Category Archives: General Microbiome

Human microbiome, August 26, 2014

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Gut microbiome structure in the first years of life, lung microbiome in pneumonia and tuberculosis, why iron supplements might not always be a good thing, and the Microbiome Diet Book.

Pregnancy and birth

* The Intestinal Microbiome in Early Life: Health and Disease – Marie-Claire Arrieta – Frontiers in Immunology

“This review describes the gut microbiome structure and function during the formative first years of life, as well as the environmental factors that determine its composition.”

Oral microbiome

Review: The oral microbiome diversity and its relation to human diseases – Jinzhi He – Folia Microbiologica

“In this review, we focus on the recent progress in this field, including the oral microbiome composition and its association with human diseases.”

Respiratory microbiome

Single-Molecule Long Read 16S Sequencing to Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia – Ian Toma – Journal of Clinical Microbiology

“The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia.”

* Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis – Luz Elena Botero – Microbiome Journal

“Most V1-V2 16S rRNA gene sequences belonged to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria, with differences in relative abundances and in specific taxa associated with each sample type. “

Gut microbiome

* Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants – Tanja Jaeggi – Gut

“Using pyrosequencing, +FeMNPs increased enterobacteria, particularly Escherichia/Shigella (p=0.048), the enterobacteria/bifidobacteria ratio (p=0.020), and Clostridium (p=0.030).”

Animal models of microbiome research

Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition – Jordan S. Mar – Gut Microbes

“Microbiota profiling revealed distinct bacterial community compositions in the ileum, cecum and colon of control untreated animals”

Commensal Bacteria Regulate Thymic Aire Expression – Akihito Nakajima – PLOS ONE

“autoimmune regulator (Aire) expression in thymic epithelial cells (TECs), main components of the thymic microenvironment, was decreased in comparison to specific pathogen-free (SPF) mice and Nod1 wild-type (WT) mice, respectively. “

Microbiome in the News

* Overselling the Microbiome Award: The Microbiome Diet Book – Jonathan Eisen – The Tree of Life

“Sound too good to be true? Well, that is because it is.”

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Microbiome Digest, August 22, 2014

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

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

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

Human skin microbiome

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

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

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

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

Human gut microbiome

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

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

Human vaginal microbiome

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

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

Animal models of microbiome research

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

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

Animal microbiome

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

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

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

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

Food microbiology

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

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

Metabolomics

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

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

Bioinformatics

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

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

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

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

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

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

Microbes in the news

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

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

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

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

Bik’s Picks

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

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

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

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

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

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

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

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

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Microbiome digest, August 21, 2014

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

Postmortem human microbiome

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

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

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

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

Invertebrate microbiome

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

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

Soil microbiome

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

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

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

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

Water microbiome

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

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

Food microbiology

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

Fungi

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

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

 

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

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

Microbes in the news

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

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

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

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

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

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

Science and career

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

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

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

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

Bik’s Picks

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

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

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

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

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

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

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Microbiome digest, August 20, 2014

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Ocular microbiome, life under ice, and gut microbiome and behavior.

Human ocular microbiome

Assessment of ocular surface microbiota in keratoconus patients – a pilot study – M Gajecka – Acta Ophthalmologica

“Culture-based microbiology methods are used in the investigation to preliminary examine the OS microbiota. Simultaneously, microbial genetic material is extracted from the eye swabs for further qualitative and quantitative analyzes using molecular biology methods (real-time PCR, NGS).”

Microbial detection in clinical samples

Elevated Levels of Circulating DNA in Cardiovascular Disease Patients: Metagenomic Profiling of Microbiome in the Circulation – Vasudevan Dinakaran – PLOS ONE

“This work was aimed to study the circulating human microbiome in CVD patients and healthy subjects.”

Animal models of microbiome

A Possible Link between Food and Mood: Dietary Impact on Gut Microbiota and Behavior in BALB/c Mice – Bettina Pyndt Jørgensen – PLOS ONE

“Behavioral changes were accompanied by a significant change in GM composition of mice fed a high-fat diet” “Denaturation gradient gel electrophoresis (DGGE) was used to investigate differences in the composition of the GM.”

Mammalian microbiome

Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus – Jana Sachsenröder – Journal of General Virology

“Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids.”

