Methods

“Pyroprinting relies on the simultaneous pyrosequencing of polymorphic multicopy loci, such as the intergenic transcribed spacer regions of rRNA operons in bacterial genomes.”

Bioinformatics

OrthoClust: an orthology-based network framework for clustering data across multiple species – Koon-Kiu Yan – Genome Biology

“We demonstrate the application of OrthoClust using the RNA-Seq expression profiles of Caenorhabditis elegans and Drosophila melanogaster from the modENCODE consortium.”

Viruses and Phages

Review: Factors affecting virus dynamics and microbial host–virus interactions in marine environments – Kristina D.A. Mojica and Corina P.D. Brussaard – FEMS Microbiology Ecology

“The goal of the present minireview was to contribute to the evolution of marine viral ecology, through the assimilation of available data regarding the manner and degree to which environmental factors affect viral decay and infectivity as well as influence latent period and production.”

More Microbes

Dead or Alive: Molecular Assessment of Microbial Viability – Gerard A. Cangelosi and John S. Meschke – Applied and Environmental Microbiology

“This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.”

Bacteria in the news

Is your body mostly microbes? Actually, we have no idea – Peter Andrey Smith – The Boston Globe

“There’s only one problem: The oft-cited 10-to-1 figure is almost certainly inaccurate.”

The Death Microbiome Could Inform Forensic Science And Medicine – Randall Mayes – Design & Trend

“For pathologists working out the time of death, research has focused on the way that insects and microbes from a corpse’ environment take up residence in the flesh.”

Tiny hitchhikers, big health impact: Studying the microbiome to learn about disease – Krista Conger – ScopeBlog Stanford

Got microbes? Meet some of the tiny life forms that call you home and may make antibiotics for you (with annoying 5 questions if you want to read the whole article) – Susannah Bodman – Oregon Live

Fighting Poisons With Bacteria – Going Inside the Rice Microbiome – Carina Storrs – NY Times

“Dr. Bais is working to develop rice plants that take up less arsenic, a common contaminant in the fields of his native India and other Asian countries.”

Possum faeces may cause flesh-eating ulcers in humans, Victorian researchers say – ABC Australia

“Infectious disease researchers at Victoria’s Barwon Health have found that possums can carry the buruli bacteria, which can cause major skin ulcers in humans.”

Scientific publishing

Ten Simple Rules for Better Figures – Nicolas P. Rougier – PLOS Computational Biology

“we aim to provide a basic set of rules to improve figure design and to explain some of the common pitfalls.”

The digital toolbox – Nature Editorial

“A new section of Nature examines the software and websites that make research easier.”

Scientific career

There is life after academia – Nature Editorial

“With high numbers of postdocs emerging from universities, prospective PhD students must be prepared for the fact that they will probably not end up with a career in research.”

Bik’s Picks

PBS: Video on the science behind brewing beer hops to it – CNET

“PBS series “It’s Okay To Be Smart” takes a look at how beer is made, and what external factors influence the final product.”

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis -France Denoeud – Science

“We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. “

On the Other Hand – Bob Grant – The Scientist

“Handedness, a conspicuous but enigmatic human trait, may be shared by other animals. What does it mean for evolution and brain function?”

[hr]

General microbiology and science, August 26, 2014

Posted on by

Here, we have CRISPRs, phages, marine metagenomics, a universal bacterial/archaeal primer (The One?), single-cell genomics, light and bacteria, and Bik’s Picks.

Phages and CRISPRs

Abundant and Diverse Clustered Regularly Interspaced Short Palindromic Repeat Spacers in Clostridium difficile Strains and Prophages Target Multiple Phage Types within This Pathogen – Katherine R. Hargreaves – mBio

“We detected multiple matches between spacers and regions in 31 C. difficile phage and prophage genomes”

Evolutionary consequences of intra-patient phage predation on microbial populations –
Kimberley D Seed – eLife

“Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients.”

Metagenomics

* Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery
Rosalba Barone – Frontiers in Marine Science

“We report examples of several hydrolytic enzymes and natural products isolated by functional sequenced-based and function- screening strategies assisted by new high-throughput DNA sequencing technology and recent bioinformatics tools.”

Bioinformatics

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data – Peter Skewes-Cox – PLOS ONE

“Here, we constructed HMMER3-compatible profile hidden Markov models (profile HMMs) from all the virally annotated proteins in RefSeq in an automated fashion using a custom-built bioinformatic pipeline. “

 

Techniques

I hope they developed two primers, not just one! Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing – Shunsuke Takahashi – PLOS ONE

“Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace×Large white×Duroc) using an Illumina MiSeq next-generation sequencer.”

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods – Charles F. A. de Bourcy – PLOS ONE

“Here, we compare three state-of-the-art methods on both bulk and single-cell samples of E. coli DNA: Multiple Displacement Amplification (MDA), Multiple Annealing and Looping Based Amplification Cycles (MALBAC), and the PicoPLEX single-cell WGA kit (NEB-WGA). “

This abstract is so vague, I am not sure where to file this under – A Robust and Adaptable High Throughput Screening Method to Study Host-Microbiota Interactions in the Human Intestine – Tomas de Wouters – PLOS ONE

“In this study, we developed a robust and reproducible methodology to combine these two biological systems for high throughput application”

LC Sciences and Norgen Biotek will be conducting a free informational webinar describing 16S rRNA Sequencing and presenting a few application examples.

“If you are interested in attending the webinar, simply reply to news@lcsciences.com and we would be happy to send the webinar details.”

More microbiology

The Immune System in Children with Malnutrition — A Systematic Review
Maren Johanne Heilskov Rytter – PLOS ONE

“A systematic literature search was done in PubMed, and additional articles identified in reference lists and by correspondence with experts in the field. “

Photodynamic Therapy Using Systemic Administration of 5-Aminolevulinic Acid and a 410-nm Wavelength Light-Emitting Diode for Methicillin-Resistant Staphylococcus aureus-Infected Ulcers in Mice – Kuniyuki Morimoto – PLOS ONE

“5-aminolevulinic acid photodynamic therapy accelerated wound healing and decreased bacterial counts on ulcer surfaces; in contrast, vancomycin treatment did not accelerate wound healing.”

Light Scattering Sensor for Direct Identification of Colonies of Escherichia coli Serogroups O26, O45, O103, O111, O121, O145 and O157 – Yanjie Tang- PLOS ONE

“SMAC was chosen for exhaustive scatter image library development, and 36 additional strains of O157:H7 and 11 non-O157 serovars were examined, with each serogroup producing unique differential scatter patterns.”

Science and publishing

Protecting human research participants in the age of big data – Susan T. Fiskea, and Robert M. Hauser – PNAS USA

“IRB review does not apply to Facebook and other private enterprises, yet they generate data that can benefit humanity”

Bik’s Picks

* Magpies don’t like shiny things – Sarah Zielinski – Science News

“Magpies deserve our apology. Apparently humans have been unnecessarily maligning the birds for centuries. “

Richard III ate like a king before biting the dust – Bruce Bower – Science News

“Well-known royal’s brief reign included a sudden shift to fancy food and drink”

What type of researcher are you? Take the Quiz – Roche Life Science

[hr]