Category Archives: Microbes in the News

Microbiome digest, September 22, 2014

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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.”

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Microbiome digest, September 19, 2014

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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.”

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Microbiome digest, September 18, 2014

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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.”

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General microbiology and science digest, September 16, 2014

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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.”

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General microbiology and science, September 15, 2014

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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?”

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General microbiology and science, August 26, 2014

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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

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General microbiology and science, August 25, 2014

Posted on by

Microbial networks, proteomics of Fusobacterium, ants carrying pathogens into hospitals, and what’s in your lab freezer?

Bioinformatics

Sparse and compositionally robust inference of microbial ecological networks – Zachary D. Kurtz – arXiv at Cornel University Library

“Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological interactions from metagenomic datasets that addresses both of these issues. “

Metabolomics / proteomics

Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota – Helen Kettle – Environmental Microbiology

“We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. “

Proteomics of Fusobacterium nucleatum within a model developing oral microbial community  – Erik L. Hendrickson – MicrobiologyOpen

“About 1210 F. nucleatum proteins were detected in single species F. nucleatum control samples, 1192 in communities with P. gingivalis, 1224 with S. gordonii, and 1135 with all three species.”

Techniques

* (Preprint) Sources of PCR-induced distortions in high-throughput sequencing datasets – Justus M Kebschull, Anthony M Zador – bioRXiv

“We examined the effects of bias, stochasticity, template switches and polymerase errors introduced during PCR on sequence representation in next-generation sequencing libraries. “

More microbes

* Ants as vectors of pathogenic microorganisms in a hospital in Sao Paulo county, Brazil – Heros J Máximo – BMC Research Notes

“Ants in hospitals may carry both Gram-positive and Gram-negative bacteria, and methods of controlling urban ants should be adopted and strictly adhered to, to minimize the risk of infection in hospital patients.”

Microbes in the news

What’s in your laboratory freezer? – Timothy J. Donahue – American Society of Microbiology

“I ask all microbiologists to make sure that you and your colleagues know what they have in the lab (freezer, refrigerator, store room, etc).”

* Hot Spring Bacteria Can Live Off Invisible Light Alone – Brian Stallard – Nature World News

“Researcher(sic) studying cyanobacteria in hot springs have discovered that the potentially harmful algae can live in near-darkness, absorbing far-red light and converting it into energy while releasing oxygen. “

Insect-borne bacteria destroy ancient Italian olive groves – Tom Kington – GulfNews

“The ancient olive groves of southern Italy, which provide much of the oil the country exports, are being destroyed by deadly, insect-borne bacterium that has already infected nearly half a million trees and has no known cure.”

Uncultured Bacteria (with video) – Serious Science

“Northeastern University Prof. Kim Lewis on great plate count anomaly, siderophores, and human microbiome”

#BacteriaHysteria

* How to Keep Bacteria Out of Your Child’s Lunchbox – FoodSafetyNews

“If possible, a child’s lunch should be stored in a refrigerator during school, but the lid should be left open so that cold air can better circulate and keep the food cold.”

* Chick-fil-A incorporates bacteria-killing copper into restrooms – The News Herald

“Seidel said that Chick-fil-A Owner and Operator Dallas Stoudenmire has realized his responsibility to keep customers bacteria free and is taking the right steps to do so.”

Science and publishing

Concerns Raised Online Linger – Kate Yandell – The Scientist

“The great majority of comments point out some kind of problem,” PubPeer moderators wrote in an e-mail to The Scientist.

Bik’s Picks

Eye implant developed at Stanford could lead to better glaucoma treatments – Bjorn Carey – Stanford News

“A tiny eye implant developed by Stephen Quake’s lab could pair with a smartphone to improve the way doctors measure and lower a patient’s eye pressure.”

Scientists grow an organ in an animal from cells created in lab – Science Daily

“The researchers have created a thymus — an organ next to the heart that produces immune cells known as T cells that are vital for guarding against disease.”

Mozzarella and cheddar are the perfect pizza toppers, according to science – Jenn Harris – LA Times

“Understanding the value of a pie spotted with perfectly crisp cheese, a group of scientists in New Zealand set out to find which cheeses create the perfect topping.”

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Human microbiome digest, August 25, 2014

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Oral microbiome in the settings of periodontitis, smoking and antibiotic resistance, respiratory microbiome in Cystic Fibrosis, a decade of molecular papers on vaginal microbiome, and gut bacteria protecting against food allergies.