Water microbiome

A microbial ecosystem beneath the West Antarctic ice sheet – Brent C. Christner – Nature

“Heterotrophic and autotrophic production data together with small subunit ribosomal RNA gene sequencing and biogeochemical data indicate that SLW is a chemosynthetically driven ecosystem inhabited by a diverse assemblage of bacteria and archaea. “

See also: Lakes under the ice: Antarctica’s secret garden – Douglas Fox – Nature

“Samples from a lake hidden under 800 metres of ice contain thousands of microbes and hint at vast ecosystems yet to be discovered.”

Bioinformatics

A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis – Liviu P. Dinu – PLOS ONE

“This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD). The rank-based aligner proposed in this work aims to improve correctness over speed. “

Viruses and phages (see also the rat/rotavirus paper above)

Unveiling viral–host interactions within the ‘microbial dark matter’ – Manuel Martínez-García – Nature Communications

“Using this method, we pinpoint viruses infecting the ubiquitous hyperhalophilic Nanohaloarchaeota, included in the so-called ‘microbial dark matter’ (the uncultured fraction of the microbial world).”

Microbes in the news

Archiving: Don’t let microbial samples perish – Noah Fierer and Craig Cary – Nature

“Microbial ecologists must coordinate to archive sample collections and genetic material.”

Microbiology: Microbiome science needs a healthy dose of scepticism – William P. Hanage – Nature

“To guard against hype, those interpreting research on the body’s microscopic communities should ask five questions”

Science, publishing and career

Editorial: Finding the root – The NIH is right to investigate whether bias makes grant awards unfair – Nature

“The idea that scientists who volunteer time and energy to review NIH grants could be biased against qualified minority researchers is a tough pill to swallow. “

Today’s YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015 – Jonathan Eisen – The Tree of Life

“Yay.  All men.  How wonderful.  Because, you know, there are no women working on the microbiome and nutrition right?  Ugg. “

 

Equally productive women are tenured less -Beryl Lieff Benderly – Science

“Women received tenure less often than men with equal productivity in three disciplines studied by Kate Weisshaar, a Ph.D. student in sociology at Stanford University.”

Bik’s Picks

Solar energy that doesn’t block the view – Science Daily

“Researchers have developed a new type of solar concentrator that when placed over a window creates solar energy while allowing people to actually see through the window. “

If Seals Hadn’t Introduced Tuberculosis To The New World, Europeans Would Have – Science 2.0

“A new study documents that again, finding isolated Mycobacterium pinnipedii from skeletons found in Peru which are at least 1000 years old. The pathogen is a relative of the TB bacterium that affects seals, so it likely that seals carried the pathogens from Africa to the Peruvian coast.”

Which Hot New Lab Coat Should You Buy This Season? – Fake Science

“We’ve found the hottest coats from Paris, Milan, and Batavia, Illinois and put them into our patented quiz. Take it and find out which lab coat will have you steaming up the beakers!”

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Microbiome digest, August 15, 2014

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Today we got donkey, goat, and camel milk, deodorants, kitten microbiomes, and coffee as a new mouth rinse.

Pregnancy and birth

Gut microbiota in preterm infants with gross blood in stools: A prospective, controlled study – Mohamed Ben Said – Early Human Development

“Each case was paired with two controls who were hospitalized in the same unit and were matched for gestational age and birth weight. The diversity of the gut microbiota was analyzed using 16S rRNA gene PCR and temporal temperature gel electrophoresis. “

Human oral microbiome

Antibacterial effect of coffee: calcium concentration in a culture containing teeth/biofilm exposed to Coffea Canephora aqueous extract – N. Meckelburg – Letters in Applied Microbiology

“This study revealed an inhibitory action of Coffea canephora against dental biofilm. This coffee species caused bacterial lysis and consequent release of calcium into the medium.”

Human gut microbiome

Review: Exploring gut microbes in Human health and disease: pushing the envelope
Jun Sun, Eugene B. Chang – Genes & Diseases

“In this review and commentary, we highlight recent progress in our understanding of the intestinal microbiome in the context of health and diseases, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.”

Review: Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology – Alexander Khoruts, Alexa R. Weingarden – Immunology Letters

“Mechanistic understanding will be required in development of next generation microbiota therapeutics, which may include FMT or defined microbial consortia.”

