Category Archives: Bik’s Non-Microbiology Picks

Microbiome digest, 31 October 2014

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Happy Halloween! Today we have fungal communities in mammals, more on the TMAO story, some microbiome reviews, honey bee colonization, and microbophobia papers.

General human/mammalian microbiome

* Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto, Carlotta De Filippo and Duccio Cavalieri – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers, and pathogens based on the interaction of these fungi with the human immune system.”

Prognostic Value of Elevated Levels of Intestinal Microbe-Generated Metabolite Trimethylamine-N-Oxide in Patients With Heart Failure – Refining the Gut Hypothesis – W.H. Wilson Tang – Journal of the American College of Cardiology

“High TMAO levels were observed in patients with HF, and elevated TMAO levels portended higher long-term mortality risk independent of traditional risk factors and cardiorenal indexes.”

* Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches – Yihwan Kim – Methods

“This review examines computational methods that are valuable for the analysis of human microbiome, and highlights the results of several large-scale human microbiome studies.”

Human gut microbiome

Novel opportunities for the exploitation of host–microbiome interactions in the intestine – Ingmar JJ Claes – Current Opinion in Biotechnology

“New sequencing technologies have dramatically increased our knowledge on the composition of the human intestinal microbiota in health and disease. ”

Animal microbiome

* Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

“Colonization patterns were evaluated using quantitative real-time PCR (qPCR) to assess community sizes and using deep sequencing of 16S rRNA gene amplicons to assess community composition.”

Soil microbiome 

Landscape-scale Variation in Pathogen-suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica – Kristen K. Becklund – Biotropica

“To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil-borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde)”

Microbes in the news

More scary than Halloween: this month in germophobia microbophobia – Jonathan Eisen – MicroBEnet

“It seems that any time a holiday comes around in the US, the press starts to ramp up the writing of stories about evil microbes that are lurking all around us. “

MSU and Detroit analyze tiny bacteria to investigate murders – Kate Wells – Michigan Rado

““Can we use these communities to identify whether a person is from a certain location or if they’ve been to a location?” asks Benbow”

Science and career

Satire: Sixth Person Dies As Another “Dance Your PhD” Video Goes Wrong – The Allium

“Principal Investigator, Professor Tom Morrow (61) slipped as he was mimicking a helix-turn-helix motif as part of a much larger transcription factor protein.”

10 Creative Careers That Rely on Science and Math – Alexandra Ossola – The Atlantic

“Knowledge of STEM subjects isn’t just essential for physicists or computer engineers. Fashion designers, zookeepers, and deep-sea divers also use it every day.”

Bik’s Picks

Lava Flow In Hawaii Spares Homes, But Threatens To Cut Off Community – Scott Neuman – NPR

“Officials in Hawaii are sending National Guard troops to the town of Pahoa on the Big Island, where a lava flow is creeping toward a main road, threatening to cut off the community.”

100-Year-Old Time Capsule Discovered – Clapway

“A 100-year old time capsule was found at Baltimore’s Washington Monument during a restoration project. And it seems officials are hesitant to even open it because of how old it is.”

Researchers: Science says girls’ sexualized Halloween costumes are scary – Rebecca C Bigler and Sarah McKenney – Dallas News

“Parents could also foster girls’ creativity by encouraging them to make their own costumes. “

And, related to the post above, make sure to read the hilarious comments here:
Delicious Women’s Phd Darling Sexy Costume – Amazon

“Sexy graduation gown is a micro mini with zip up front. Gold sash, hat, and diploma included”

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Microbiome digest, October 30, 2014

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Bacteriocins in human metagenomic libraries, freezing/thawing effects on community composition, microbiome of preterm neonates, and bacteria in soil.
Multiple-site human microbiome

Diversity and dynamics of bacteriocins from human microbiome – Jinshui Zheng – Environmental Microbiology

“We employed bioinformatic analyses to identify putative bacteriocin sequences in metagenomic sequences obtained from different human body sites. “

Human respiratory microbiome

* Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses – Leah Cuthbertson – Journal of Cystic Fibrosis

“Following each cycle, an aliquot was removed and treated with propidium monoazide (PMA) prior to DNA extraction and 16S rRNA gene pyrosequencing.”

