General microbiology and science digest, October 27, 2014

A new Shiny R tool for microbial communities, virus-like pictures in human distal gut, interaction between oral bacteria, dancing your PhD, and X-ray movies of human joints in action.

Bioinformatics

* Seed: a user-friendly tool for exploring and visualizing microbial community data
Daniel Beck – Bioinformatics

“Seed is written in R using the Shiny library. This provides access to powerful R based functions and libraries through a simple user interface. “

Viruses and phages

With cool pictures: Characterization of virus-like particles associated with the human faecal and caecal microbiota – Lesley Hoyles – Research in Microbiology

“Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery.”

Transcriptomics / Proteomics / Metabolomics

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis – Yu Xia – Scientific Reports

“The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified.”

Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis – Kazuhiko Maeda – Journal of Proteome Research

“Here, using shotgun proteomics we examined the molecular basis of mixed-biofilm formation by P. gingivalis with Streptococcus oralis.”

Review: Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach – Wanping Aw, Shinji Fukuda – Seminars in Immunopathology

“In this review, we discuss in detail the relationship between gut microbiota and its metabolites … in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. “

More Microbiology

Biofilms: Five-Star Accommodations for the Aerobically Challenged – Robert A. Cramer – Current Biology

“A recent study finds that fungal biofilms are capable of supporting growth of anaerobic bacteria, suggesting that these fungi can promote bacterial growth in otherwise toxic environments.”

Microbes in the news

* Sorry, Your Gut Bacteria Are Not the Answer to All Your Health Problems – Gabrielle Canon – Mother Jones

“We’re told that tweaks to the microbiome can cure everything from allergies to Ebola. Not exactly, say experts. …despite the optimism, some researchers caution that much of what we hear about microbiome science isn’t always, well, science. “

* Orthopedic surgeon studies bear bacteria to aid bear attack victims – Healio

“Working with the Montana Fish, Wildlife & Parks, Iwersen has been collecting cultures of bacteria from the mouths of grizzly bears and correlating them with the types of bacteria found in the bear bites on patients. “

Mexican scientist investigates intestinal bacteria – BetaWired

“Recent findings of the investigator Xicotencatl Gracida Canales…at Harvard University in Cambridge, USA, suggest that in the absence of an intestinal shield, variations in bacterial metabolism can affect reproductive cells and cause infertility in an animal model called C. Elegans.”

Algae-Based Material Takes On Body Odor – Dana Dovey – NewsWeek

“A team of Swedish researchers from the KTH Royal Institute of Technology has found a way to eliminate the growth of this smell-inducing bacteria using one of nature’s best antimicrobials, algae.”

MoBE Postdoctoral Fellowship: From Source to Tap: Linking the Drinking Water Microbiome to Human Health – Sarah Haig – MicroBEnet

“We hypothesize that the microbial communities in municipally treated drinking water are a source of opportunistic pathogens, posing a risk to people with cystic fibrosis”

Science, publishing, career

Is NIH policy the best way to sex equality in studies? – Bethany Brookshire – Science News

“The end goal will be to make sure that NIH-funded scientists “balance male and female cells and animals in preclinical studies in all future [grant] applications” to the NIH.”

Some suggestions for having diverse speakers at meetings – Jonathan Eisen – The Tree of Life

“Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway “

‘Dance Your Ph.D.’ finalists announced – John Bohannon – Science

“Rather than reading a paper about it, why not watch a dance? A ballet and a modern dance on those very topics have made it into the finals of this year’s “Dance Your Ph.D.” contest.”

Bik’s Picks

Interactive world map of vaccine-preventable outbreaks – Council for Foreign Relations

“This interactive map visually plots global outbreaks of measles, mumps, whooping cough, polio, rubella, and other diseases that are easily preventable by inexpensive and effective vaccines.”

Dietary cocoa flavanols reverse age-related memory decline in mice – Science Daily

“Dietary cocoa flavanols —- naturally occurring bioactives found in cocoa —- reversed age-related memory decline in healthy older adults, according to a new study. Flavanols are also found naturally in tea leaves and in certain fruits and vegetables”

Amazing X-ray GIFs Show Joints In Motion – Lisa Winter – IFL Science

“Cameron Drake of San Francisco has created a collection of magnificent images showing joints in motion. He was aided by orthopedic physician Dr. Noah Weiss and the finished product is completely amazing. “

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Microbiome digest, October 21, 2014

Human oral microbiome

Abstract 4834: Microbiome in Oral Epithelial Dysplasia and Squamous Cell Carcinoma
Deepak Saxena – Cancer Research

“PCR amplicons targeting V3-V5 region of 16S rRNA gene were sequenced by 454 pyrosequencing. “

Human respiratory microbiome

Microbial Communities in the Upper Respiratory Tract of Patients with Asthma and Chronic Obstructive Pulmonary Disease – HeeKuk Park – PLOS ONE

“To account for the qualitative and quantitative diversity of the 16S rRNA gene in the oropharynx, the microbiomes of 18 asthma patients, 17 COPD patients, and 12 normal individuals were assessed using a high-throughput next-generation sequencing analysis.”