Gut Bacteria May Play a Role in Autism – Melinda Wenner Moyer – Scientific American

“One open question is whether these microbial differences drive the development of the condition or are instead a consequence of it. “

Skin microbiome

Deodorants and antiperspirants affect the axillary bacterial community – Chris Callewaert — Archives of Dermatological Research

“The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics.”

Goat and Ass Milk microbiome

Analysis of raw goat milk microbiota: Impact of stage of lactation and lysozyme on microbial diversity – Elizabeth A. McInnis – Food Microbiology

“Milk from transgenic goats containing lysozyme had a similar microbiota over time.”

Fasscinating stuff: Cleopatra took daily baths in assmilk to keep her skin wrinklefree. Maybe lactic acid bacteria were her secret?  Biotyping of cultivable lactic acid bacteria isolated from donkey milk – D. Carminati – Letters in Applied Microbiology

“The large amounts of antimicrobial components and defence factors present in donkey’s milk provide protection from microbial infections and distinguish donkey’s milk from the milks of other mammals”

The Kitten Microbiome Project

“Keeping track of the cutest, fluffiest microbiome project around”

Insect microbiome

Microbial impacts on insect evolutionary diversification: From patterns to mechanisms
Fabrice Vavre, Natacha Kremer – Current Opinion in Insect Science

“Symbiosis can favor rapid shifts in host phenotypic traits, particularly through the contribution of symbionts to the host’s physiology.”

How resident microbes modulate ecologically-important traits of insects
Kerry M. Oliver, Adam J. Martinez – Current Opinion in Insect Science

“In addition to their better-known roles in nutrient provisioning and degrading plant polymers, there is emerging evidence that microorganisms also aid herbivores in countering plant defenses. “

Metabolomics

Building blocks for automated elucidation of metabolites: natural product-likeness for candidate ranking – Kalai Vanii Jayaseelan and Christoph Steinbeck – BMC Bioinformatics

“In this study, we investigated whether additional existing knowledge, such as the fact that the unknown compound is a natural product, can be used to improve the ranking of the correct structure in the result list after the structure elucidation process.”

Phages and viruses

Bacteriophage as effective decolonising agent for elimination of MRSA from anterior nares of BALB/c mice – Sanjay Chhibber – BMC Microbiology

“Phage MR-10, given along with mupirocin showed an additive effect and the combination was able to effectively eradicate the colonising MRSA population from the nares of mice by day 5.”

Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target – Sabin Mulepati, Annie Héroux, Scott Bailey – Science

“The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. “

Bik’s Picks – weekend edition

15 Real-Life Scientists Share Their Favorite Science Fiction Books, Movies – Jacqueline Howard – Huffington Post

“There’s a big difference between science and science fiction, but there’s abundant evidence to suggest that sci-fi books and movies can spark a lifelong interest in science.”

After donkey and goat milk, this one was only appropriate: A Nice Tall Glass of Camel’s Milk – Olga Khazan – The Atlantic

“An oasis in the dromedary-dairy desert?”

Male Mathematicians Agree That Fields Medal Gender Balance Is Now OK – The Allium

“Now that a woman has won the fields medal, there is true and genuine equality and there is no need to worry any more about it.”

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Human microbiome, August 11, 2014

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Microbiome of Hadza Hunter, the premature infant gut, neonatal sepsis, skin and respiratory microbiome.

Microbiome general

BacterioFiles 178 – Hadza Hunters Have Heterogeneous Helpers (14 min) – Jesse Noar – BacterioFiles

“This episode: Modern hunter-gatherers have very different gut microbes from people from agricultural societies! “

“What is the FDA Going to Think?” – Negotiating Values through Reflective and Strategic Category Work in Microbiome Science – Katherine W. Darling – Science, Technology & Human Values

“Here, we describe how values are conceptualized and negotiated within microbiome research.”

Pregnancy and Birth microbiome

Patterned progression of bacterial populations in the premature infant gut – Patricio S. La Rosa – PNAS USA

“We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes“

Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis – Marre van den Brand – Journal of Microbiological Methods

“we developed a real-time multiplex PCR assay tailored to LOS diagnosis which is easy-to-use, is applicable on small blood volumes and provides species-specific results within 4 h.”