Human gut microbiome

Immune Homeostasis, Dysbiosis and Therapeutic Modulation of the Gut Microbiota – Christine T. Peterson – Clinical & Experimental Immunology

“This review discusses host-microbiota homeostasis, consequences of its perturbation, and the associated challenges in therapeutic developments that lie ahead.”

Microbiome of pregnancy and birth

* Intestinal Microbiota Development in Preterm Neonates and Effect of Perinatal Antibiotics – Silvia Arboleya – The Journal of Pediatrics

“We used 16S ribosomal RNA gene sequence-based microbiota analysis and quantitative polymerase chain reaction to evaluate the establishment of the intestinal microbiota. “

Animal microbiome

Hidden Population Structure and Cross-species Transmission of Whipworms (Trichuris sp.) in Humans and Non-human Primates in Uganda – Ria R. Ghai – PLOS Neglected Tropical Diseases

“We examined the phylogenetic structure of whipworms in a multi-species community of non-human primates and humans in Western Uganda, using both traditional microscopy and molecular methods.”

Soil microbiome

Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes – Renata Carolini Souza – Applied Soil Ecology

“in this study we used a shotgun metagenomic approach to compare different soil…, and crop … managements in a 13-year-old field experiment in southern Brazil. “

Evaluating T-RFLP protocols to sensitively analyze the genetic diversity and community changes of soil alkane degrading bacteria – Julia Giebler – European Journal of Soil Biology

“This study aimed at identifying a reliable, highly resolving fingerprinting method to monitor alkane degrading communities in soil.”

Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms – Simonetta Bagella – Comptes Rendus Biologies

“Species richness decreased with increasing land use intensity, the Shannon index showed the highest values in grasslands and hay crops.”

Food microbiology

Characterization and use of microbial communities in Doenjang to control the unpleasant odor of Ginkgo epicarp – Sunhyun Park – Food Science and Biotechnology

“Microbes in doenjang were probably responsible for the reduction in the butyric acid content. Microbial communities were analyzed during fermentation.”

Bioreactor microbiology

Thermophilic anaerobic digestion of thermal pretreated sludge: role of microbial community structure and correlation with process performances – M.C. Gagliano – Water Research

“16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses allowed us to identify the majority of bacterial and archaeal populations. “

Bioinformatics

Fast dendrogram-based OTU clustering using sequence embedding – Thuy-Diem Nguyen – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. “

Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant features – Julia Warnke – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We present Focus, a new multilayer graph model for short read analysis and extraction of biologically relevant features. “

The UniFrac significance test generates different outputs given semantically equivalent inputs – Jeffrey Long – Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

“We identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.”

Microbes in the news

SpaceX 4 splashes down, returns bacteria samples to Earth – Josh Barrett – WaayTV

“HudsonAlpha’s Genomic Sciences Lab will be sequencing the genomes of E. coli bacteria that were aboard the ISS. For some reason, bacteria are not as susceptible to antibiotics in space.”

Bik’s Picks

Why Millennials &%#@! Love Science – Alexandra Ossola – The Atlantic

“Today’s young adults see new discoveries both as a source of awe and a means for innovation.”

1,000 Flavors of Banana: the New Science of Food Additives – Annie Gasparro – The Wall Street Journal

“Rather than sourcing the jalapeño or poblano pepper, you can create it with a flavor house, and just apply it over a corn chip,” said Jared Simon, marketing director for Hain Celestial Group Inc. ’s snacks and bakery division, which uses natural flavors for its foods such as Terra vegetable chips.”

Spooky Science: The Sounds of Halloween – Science Buddies – Scientific American

“In this science activity, you will investigate what goes into the composition of a perfect creepy soundtrack. “

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Microbiome Digest, October 29, 2014

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The genome of Mycoplasma Mnola, helminths in wild rats, fungi in strawberry roots, and the top 100 most cited papers of all time. Can you guess which one is #1?

Human genital microbiome

An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease – Jennifer M. Fettweis – PLOS ONE

“In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease.”