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 analyzed for the presence of >250 species/phylotypes using HOMIM. “

Smoking decreases structural and functional resilience in the subgingival ecosystem – Vinayak Joshi – Journal of Clinical Periodontology

“16S cloning and sequencing was used for bacterial identification and multiplexed bead-based flow cytometry was used to quantify the levels of 27 immune mediators.”

Extended-spectrum beta-lactamase-producing bacteria are not detected in supragingival plaque samples from human fecal carriers of ESBL-producing Enterobacteriaceae – Arne Søraas – Journal of Oral Microbiology

“No ESBL-producing bacteria or ESBL genes were detected using culture-based and molecular methods. “

Clonality of bacterial consortia in root canals and subjacent gingival crevices – Nipuna B. Parahitiyawa – Journal of Investigative and Clinical Dentistry

“The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. “

Respiratory microbiome

* Antimicrobial resistance in the respiratory microbiota of people with cystic fibrosis –
Laura J Sherrard – The Lancet

“Strategies to manage antimicrobial resistance consist of new antibiotics or localised delivery of antimicrobial agents, iron sequestration, inhibition of quorum-sensing, and resistome analysis.”

Evidence that Intraspecific Trait Variation among Nasal Bacteria Shapes the Distribution of Staphylococcus aureus – Ben Libberton – Infection and Immunity

“We characterized S. aureus growth inhibition by the culturable bacterial aerobe consortia of 60 nasal microbiomes, and this revealed intraspecific variation in growth inhibition and that inhibitory isolates clustered within communities that were culture negative for S. aureus. “

Gary Huffnagle: rewriting the rules on the lung microbiome – David Holmes – The Lancet

“The ideas being generated by Huffnagle at the moment are all about the lung microbiome and its role in the pathogenesis of everything from chronic obstructive pulmonary disease (COPD) to asthma, and they’re starting to make waves.”

Vaginal microbiome

* The Vaginal Microbiota: What Have We Learned after a Decade of Molecular Characterization? – Janneke H. H. M. van de Wijgert – PLOS ONE

“We conducted a systematic review of the Medline database … to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions.”

Gut microbiome

Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota – Helen Kettle – Environmental Microbiology

“We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. “

Animal models of human microbiome

Commensal bacteria protect against food allergen sensitization – Andrew T. Stefka – PNAS USA

“By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. “

Pregnancy and Birth

Researcher Granted $1 Million to Study Deadly Bacteria Passed to Babies From 25 Percent of Mothers – Infection Control Today

“Narayana Sthanam, PhD, professor of structural biology in the Department of Optometry, has been awarded a four-year, $1 million R01 grant from the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, to further Group B Streptococcus research.”

Microbiome News

* Satire: Study Reveals Microbiome To Be Master-Controller Of All Humanity – The Allium

“Science has already found out that your microbiome at birth decides your taste in clothes and music, whether you are going to be great footballer like David Beckham or a great political leader like Sarah Palin.”

9 questions you were too grossed out to ask about the bacteria living on you – Susannah Locke – Vox

“What researchers have discovered is that our bodies are essentially complex ecosystems of tiny living things. “

Interview with Prof. Yolanda Sanz, project coordinator of My New Gut – Kristina Campbell – Gut Microbiota For Health

“Professor Yolanda Sanz has been appointed MyNewGut’s project coordinator and leads the project’s human intervention trials on the gut microbiome’s ability to metaolise (sic) nutrients and influence energy balance. “

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Microbiome Digest, August 22, 2014

Posted on by

The microbiome of the human eye,  chronic lung diseases, ticks, trout, the air in wineries, and Bik’s Picks. Have a good weekend!
Pregnancy and birth

The human microbiome and the great obstetrical syndromes, a new frontier in maternal fetal medicine – Ido Solt – Best Practice & Research Clinical Obstetrics & Gynaecology

“The transmission of maternal microbiomes to the neonate, according to vaginal delivery or cesarean section, is shown to affect health from birth to adulthood.”

Human skin microbiome

Considerations in Understanding the Ocular Surface Microbiome – Michael E. Zegans – American Journal of Ophthalmology

“In ophthalmology, the question naturally arises as to whether or not the ocular surface, like other mucous membrane surfaces, has a resident microbiota, and, if so, what role it plays in ocular surface physiology. This question has provoked much debate over many years. “

Human respiratory microbiome
* The role of the microbiome in exacerbations of chronic lung diseases – Robert P Dickson – The Lancet

“We propose that exacerbations are occasions of respiratory tract dysbiosis—a disorder of the respiratory tract microbial ecosystem with negative effects on host biology.”