Respiratory microbiome

Uncovering the hidden villain within the human respiratory microbiome – Chun Kiat Lee, Stephen James Bent – Diagnosis

“The review herein presents the current status of human airway microbiome research and highlights potential gaps which can be translated into research possibilities for future work on respiratory tract infection diagnosis”

Skin microbiome

The skin microbiome: potential for novel diagnostic and therapeutic approaches to cutaneous disease – Elizabeth A. Grice – Skin and Allergy News

“It is increasingly apparent that this collective set of microorganisms and their genetic material, the “microbiome”, contributes genetic diversity, modulates disease, influences metabolic processes, and is essential for immunity.”

Animal models of human microbiome

Citrobacter rodentium: infection, inflammation and the microbiota – James W. Collins – Nature Reviews Microbiology

“In this Review, we discuss recent studies in which C. rodentium has been used to study mucosal immunology, including the deregulation of intestinal inflammatory responses during bacteria-induced colitis and the role of the intestinal microbiota in mediating resistance to colonization by enteric pathogens. “

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Microbiome digest, August 7, 2014

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Microbiome and caries, colorectal cancer, and inflammatory bowel diseases. Microbiomes of fish, dogs, and mosses, microscopic life in an asphalt lake, and the Picks.

Human mouth microbiome

Identification of the Microbiota in Carious Dentin Lesions Using 16S rRNA Gene Sequencing – Junko Obata – PLOS ONE

“In the present study, the bacterial communities in the carious dentin of Japanese subjects were analyzed comprehensively with molecular approaches using the 16S rRNA gene.”

Human gut microbiome

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer – Joseph P. Zackular, Mary A.M. Rogers, Mack T. Ruffin IV, and Patrick D. Schloss – Cancer Prevention Research

“Analysis of the gut microbiome from stool samples revealed both an enrichment and depletion of several bacterial populations associated with adenomas and carcinomas.”

Manipulation of Microbiome, a Promising Therapy for Inflammatory Bowel Diseases – Dapeng Jin, Hongyu Zhang, and Jun Sun – Clinical & Cellular Immunology

“In this review, we summarize the current knowledge of how changes in microbiota may affect the pathogenesis of IBD. “

A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota – Bruce R. Hamaker, Yunus E. Tuncil – Journal of Molecular Biology

“the article encourages the building of a framework of information to manipulate the colon microbiota in a predicted way for improved health”

 

Human microbiome after death

Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans – Ismail Can – Journal of Microbiological Methods

“We compared the effectiveness of two methods by amplifying the 16S rRNA genes and sequencing the amplicons from four cadavers”

Animal models of human microbiome

Disturbance of the gut microbiota in early-life selectively affects visceral pain in adulthood without impacting cognitive or anxiety-related behaviors in male rats
S.M. O’Mahony – Neuroscience

“Neonatal antibiotic treatment leads to an increase in visceral sensitivity in adulthood in rats.”

Dog microbiome

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque – Ian J Davis, Christopher Bull, Alexander Horsfall, Ian Morley and Stephen Harris – BMC Microbiology

“Using a quantitative polymerase chain reaction (qPCR) directed approach a range of microbiological media were screened and optimized to enrich for previously uncultivated target species. A systematic screening methodology was then employed to isolate the species of interest. ‘

Fish microbiome

Characterization of Microbiota Composition and Presence of Selected Antibiotic Resistance Genes in Carriage Water of Ornamental Fish – Lenka Gerzova – PLOS ONE

“In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents.”

Insect microbiome

The mosquito microbiota influences vector competence for human pathogens – Nathan J Dennison, Natapong Jupatanakul, George Dimopoulos – Current Opinion in Insect Science

“Understanding the interaction between the vector, its microbiota and transmitted pathogens will provide novel opportunities to limit disease transmission.”

Plant microbiome

Bacterial-biota dynamics of eight bryophyte species from different ecosystems
Faisal Hammad Mekky Koua – Saudi Journal of Biological Sciences

“..we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan.”

Soil and water microbiome

Two Neumann U students discover new types of viruses – CatholicPhilly.com

“They collected arthrobacter (a bacteria present in soil) from under trees and near lakes, found and filtered out the phages that were present, and then studied phage anatomy and life cycles.”