Human gut microbiome

Bacteriology and Changes in Antibiotic Susceptibility in Adults with Community-Acquired Perforated Appendicitis – Hong Gil Jeon – PLOS ONE

“We retrospectively reviewed records of adult patients diagnosed with perforated appendicitis at an 800-bed teaching hospital between January 2000 and December 2011. “

Animal microbiome

Changes in the intestinal bacterial community during the growth of white shrimp, Litopenaeus vannamei – Zhaobin Huang – Aquaculture Research

“In this study, we documented the changes in the intestinal bacterial community at four stages in Litopenaeus vannamei…, using 454 pyrosequencing techniques. “

* Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics – Ryusei Tanaka – PLOS ONE

“In this study, we assessed parasite diversity in wild rats using 18S rDNA-based metagenomics. 18S rDNA PCR products were sequenced using an Illumina MiSeq sequencer and the analysis of the sequences using the QIIME software successfully classified them into several parasite groups.”

Soil microbiome

Linking soil microbial communities to vascular plant abundance along a climate gradient – Luca Bragazza – New Phytologist

“Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance.”

* Influence of Soil Type, Cultivar and Verticillium dahliae on the Structure of the Root and Rhizosphere Soil Fungal Microbiome of Strawberry – Srivathsa Nallanchakravarthula – PLOS ONE

“In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing.”

Metagenomics / Bioinformatics

* Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes – Ying Yang – PLOS ONE

“A hybrid annotation pipeline proposed previously for taxonomic assignments was evaluated in this study for metagenomic sequences annotation of specific functional genes, such as antibiotic resistance genes, arsenic resistance genes and key genes in nitrogen metabolism. “

Metabolomics

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

“Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. “

Phages and viruses

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting – Gregory W. Goldberg – Nature

“Here we show that the Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phages. “

Science, publishing and career

The top 100 papers – Richard Van Noorden – Nature

“To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time.”

Bibliometrics: Is your most cited work your best? – John P. A. Ioannidis – Nature

“John P. A. Ioannidis and colleagues asked the most highly cited biomedical scientists to score their top-ten papers in six ways.”

Recommendations for the Role of Publishers in Access to Data – Jennifer Lin, Carly Strasser – PLOS Biology

“As appeals for public access of research data continue to proliferate, many scholarly publishers—alongside funders, institutions, and libraries—are expanding their role to address this need. “

How to Make More Published Research True – John P. A. Ioannidis – PLOS ONE

“Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted.”

* Prominent Geomicrobiologist Dies – Tracy Vence – The Scientist

“Katrina Edwards, whose research focus was on discovering life beneath the ocean floor, has passed away at age 46.”

Bik’s Picks

* The Art of Science: Popsicles Go Viral – The Finch and Pea

“Lick a virus? Probably not a good idea, unless it’s a Dangerous Popsicle, a sweet treat created by artist and designer Wei Li. “

Dozens of genes associated with autism in new research – Science Direct

“Two major genetic studies of autism, involving more than 50 laboratories worldwide, have newly implicated dozens of genes in the disorder. “

Antares Rocket Explosion Destroyed These Kids’ Science Projects – Rheana Murray – ABC News

“Students across the nation watched their science projects go up in flames as the rocket bound for the International Space Station exploded moments after takeoff.”

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General microbiology and science digest, October 28, 2014

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Viruses in humans and caribous, metabolomics of losing weight, and microbes on rough surfaces.
Metabolomics

Impact of a 6-week very low-calorie diet and weight reduction on the serum and fecal metabolome of overweight subjects – Mette S. Schmedes – European Food Research and Technology

“NMR-based metabolomics was carried out on serum and fecal samples obtained from healthy female subjects pre- and post-weight reduction. “

Book with lots of plagiarized text (in at least 3 chapters), so not worth the $25 for the physical book, or even the free download:
Metabonomics and Gut Microbiota in Nutrition and Disease – Springer Link

Metagenomics

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – PeerJ Preprints

“Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. “

Viruses and phages

Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources – Michael J. Strong, Zhen Lin, Erik K. Flemington – mBio

“We thank Ladner and colleagues for their conversation about standardizing viral genome sequences derived from high-throughput (HT) sequencing technology.”

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice – Robert H. Yolken – PNAS USA

“Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. “

* Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch – Terry Fei Fan Ng – PNAS USA

“Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. “

Microbial Ecology

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces – Gang Wang, Dani Or – Scientific Reports

“A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields.”