Human gut microbiome

* Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates – Erica D. Sonnenburg, Justin L. Sonnenburg – Cell Metabolism

“The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. “

Human vaginal microbiome

Rectal Lactobacillus Species and Their Influence on the Vaginal Microflora: A Model of Male-to-Female Transsexual Women – Ljubomir Petricevic – The Journal of Sexual Medicine

“We undertook this observational study to characterize the Lactobacillus species present in the neovagina and rectum of male-to-female transsexual women and to determine the degree of neovaginal-rectal co-colonization in order to gain a better understanding of the potential role of the gut as a reservoir for genital lactobacilli.”

Animal models of microbiome research

Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases – Shannon L. Russell – Journal of Allergy and Clinical Immunology

“Disease severity was assessed by measuring lung inflammation, pathology, cytokine responses, and serum antibodies. Microbial community analyses were performed on stool samples via 16S ribosomal RNA pyrosequencing and correlations between disease severity and specific bacterial taxa were identified.”

Animal microbiome

The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal – Xue-Chao Zhang – Ticks and Tick-borne Diseases

“By 16S rRNA Illumina sequencing, we investigated the microbiome of I. persulcatus and assessed the variation of the microbiome before and after blood feeding.”

Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss) – Hans-Christian Ingerslev – Fish & Shellfish Immunology

“This study investigated the influence of the rainbow trout (Oncorhynchus mykiss) commensal intestinal microbiota in connection to an experimental Yersina ruckeri infection, the causative agent of enteric redmouth disease.”

Food microbiology

* Microbial communities in air and wine of a winery at two consecutive vintages – Fátima Pérez-Martín – International Journal of Food Microbiology

“The microbial composition was determined by using both a culture-dependent method and a culture-independent method, PCR-denaturing gradient gel electrophoresis (PCR-DGGE).”

Metabolomics

* Microbial catabolism of procyanidins by human gut microbiota – Keqin Ou – Molecular Nutrition & Food Research

“The objective of this study was to identify and quantify the microbial metabolites of procyanidins after anaerobic fermentation with human microbiota.”

Bioinformatics

* Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model – Andries J. van Tonder – PLOS Computational Biology

“The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. “

* Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr, Elhanan Borenstein – PLOS ONE

“Overall, our findings provide a first comprehensive evaluation of the capabilities and limitations of functional metagenomic annotation, providing crucial goal-specific best-practice guidelines to inform future metagenomic research.”

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era
Andre J. Aberer – Molecular Biology and Evolution

“We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on datasets of arbitrary size.”

Microbes in the news

Behold 50 shades of Gross: A guide to Germaphobia! – Katherine Dahlhausen – MicroBEnet

“So logically, I began researching germaphobic practices. Some of them are just too good not to share! “

California Trees Nailed As The Source Of Mystery Infections – Nancy Shute – NPR

“”We had a good idea that the fungus was going to be associated with trees,” says Deborah Springer, a postdoctoral fellow at Duke University who studies C. gatti. “

Bik’s Picks

Pulling teeth from history: DNA from ancient teeth can help to yield information about our ancestors’ health, diet and diseases – Philip Hunter – EMBO Reports

“Teeth have proven to be an excellence source of ancient DNA. New analytical tools are helping to exploit this treasure trove to address questions about the link between diet and health, and the impact of historical epidemics with clear relevance for human health today.”

Ten Simple Rules of Live Tweeting at Scientific Conferences – Sean Ekins, Ethan O. Perlstein – PLOS Computational Biology

“Increasingly, some scientists are using Twitter as a vehicle to summarize presentations and posters at conferences in real time, which is defined as “live tweeting.””

Why the World Smells Different After It Rains – Behold, the wonders of petrichor.
Megan Garber – The Atlantic

“In the video above, PBS’s Joe Hanson describes the biology that leads to petrichor.”

Scientist Mistakenly Does “Dry-Ice Bucket Challenge” – The Allium

“Sad news has come to us today at The Allium, when we learned that scientist Dr. Liv Good, has mistakenly carried out a Dry-Ice Bucket challenge.”

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Microbiome digest, August 21, 2014

Posted on by

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

Postmortem human microbiome

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

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

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

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

Invertebrate microbiome

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

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

Soil microbiome

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

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

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

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

Water microbiome

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

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

Food microbiology

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

Fungi

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

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

 

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

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

Microbes in the news

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

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

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

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

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

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

Science and career

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

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

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

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

Bik’s Picks

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

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

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

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

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

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

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