Water droplets in oil are microhabitats for microbial life – Rainer U. Meckenstock – Science

“In Pitch Lake, Trinidad and Tobago—the world’s largest asphalt lake—we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. “

Microbiome of the built environment

Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings – Jörg D. Ettenauer – PLOS ONE

“In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques.”

Metagenomics

High-resolution metagenomics – Eran Mick & Rotem Sorek – Nature Biotechnology

In this issue, Nielsen et al. present a powerful method for interpreting metagenomic data at the level of individual genomes without relying on reference sequences of cultured isolates, which can be generated for only a small fraction of microbial life.

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

“But as I read the journal Genome Biology today, I decided that someday I might surrender to the Quantified Self movement. I’ll just have to wait till I can track my trillions of microbes from one day to the next.”

Science and Career

Ph.D.’s, come out of the closet! – Lina Nilsson – Science

“If you promise not to tell Fisher’s Ph.D. adviser (or mine), I’ll let you in on this well-hidden truth: Fisher isn’t planning to pursue an academic career.”

Bik’s Picks

Stress during pregnancy can be passed down through generations, rat study shows – Science Daily

“Scientists investigating pregnancies in four generations of rats show that inherited epigenetic effects of stress could affect pregnancies for generations.”

This Is Your Brain on Fish – James Hamblin – The Atlantic

“Thicker, stronger, and more resilient. Once a week is all it takes, new research says.”

10 Great Novels That Will Make You More Passionate About Science – Charlie Jane Anders – io9

“A lot of the best science fiction features scientists who solve problems and make breakthroughs.”

Scientist looking forward to weekend of binge-experimenting – The Allium

“Imperial college Scientist Dr. Lou Pole announced earlier today that he was going to spend the entirety of this weekend binge-experimenting.”

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Microbiome digest, July 31

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A snapshot of the human microbiome, a robot helping the Knight lab process samples (I want one!), and finally something that does NOT involve the microbiome.

Human microbiome general

SnapShot: The Human Microbiome – Antonio González – Cell

“This SnapShot presents several aspects of the human microbiome, including the characterization of the microbial species populating different body sites, the distribution of microbes across different geographic locations, and how the microbiome can be altered by a physiological process, exemplified by pregnancy.”

 

Animal models of microbiome

Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4 – Madhukumar Venkatesh – Immunity

“Here we showed that microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR).”

Bacterial Sensor Nod2 Prevents Inflammation of the Small Intestine by Restricting the Expansion of the Commensal Bacteroides vulgatus – Deepshika Ramanan – Immunity

“Here, we identified several abnormalities in the small-intestinal epithelium of Nod2−/− mice including inflammatory gene expression and goblet cell dysfunction, which were associated with excess interferon-γ production by intraepithelial lymphocytes and Myd88 activity.”

Effect of virgin and refined olive oil consumption on gut microbiota. Comparison to butter – M. Hidalgo – Food Research International

“Evolution of symbiont population in feces was studied using culture-dependent and culture-independent methods. In the latter, the V3 region of 16S rDNA was amplified and separated by Denaturing Gradient Gel Electrophoresis; followed by sequencing of the most representative bands. “

Animal gut microbiome

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture – D.W. Pitta – Anaerobe

“Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. “

Metabolomics

The cross talk between microbiota and the immune system: metabolites take center stage – Hagit Shapiro – Current Opinion in Immunology

“While most attention has focused on the innate recognition of immune-stimulatory bacterial molecules, such as cell wall components and nucleic acids, we emphasize here the impact of diet-dependent microbial metabolites on the development and function of the immune system.”

Bioinformatics tools

eSNaPD: A Versatile, Web-Based Bioinformatics Platform for Surveying and Mining Natural Product Biosynthetic Diversity from Metagenomes – Boojala Vijay B. Reddy – Chemistry & Biology

“Environmental Surveyor of Natural Product Diversity (eSNaPD) is a web-based bioinformatics and data aggregation platform that aids in the discovery of gene clusters encoding both novel natural products and new congeners of medicinally relevant natural products using (meta)genomic sequence data. “

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA – Imogen A. Wright and Simon A. Travers

“To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA”

Computational integration of genomic traits into 16S rDNA microbiota sequencing studies – Alexander Keller – Gene

“Here, we show in a proof-of-concept that computational approaches are able to retain functional information about microbial communities assessed through 16S rDNA (meta)barcoding by referring to reference genomes.”