Human gut microbiome

Decreased bacterial diversity characterizes an altered gut microbiota in psoriatic arthritis and resembles dysbiosis of inflammatory bowel disease – Jose U. Scher – Arthritis & Rheumatology

“High-throughput 16S rRNA pyrosequencing was utilized to compare community composition of gut microbiota in PsA patients, subjects with psoriasis of the skin and healthy, matched-controls. “

Pregnancy and birth

The Salivary Scavenger and Agglutinin in Early Life: Diverse Roles in Amniotic Fluid and in the Infant Intestine – Martin Parnov Reichhardt – Journal of Immunology

“The present study revealed that SALSA was present in the amniotic fluid (AF) and exceptionally enriched in both meconium and feces of infants. “

Animal microbiome

* Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts – Kevin D. Kohl – FEMS Microbiology Ecology

“We used 16S rRNA sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. “

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (HMA, LMA) and seawater – Kristina Bayer – FEMS Microbiology Ecology

“By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified”

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges – Kathleen M Morrow – ISME Journal

“The corals Acropora millepora and Porites cylindrica were less abundant and hosted significantly different microbial communities at the CO2 seep than at nearby control sites <500 m away.”
Plant microbiome

Phylogenetic conservatism in plant-soil feedback and its implications for plant abundance – Brian L. Anacke – Ecology Letters

“We conclude that soil biota influence the abundance of close plant relatives in nature.”

Bioreactor microbiome

Influence of Acidic pH on Hydrogen and Acetate Production by an Electrosynthetic Microbiome – Edward V. LaBelle – PLOS ONE

“Production of hydrogen and organic compounds by an electrosynthetic microbiome using electrodes and carbon dioxide as sole electron donor and carbon source, respectively, was examined after exposure to acidic pH (~5). “

Metagenomics / Transcriptomics / Bioinformatics

Census-based rapid and accurate metagenome taxonomic profiling – Amirhossein Shamsaddini – BMC Genomics

“We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. “

Metatranscriptomes from diverse microbial communities: assessment of data reduction techniques for rigorous annotation – Andrew Toseland – BMC Genomics

“To investigate the effect of such techniques on the annotation of metatranscriptome data we assess two commonly employed methods: clustering and de-novo assembly. To do this, we also developed an approach to simulate 454 and Illumina metatranscriptome data sets with varying degrees of taxonomic diversity. “

Microbial Ecology

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review – Hyun-Seob Song – Processes

“In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. “

A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world – Albert Barberán† and Emilio O. Casamayor – Molecular Ecology

“We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition.”

Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment – Davi Pedroni Barreto – PLOS ONE

“The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA.”

More microbiology

From Denise Monack’s lab: Role of disease-associated tolerance in infectious superspreaders – Smita Gopinath – PNAS USA

“Using a mouse model of Salmonella infection, we show that levels of Salmonella are equivalent between antibiotic-treated superspreader and nonsuperspreader hosts; however, superspreader hosts are uniquely able to tolerate antibiotic treatment, unlike nonsuperspreader hosts. “

*Also see:  Antibiotics may help Salmonella spread in infected animals, scientists learn – Stanford Medicine News

Spatial organization of bacterial chromosomes – Xindan Wang, David Z Rudner – Current Opinion in Microbiology

“Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.”

Bacterial healers: Microbes can redeem themselves to fight disease – Susan Gaidos – Science News

“It’s just a matter of time before bacterial-based treatments become a routine part of a doctor’s toolkit, says microbiologist Robert Britton of the Baylor College of Medicine in Houston, who is studying the relationship between microbes and human health. “

Techniques

Rapid fingerprinting of methanogenic communities by high-resolution melting analysis – Jaai Kim, Changsoo Lee – Bioresource Technology

“The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel.”