Scaling laws governing stochastic growth and division of single bacterial cells – Srividya Iyer-Biswas – PNAS USA

“Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. “

Microbes in the news

Gut feelings – Microbiome and mental health – Fabio Piccini – Wall Street International

“Might people suffering from certain forms of mental health problems benefit from a fecal transplant from someone with more happy-go-lucky bacteria? “

Small Things Considered: Bacteria Allow Woodrats to Eat Poison – Anne A. Madden – ASM blog

“Despite such dire consequences, woodrats ingest enough of these plant toxins to kill a lab rat. Every day. But the desert is not littered with woodrat corpses, so clearly they are able to detoxify this poisonous salad somehow. “

Saving The Bees Using Microscopic Bugs – RedOrbit

“Phages are the most abundant life form on the planet and each phage has a unique bacteria that it will attack,” said Sandra Burnett, BYU professor of microbiology and molecular biology. “This makes phage an ideal treatment for bacterial disease because it can target specific bacteria while leaving all other cells alone.”

Science, publishing, and career

Reputation and impact in academic careers – Alexander Michael Petersen – PNAS USA

“Here, we develop a framework for quantifying the influence author reputation has on a publication’s future impact.”

NPRs All Things Considered (Podcast, 5 min): Is ‘Leaning In’ The Only Formula For Women’s Success In Science? – Kelly McEvers – NPR

“Don’t wait to be invited or encouraged to make a career in science, engineering or technology, Frances Arnold advises the young women she teaches at the California Institute of Technology. “

Bik’s Picks

Doctors Making Housecalls: Better, Cheaper Care at Home? – Jennifer Ferris – MedPageToday

“In a little over a decade the practice has exploded in popularity — with Taavoni and more than 40 other providers in North Carolina innovating new ways to bring healthcare home.”

Oil platforms off California are among the most productive marine fish habitats globally –
Jeremy T. Claisse – PNAS USA

“Here, we find that fish communities living on the complex hardscape habitat created throughout the water column by the structure of oil and gas platforms off California have the highest secondary production per unit area of seafloor of any marine ecosystem for which similar estimates exist.”

Can Science Perfect Food? – Daniela Galarza – Eater.com

“A research team in Japan is blowing past molecular gastronomy to discover new ways of perfecting already flawless dishes.”

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General microbiology and science digest, October 27, 2014

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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 24, 2014

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Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”

Metagenomics

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”

Metabolomics 

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”

Microbiome Digest, October 23, 2014

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Not much microbiome news today – which was good because I got time to watch the solar eclipse and a huge solar storm at the same time.  Enjoy the read!

Animal models of microbiome research

Lyn Deficiency Leads to Increased Microbiota-Dependent Intestinal Inflammation and Susceptibility to Enteric Pathogens – Morgan E. Roberts – Journal of Immunology

“Lyn2/2 mice exhibited profound cecal inflammation, bacterial dissemination, and morbidity following S. Typhimurium challenge and greater colonic inflammation throughout the course of C. rodentium infection.”

Rock microbiome

* Halophilic Archaea Cultivated from Surface Sterilized Middle-Late Eocene Rock Salt Are Polyploid – Salla T. Jaakkola – PLOS ONE

“We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase.”

More Microbiology

Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria – Felix J. H. Hol, Cees Dekker – Science

“Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities.”

Review: Theory and Empiricism in Virulence Evolution – James J. Bull, Adam S. Lauring – PLOS Pathogens

“Our purpose here is to offer a brief introduction to virulence theory, explain some of its strengths and weaknesses, and suggest how theory might be united with empiric data”

Techniques

Comparing the new 16S rRNA V4 and ITS primers to the old primers-RESULTS! – Embriette Hyde – MicroBEnet

“The Knight lab has been working hard testing new primers for 16S rRNA amplicon production and its time to share our progress.”

Microbes in the News

As permafrost soils thaw, soil microbes amplify global climate change – Science Daily

“Now, research by an international team of scientists from the U.S., Sweden and Australia, led by University of Arizona scientists, shows that a single species of microbe, discovered only very recently, is an unexpected key player in climate change.”

* The Scientist: Prof. Esther Angert Studies Extreme Bacteria – Siddesh Ramesh – Cornell Sun

“While the majority of bacteria cannot be seen without a microscope, there exists a group of bacterial species that is visible to the naked eye. Known as Epulopiscium, they are “an extreme on the spectrum of diversity of bacterial life in existence,” according to Prof. Esther Angert, microbiology.”