Viruses and helminths

How helminths go viral – Rick M Maizels1, William C Gause

“On pages 573 and 578 of this issue, Reese et al. (3) and Osborne et al. (4), respectively, provide fine detail on how helminth worms can substantially enhance and reactivate viral infection, with major health implications for tropical medicine.”

Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter – T. A. Reese – Science

“We found that helminth infection, characterized by the induction of the cytokine interleukin-4 (IL-4) and the activation of the transcription factor Stat6, reactivated murine γ-herpesvirus infection in vivo.”

Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation – Lisa C. Osborne – Science

“Helminth coinfection resulted in impaired antiviral immunity and was associated with changes in the microbiota and STAT6-dependent helminth-induced alternative activation of macrophages. “

More Microbiology

Larger Mammalian Body Size Leads to Lower Retroviral Activity – Aris Katzourakis – PLOS Pathogens

“Body size explains 37% of the variance in ERV integration rate over the last 10 million years, controlling for the effect of confounding due to other life history traits. “

Microbes in the news

Researcher: Bacteria Ate Some Gulf Spill Toxins, but Worst Remain – Sandy Smith – EHS Today

“In two new studies conducted in a deep sea plume, Assistant Professor Olivia Mason found a species of bacteria called Colwellia likely consumed gaseous hydrocarbons and perhaps benzene, toluene, ethylbenzene and xylene compounds that were released as part of the oil spill. “

Baxter breaks out – Hal Hodson – New Scientist
http://www.sciencedirect.com/science/article/pii/S0262407914614342

“Baxter is even turning its grippers to lab work. Correll is working with UCB’s Rob Knight to teach Baxter the job of preparing faeces samples for research.”

Science and Career

The stressed-out postdoc – Carrie Arnold – Science

“After he defended his dissertation and moved to a new lab for his postdoc, Ian Street hoped his battles with anxiety and depression were over.”

Bik’s Picks

Africa Needs Science, Not Aid – Nkem Khumbah and Melvin P. Foote –  The New York Times

“Scientific and technological advancement will help eradicate poverty and promote homegrown economic development by providing Africa with the tools to address its own challenges and expand its industrial productivity. “

DDT Linked To Obesity In Female Mice Long After Exposure – Hank Campbell – Science 2.0

“A new epidemiology paper in PLOS One doesn’t try to prove that, the authors instead correlate DDT use from generations ago with increased waistlines of today.  DDT exposure may have made you fat, they conclude.”

 

A Lick Of The Tongue Changes This Ice Cream’s Color – Loren Grush – Popular Science

“The result was Xamaleón, which is Spanish for “chameleon.” With a patent pending, Linares is staying tight-lipped on the recipe, but apparently there’s a special ingredient dubbed the “love elixir,” which must be spritzed on the ice cream before it’s eaten. “

 

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Scientists explain mystery of our ‘lemon Moon’ – James Vincent – The Independent

“A new accurate map of the Moon has shown that it bulges slightly at one side and is flattened at the top and bottom – but how did it get this way?”

 

 

 

Microbiome digest, July 30

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Host diet, sex, and the microbiome, smoking cessation, eukaryotic microbes, CRISPRs and my picks.

Gut microbiome

Individual diet has sex-dependent effects on vertebrate gut microbiota – Daniel I. Bolnick – Nature Communications

“Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. “

Smoking Cessation Alters Intestinal Microbiota: Insights from Quantitative Investigations on Human Fecal Samples Using FISH – Biedermann L – Inflammatory Bowel Diseases

“As determined by fluorescence in situ hybridization, an independent direct quantitative microbial approach, we could confirm that intestinal microbiota composition in humans is influenced by smoking.”

More microbiology

Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria – Jean-David Grattepanche – Trends in Microbiology

“High-throughput sequencing tools underestimate the diversity of eukaryotes by removing morphospecies.”

Microbes in the news

A Trip Overseas Could Change The Bugs Living In Your Gut – Bahar Gholipour – Huntington Post

“I was amazed to see how profoundly a single food poisoning event impacted the gut bacteria,” David, who was a researcher at Harvard University at the time of the study, said in a statement.