Microbes in the news

Our unique ‘microbial aura’ travels with us wherever we go – Science Friday – PRI

“Unless you lived exactly the same life as me, you would not have the same microbiome. You are, in essence, microbially unique,” explains Jack Gilbert

We’re making a Microbiome Documentary Series and could use your Help – Jamie – Reddit

“My name’s Jamie and I’m part of a team trying to crowdfund a documentary series on the human microbiome titled: ‘Redefining Human’.”

Building houses with bacteria – Euronews

“Houses of the future could be partially built with bacteria. It sounds like science fiction but researchers involved in an EU-backed project in Madrid are working towards making this a concrete reality.”

Bik’s Picks

The Role of Surface Chemistry in Adhesion and Wetting of Gecko Toe Pads – Ila Badge – Scientific Reports

“As expected, under wet conditions, adhesion on a hydrophilic surface (glass) was lower than that on a hydrophobic surface (alkyl-silane monolayer on glass).”

Scientists prepare for an 8-month mission to Mars – on Earth soil- BetaWired

“There’s a new experiment commencing in Hawaii, and the results will help NASA better prepare its astronauts for a lengthy mission to Mars.”

White rhino subspecies is down to one breeding male – Andrea James – BoingBoing

“Sad news from Kenya: the northern white rhino subspecies is down to one breeding male with the death of Suni this month. Only six remain.”

Scientists restore hearing in noise-deafened mice, pointing way to new therapies – ScienceDirect

“Scientists have restored the hearing of mice partly deafened by noise, using advanced tools to boost the production of a key protein in their ears.”

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Human microbiome digest, October 7, 2014

Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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Microbiome digest, August 27, 2014

Not many microbiome papers today, just some other interesting topics: does dirt make you happy, definition of preterm labor, cheese cultures, and solving a Death Valley mystery.

Pregnancy and birth 

The Problem With What Doctors Call Preterm Labor – Catherine Pearson – Huffington Post

“”We have been thinking of preterm birth as though it is one condition, and this is not the right way of thinking about the problem,” Dr. Roberto Romero, chief of the perinatology research branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, told The Huffington Post.”

Insect microbiome

* Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology

“Using 454-pyrosequencing of the 16S rRNA gene, we show that gut communities have representatives of 26 bacterial phyla and are dominated by Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria and Synergistetes”

Microbes in the news

* Does Dirt Make You Happy? – Anna Brones – Modern Farmer

“We benefit from being outdoors and exposed to things like soil and animals, because of the fact that we’re exposed to microorganisms.”

* Scientists and cheesemakers gather for (microbial) culture – Ewen Callaway – Nature News

““I fall in love every time I look at a cheese rind. They’re wonderful microbial ecosystems,” she says.”

Transcriptomics

Comparative analysis of the transcriptome across distant species – Mark B. Gerstein – Nature

“To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. “

Bik’s Picks

This has intrigued me for years – very happy to see this paper.
Sliding Rocks on Racetrack Playa, Death Valley National Park: First Observation of Rocks in Motion – Richard D. Norris – PLOS ONE

“the process of rock movement that we have observed occurs when the thin, 3 to 6 mm, “windowpane” ice sheet covering the playa pool begins to melt in late morning sun and breaks up under light winds of ~4–5 m/s.”

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General microbiology and science, August 14

A metabolic map of Faecalibacterium prausnitzii, bacteria injections to cure cancer, a researcher smuggling live bacteria in a lunchbox,  and a scientist in trouble for posting a PhD thesis.

Metabolomics

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe – Almut Heinken – Journal of Bacteriology

“In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms.”

Transcriptomics

Pervasive transcription: illuminating the dark matter of bacterial transcriptomes – Joseph T. Wade & David C. Grainger – Nature Reviews Microbiology

“In this Opinion article, we discuss our current understanding of pervasive transcription, its genetic origin and its regulation. “

More microbiology

Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses
Nicholas J. Roberts – Science Translational Medicine

“On the basis of these encouraging results, we treated a human patient who had an advanced leiomyosarcoma with an intratumoral injection of C. novyi-NT spores. This treatment reduced the tumor within and surrounding the bone. “

Canadian ex-researcher pleads guilty in attempted bacteria-smuggling case – Lee-Anne Goodman

“With his wife in the passenger seat, they discovered in his suitcase 17 vials of live Brucella — contained in a block of ice and swathed in bubble wrap in a children’s lunch bag — and a substantial quantity of goat’s blood.”