Bik’s Picks

Flare Alert: Monster Sunspot Turns Toward Earth – Ian O’Neill – Discovery

“Amateur astronomers have been wowed by a vast sunspot that has rotated to face Earth, the largest since this solar cycle began in 2008, and solar observatories (on the ground and orbiting Earth) are closely monitoring the region.“

Watch cell division with new, remarkable resolution: Nobel winner Betzig strikes again – Tech Times

“Just weeks after sharing the Nobel Prize in chemistry for his work involving high-resolution microscopes, a U.S. researcher has again stunned the scientific world with a new technique that peers deeply into living cells.”

Ancient Europeans do not drink milk according to new study – BetaWired

“Almost everyone drinks milk today but a new study shows that ancient Europeans were not milk lovers back in the old days. According to a DNA analysis result, ancient Europeans are lactose intolerant.”

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Microbiome digest, October 22, 2014

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Microbes in the mouth of patients with heart disease, bile and gall bladder microbiome of pigs, precisely restoring resistance to Clostridium difficile infection, and networks between fungi and plants. And don’t forget the solar eclipse tomorrow PM for most of the US.

Human oral microbiome

Microbial Diversity Similarities in Periodontal Pockets and Atheromatous Plaques of Cardiovascular Disease Patients – Wagner Serra e Silva Filho – PLOS ONE

“Subgingival biofilm and coronary balloons used in percutaneous transluminal coronary angioplasty were collected from 18 subjects presenting with generalized moderate to severe periodontitis and OCAA. DNA was extracted and the gene 16S was amplified, cloned and sequenced.”

Human gut microbiome

Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects – Ling Chun Kong – PLOS ONE

“We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.”

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men – Anne Salonen – ISME Journal

“Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet.”

Animal models of microbiome research

* Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

“..we determine that Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion.”

* Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs – Marc A. Sze – PLOS ONE

“Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation.”

Specific Microbiome Changes in a Mouse Model of Parenteral Nutrition Associated Liver Injury and Intestinal Inflammation – J. Kirk Harris – PLOS ONE

“Microbiome analysis in the PNALI mouse identified specific alterations within colonic microbiota associated with PNALI and further association of these communities with the lipid composition of the PN solution. “

Animal microbiome

Characterization of the bile and gall bladder microbiota of healthy pigs – Esther Jiménez – Microbiology Open

“We have studied, by culture-dependent techniques and a 16S rRNA gene-based analysis, the microbiota present in the bile, gall bladder mucus, and biopsies of healthy sows”

Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia – Petra Videnska – PLOS ONE

“In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. “

Plant microbiome

* Assembly of complex plant–fungus networks – Hirokazu Toju – Nature Communications

“The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. “

Soils and sediments

The long-term adaptation of bacterial communities in metal-contaminated sediments: a metaproteogenomic study – David C. Gillan – Environmental Microbiology

“Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels (MetalEurop: 3218 mg Zn kg−1; 913 mg Pb kg−1) were compared by shotgun metaproteogenomics. “

Bioinformatics / metabolomics

* Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment – A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses – Diogo M. O. Ogawa – PLOS ONE

“We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. “

Estimating coverage in metagenomic data sets and why it matters – Luis M Rodriguez-R and Konstantinos T Konstantinidis – ISME Journal

“We demonstrate here how available solutions can determine the level of sequencing coverage obtained by metagenomic data sets and thus, guide their robust analysis and comparison.”

Immunology

* Fall issue of Stanford Medicine reports on the immune system’s balancing act

“If you want to understand the human immune system, try studying humans — not mice, urges Mark Davis, PhD, in a special report on the immune system in the new issue of Stanford Medicine magazine.”

Bik’s Picks

Genome sequence of a 45,000-year-old modern human from western Siberia – Qiaomei Fu – Nature

“the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. “

Sky spectacle: Partial solar eclipse coming Thursday – USA Today

“In the afternoon, a partial solar eclipse — where the moon covers a part of the sun — will be visible across much of the USA, barring any pesky clouds that could block the show.”

Go Giants! The Science of Baseball – Exploratorium

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Microbiome digest, October 21, 2014

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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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Microbiome Digest, October 20, 2014

Posted on by

Oral core microbiome, symbionts in crabs, sponges, and Drosophila, metabolites in dolphin’s breath, and retraction of a paper favored by Dr. Oz.