Researcher Using Next-Generation Sequencing, Other New Methods to Rapidly Identify Pathogens – Joe Montgomery – Kansas State University News Office – Labmanager.com

“Benjamin Hause, an assistant research professor at the Kansas State Veterinary Diagnostic Laboratory at Kansas State University, recently published an article about one of his discoveries, porcine enterovirus G, which is an important find in the United States.”

Antibiotics and resistance

Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance – Orsolya Méhi – Molecular Biology and Evolution

“To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated that the set of genes regulated by Fur change substantially in response to antibiotic treatment. “

Phages, viruses, and CRISPRs

Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages – Alexander P. Hynes – Nature Communications

“Here we demonstrate that cells can acquire spacers from defective phages at a rate directly proportional to the quantity of replication-deficient phages to which the cells are exposed.”

Dr. Bik’s Picks

Contamination hits cell work: Mycoplasma infestations are widespread and costing laboratories millions of dollars in lost research – Ewen Callaway – Nature

“A total of 11% of the samples were found to contain Mycoplasma DNA at levels indicative of contamination.”

Five daily portions of fruit and vegetables may be enough to lower risk of early death – Science Daily

“Eating five daily portions of fruit and vegetables is associated with a lower risk of death from any cause, particularly from cardiovascular disease, but beyond five portions appears to have no further effect, finds a new study.”

Lands’ End Announces Science-Themed Tees For Girls After Mom’s Letter Goes Viral – Jessica Samakow – The Huffington Post

“My daughter was very confused. Lots of her friends that are girls love science, too. Why were there no cool science shirts for girls?”

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Human microbiome, July 29

Posted on by

Papillomaviruses in human skin, gastric mucosa in cancer patients, breast milk metabolome, microbiome of a human family, and more.

Skin microbiome

Deep sequencing extends the diversity of human papillomaviruses in human skin –
Davit Bzhalava – Nature Scientific Reports

“This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses.”

Gastric microbiome

Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods – Chang Soo Eun – Helicobacter

“Gastric mucosal biopsy samples were collected from 31 patients during endoscopy. After the extraction of genomic DNA, variable region V5 of the 16S rRNA gene was amplified. PCR products were sequenced using 454 high-throughput sequencer. “

Pregnancy and Birth

Breast milk metabolome characterization in a single phase extraction, multiplatform analytical approach – Alma Villaseñor – Analytical Chemistry

“We conducted this single-phase extraction procedure on a representative pool of BM, and characterized the metabolic composition using LC-QTOF-MS and GC-Q-MS for polar and lipidic metabolites. “

Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the
Prevention of Allergy Development in Infants and on Fecal Microbiota [PDF]- Tadao Enomoto – Allergology International

“Effects of Bifidobacterial Supplementation to Pregnant Women and Infants in the Prevention of Allergy Development in Infants and on Fecal Microbiota”

Gut microbiome
The dynamics of a family’s gut microbiota reveal variations on a theme – Patrick D Schloss – Microbiome

“Here we study a chronosequence of the gut microbiota found in eight individuals from a family consisting of two parents and six children ranging in age from two months to ten years old.”

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression – Charles K. Fisher – PLOS ONE

“Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS), that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. “

Antivirulence Activity of the Human Gut Metabolome – L. Caetano M. Antunes – mBio

“We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion.”

 Metagenomic Identification of a Novel Salt Tolerance Gene from the Human Gut Microbiome Which Encodes a Membrane Protein with Homology to a brp/blh-Family β-Carotene 15,15′-Monooxygenase – Eamonn P. Culligan – PLOS ONE

“Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. “

Review: Archaea and the human gut: New beginning of an old story [DOC]- Gaci N – World Journal of Gastroenterology

“Here we provide an updated census of the archaeal diversity associated to human GIT and their possible role in the gut physiology and health.”

 

Animal models of human microbiome and disease

Maternal high protein or prebiotic fiber diets affect maternal milk composition and gut microbiota in rat dams and their offspring – Megan C. Hallam – Obesity

“Fecal microbiota was analyzed in dams at parturition and 2 weeks post-partum and in offspring at 5 and 22 weeks along with cecal digesta at termination.”

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