Techniques

Preprint: Swabs to Genomes: A Comprehensive Workflow – David A Coil – PeerJ

“The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome”

Accuracy of Next Generation Sequencing Platforms – Edward J Fox – Next Generation: Sequencing & Applications

“The ability of these technologies to disentangle sequence heterogeneity, however, is limited by their relatively high error rates”

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences — Pablo Yarza – Nature Reviews Microbiology

“Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.”

Science, Publishing, Career

Financial costs and personal consequences of research misconduct resulting in retracted publications – Andrew M Stern, Arturo Casadevall, R Grant Steen, Ferric C Fang – eLife

“We found that papers retracted due to misconduct accounted for approximately $58 million in direct funding by the NIH between 1992 and 2012, less than 1% of the NIH budget over this period. ”

Student may be jailed for posting scientist’s thesis on web – David Reay – Nature News Blog

“Colombian biology student is facing up to 8 years in jail and a fine for sharing a thesis by another scientist on a social network. Diego Gómez Hoyos posted the 2006 work, about amphibian taxonomy, on Scribd in 2011.

Study: Uncivil work environment pushing women out of the engineering field – Brigid Schulte – Washington Post

“a new National Science Foundation report released on Saturday about why so few women go into engineering, or stay in the field, highlights a key reason: a workplace culture of incivility toward women.”

Science of inclusion – Holly McDede – SFBG.com

“As Big Tech struggles with diversity, women find support and fellowship in the biotech industry.”

Bik’s Picks

Pour on the Salt? New Research Suggests More Is OK – Judy Silverman and Lisa Tolin – NBC News

“New research suggests that healthy people can eat about twice the amount of salt that’s currently recommended — or about as much as most people consume anyway. “

At Harvard, tiny robots ‘swarm’ into shape – Carolyn Y. Johnson – Boston Globe

When Harvard scientist Michael Rubenstein walks into the laboratory in the morning, he is greeted with a scene somewhere between a disco and the opening of a science fiction movie about a robot apocalypse. A constellation of LED lights blinks in the darkness — the electronic heartbeat of his 1,024-robot horde. They are ready to do his bidding.”

Newborns’ genetic code sends infection distress signal – Science Daily

“Babies suffering from life-threatening bacterial infections such as sepsis could benefit from improved treatment, thanks to a ground-breaking study. “

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General microbiology and science

Some new bioinformatic tools,  dengue response and vaccines, and host response and transcriptomics.

Host response and gene expression

Single-cell RNA-seq: advances and future challenges – Antoine-Emmanuel Saliba – Nucleic Acids Research

“Different single-cell RNA-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations.”

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes – Nadia M Davidson and Alicia Oshlack – Genome Biology

“Here we present Corset, a method that hierarchically clusters contigs using shared reads and expression, then summarizes read counts to clusters, ready for statistical testing. Using a range of metrics, we demonstrate that Corset out-performs alternative methods.”

Bioinformatics

Suffix tree searcher: exploration of common substrings in large DNA sequence sets
David Minkley – BMC Research Notes

“The program accommodates very large numbers of very large sequences, with aggregate size reaching tens of billions of nucleotides. The program makes use of pre-sorted persistent “building blocks” to reduce the time required to construct new trees.”

SnipViz: a compact and lightweight web site widget for display and dissemination of multiple versions of gene and protein sequences – Daniel Jaschob – BMC Research Notes

“SnipViz is a client-side software tool designed to disseminate multiple versions of related gene and protein sequences on web sites. SnipViz has a space-efficient, interactive, and dynamic interface for navigating, analyzing and visualizing sequence data.”

Dengue

 

Dengue vaccine trial poses public health quandary – Dennis Normile – Science

 

“The vaccine, developed by Sanofi Pasteur, proved safe, had an overall efficacy rate of 56.5%, and reduced cases of severe disease by 88.5%. But it had limited efficacy against dengue 2, one of four dengue virus serotypes in circulation.”

Predictors of hospital stay and mortality in dengue virus infection-experience from Aga Khan University Hospital Pakistan – Muhammad Abdul Khalil – BMC Research Notes

“Increasing age, coagulopathy and acute kidney injury in patients with DVI is associated with increased hospital stay.”