Pregnancy and birth

NEC in Twin Pregnancies: Incidence and Outcomes – Sathyaprasad C Burjonrappa, Brian Shea, Diya Goorah – Journal of Neonatal Surgery

“There is a remarkable higher incidence of NEC amongst twins. Abnormal colonization of the gastrointestinal tract appears to be an immediate postpartum event.”

Human oral microbiome

Intraindividual variation in core microbiota in peri-implantitis and periodontitis – Noriko Maruyama – Scientific Reports

“To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. “

Antimicrobial Effect of Lemongrass Oil against Oral Malodor Microorganisms and the Pilot Study of Safety and Efficacy of Lemongrass Mouthrinse on Oral Malodor – Panitta Satthanakul – Journal of Applied Microbiology

“Antimicrobial activity of LG mouthrinse was examined against common odorigenic microorganisms using broth microdilution assay and the disc diffusion method. A randomized double-blind clinical study was performed in 20 healthy volunteers.”

Animal microbiome

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri – Tomo-o Watsuji – ISME Journal

“A phylogenetic analysis showed that many of the bacterial 16S ribosomal RNA gene sequences obtained from the intestine were closely related to the sequences of the epibionts, thus they were probably derived from the epibionts.”

* In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors – Peter D. Newell – Frontiers in Microbiology

“We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. “

* Two distinct microbial communities revealed in the sponge Cinachyrella – Marie L. Cuvelier – Frontiers in Microbiology

“Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing.”

* Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology

“PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. “

Plant microbiome

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils – Chao Ai – Soil Biology and Biochemistry

“Wheat rhizosphere microbiome was studied by stable isotope probing and pyrosequencing.”

Environmental microbiome

Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea – Sung-Suk Suh – Ocean Science Journal

“In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. “

Bacterial community structure of a lab-scale anammox membrane bioreactor – Alejandro Gonzalez-Martinez – Biotechnology Progress

“In this study, next-generation sequencing techniques have been used for the investigation of the bacterial communities of this MBR Anammox for the first time ever. “

Metagenomics & Bioinformatics

GenomePeek: What exactly is that sequencing data? – Katelyn McNair – MicroBEnet

“I wrote the initial version of GenomePeek, and tested it with various data sets using this student’s data. I quickly found that some genes work better than others, and so currently the four genes analyzed are: 16S, recA, rpoB, and groEL.”

Metabolomics

Metabolite Content Profiling of Bottlenose Dolphin Exhaled Breath – Alexander A. Aksenov – Analytical Chemistry

“We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). “

Proteomics

Symbiosis, Dysbiosis and Rebiosis – the value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

“After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis and rebiosis of the human gut during human development, pathogenesis and aging.”

More microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

“This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.”

* Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Zhang Wang, Martin Wu – PLOS ONE

“Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria.”

Real-time video imaging as a new and rapid tool for antibiotic susceptibility testing by the disk diffusion method: a paradigm for evaluating resistance to imipenem and identifying extended-spectrum β-lactamases – Stéphanie Le Page – International Journal of Antimicrobial Agents

“..we present here for the first time video movies of the appearance of the diameter of inhibition by the disk diffusion in real-time. “

Microbes in the news

Can Microbes Help Feed the World? – Amy Mayer – BioScience

“To help meet the challenge for food, scientists are using new technologies to better understand the role that soil microbes might play in bolstering agricultural production. “

Dentists Want To See Studies On Pot-Cavity Link – CBS Local

“Patients are experiencing tooth decay, expensive dentist bills and the pain of dealing with it all. The biggest side effect is dry mouth.”

Bik’s Picks

Brain surgery, by robot, through the cheek – Science Daily

“Engineers have developed a surgical robot designed to perform brain surgery by entering through the cheek instead of the skull that can operate on a patient in an MRI scanner. Additionally, the engineers have designed the system so that much of it can be made using 3-D printing in order to keep the price low.”

* Hilarious cartoons on Imgur: Real Scientists vs. Movie Scientists 

* Authors retract green coffee bean diet paper touted by Dr. Oz – Ivan Oransky – Retraction Watch

“Two authors of a 2012 paper sponsored by a company that made grand claims about green coffee bean extract’s abilities to help people lose weight have retracted it. The study was cited by The Dr. Oz Show, and last month it cost the company a $3.5 million settlement with the Feds.”

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