 

 

Science and publishing

A crisis of trust – Pubpeer

“As PubPeer developed, and especially once we enabled anonymous posting, we were shocked at the number of comments pointing out much more fundamental problems in papers, involving very questionable research practices and rather obvious misconduct. “

Dr. Bik’s Picks

Note to Science: The GOP’s Just Not That That Into You – Jeffrey Kluger – Time

“If the Speaker, by his own admission, isn’t qualified to debate climate change, fine, he’s excused from the conversation—and he should be expected not to offer further opinion on the matter. “

The first Science Hack Day in China – Ariel Waldman – BoingBoing

“Over the course of the weekend in a Shanghai incubator space, kids, parents, scientists, artists and technologists joined forces to play with science and prototype ideas. “

Exclusive: Naked Mole Rat Filled With Regret Over Evolutionary Choices – The Allium

“In an exclusive interview with The Allium, the Naked Mole Rat has revealed its regret at some of the evolutionary choices it has made, in particular the whole nakedness and the teeth.”

 

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Human microbiome, July 22

Transcriptome in periodontitis, metabolomic analysis of breath in IBD patients, cystic fibrosis microbiome, and Clostridium difficile.

Human microbiome general

Review: Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana and Dennis L. Kasper – Journal of Clinical Investigation

“In this Review, we discuss the current state of knowledge regarding the role of the intestinal microbiota in immunologic development, highlighting mechanistic principles that can guide future work.”

Meeting report: Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 – Jacques Ravel and many others – Microbiome

“This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.”

Metabolomics

Metabolomic analysis of breath volatile organic compounds reveals unique breathprints in children with inflammatory bowel disease: a pilot study – N. Patel – Alimentary Pharmacology & Therapeutics

“Exhaled breath was collected and analysed using a selective ion flow tube mass spectroscopy (SIFT-MS) to identify new markers or patterns of IBD.”

Metabolites related to gut bacterial metabolism, peroxisome proliferator-activated receptor-alpha activation, and insulin sensitivity are associated with physical function in functionally-limited older adults – Michael S. Lustgarten – Aging Cell

“Collectively, these data suggest that gut microbial metabolism, PPAR-α activation, and insulin sensitivity may be involved in mechanisms that underlie physical function in functionally-limited older adults.”

Oral microbiome

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis – Ana E Duran-Pinedo – ISME J

“We report here the in situ genome-wide transcriptome of the subgingival microbiome in six periodontally healthy individuals and seven individuals with periodontitis.”

Respiratory microbiome

Predominant pathogen competition and core microbiota divergence in chronic airway infection – Geraint B Rogers – ISME Journal

“..we analysed 16S rRNA gene pyrosequencing data generated previously from 60 adult bronchiectasis patients, whose airway microbiota was dominated by either P. aeruginosa or H. influenzae.”

Pyrosequencing reveals transient cystic fibrosis lung microbiome changes with intravenous antibiotics – Daniel J. Smith – European Respiratory Journal

“Microbial community profiles were derived through analysis of bacterial-derived 16S ribosomal RNA by pyrosequencing and changes over time were compared.”

Review: Respiratory microbiota: addressing clinical questions, informing clinical practice – Geraint B Rogers – Thorax

“In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. “

Propionibacterium-Produced Coproporphyrin III Induces Staphylococcus aureus Aggregation and Biofilm Formation – Michael S. Wollenberg – mBio

“We observed that crude extracts of cell-free conditioned medium from Propionibacterium spp. induce S. aureus aggregation in culture. “

Gut microbiome

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection – Susana Fuentes – ISME Journal

“Global composition and network analysis of the microbiota was performed in faecal samples from nine patients with recurrent CDI. Analyses were performed before and after duodenal donor faeces infusion, and during a follow-up of 10 weeks. The microbiota data were compared with that of the healthy donors. “

Review: Clostridium difficile and the microbiota – Anna M. Seekatz and Vincent B. Young – Journal of Clinical Investigation

“Both human and animal models have demonstrated the importance of the gut microbiota’s capability of providing colonization resistance against C. difficile.”

Vaginal microbiome

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME Journal

“We conducted comparative analyses of the primate vaginal microbiome using pyrosequencing of the 16S rRNA genes of a phylogenetically broad range of primates to test for factors affecting the diversity of primate vaginal ecosystems. … humans were distinct from other primates in both microbiome composition and diversity.

Semen microbiome

The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection – Cindy M. Liu – PLOS Pathogens

“HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART.”

Antibiotic perturbation and microbiome

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations – Torey Looft – ISME Journal

“In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. “

Impact of Antibiotics on the Intestinal Microbiota and on the Treatment of Shiga-toxin-Producing Escherichia coli and Salmonella Infections – Szych, Jolanta – Current Pharmaceutical Design

“This review evaluates the current literature based on the impact of antibiotics on the intestinal microbiota and the critical role of intestinal bacteria in controlling infection and subsequent clinical disease caused by STEC and Salmonella, and the transmissibility of these important pathogens”

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