Category Archives: Metabolomics

General microbiology and science, September 15, 2014

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

Microbial Ecology

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

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

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

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

Metabolomics

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

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

Techniques

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

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

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

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

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

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

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

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

Bioinformatics

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

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

Viruses and Phages

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

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

More Microbes

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

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

Bacteria in the news

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

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

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

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

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

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

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

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

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

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

Scientific publishing

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

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

The digital toolbox – Nature Editorial

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

Scientific career

There is life after academia – Nature Editorial

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

Bik’s Picks

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

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

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

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

On the Other Hand – Bob Grant – The Scientist

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

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Microbiome Digest, August 29, 2014

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@MicrobiomDigest will be enjoying vacation for the next two weeks, so I won’t be able to post as much as usual. I might occasionally have some time and internet access at the same time, and post something, but don’t rely on this blog during that time for your daily Microbiome fix. But I will be back! Enjoy this last (short) one for now:
Human oral microbiome

Bacterial community composition of chronic periodontitis and novel oral sampling sites for detecting disease indicators – Vaia Galimanas – Microbiome

Human gut microbiome

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease – Noah W Palm – Cell

Modulation of immune development and function by intestinal microbiota – Agnieszka M. Kabat – Trends in Immunology

 

Worms, bacteria, and micronutrients: an elegant model of our diet – Lutfu Safak Yilmaz, Albertha J.M. Walhout – Trends in Genetics

 

Mammal microbiome

Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics (in flying squirrels) – Hsiao-Pei Lu – Scientific Reports

Social influences on the gut microbiome of developing monkeys – W.Z. Amaral – Brain, Behavior, and Immunity

 

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation? – AE Naas – mBio

 

Characterization of the Fecal Microbiota of Pigs before and after Inoculation with “Brachyspira hampsonii” – Matheus O. Costa – PLOS ONE

 

Sponges and corals

The versatile nature of coral-associated viruses – Bettarel Yvan – Environmental Microbiology

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

Rocks and Water Microbiome

Microbial Colonization of Bare Rocks: Laboratory Biofilm Enhances Mineral Weathering – F. Seiffert – Procedia Earth and Planetary Science

Microbial diversity and biogeochemical cycling in soda lakes – Dimitry Y. Sorokin – Extremophiles

Food microbiome

Switzerland Puts Secret Bacteria In Cheese To Catch Knockoffs – Sarah Zhang – Gizmodo

Bioinformatics

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data – Yuan Zhang – PLOS Computational Biology

Metabolomics

Taking your breath away: metabolomics breathes life in to personalized medicine
Nicholas J.W. Rattray – Trends in Biotechnology

Phages and Viruses

Identifying and analyzing bacteriophages in human fecal samples: what could we discover? – Maite Muniesa1 & Juan Jofre – Future Medicine

Microbes in the news

Hotel rooms aren’t yucky – you colonize them with your own personal bacteria within hours — Rachel Feltman – Washington Post

A touching story: The ancient conversation between plants, fungi and bacteria – David Tenenbaum – News UW Madison

Bik’s Picks

The universal ‘anger face’: Each element makes you look physically stronger and more formidable – Science Daily

Zombie Bacteria Invasion? Nothing To Worry About – Science 2.0

Report: Ice Bucket Challenge Causing Ecological Mayhem in California – The Allium (Satire)

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General microbiology and science, August 25, 2014

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

Bioinformatics

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

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

Metabolomics / proteomics

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

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

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

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

Techniques

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

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

More microbes

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

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

Microbes in the news

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

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

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

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

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

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

Uncultured Bacteria (with video) – Serious Science

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

#BacteriaHysteria

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

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

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

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

Science and publishing

Concerns Raised Online Linger – Kate Yandell – The Scientist

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

Bik’s Picks

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

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

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

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

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

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

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Human microbiome digest, August 25, 2014

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

Oral microbiome

* Microbial Signature Profiles of Periodontally Healthy and Diseased Patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

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

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

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

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

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

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

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

Respiratory microbiome

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

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

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

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

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

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

Vaginal microbiome

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

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

Gut microbiome

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

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

Animal models of human microbiome

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

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

Pregnancy and Birth

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

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

Microbiome News

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

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

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

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

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

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

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Microbiome Digest, August 22, 2014

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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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General microbiology and science, August 19, 2014

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Proteomics in biofilms at different temperatures, neonatal immune metabolic network, co-occurrence, something wonky with Unifrac, and microbiome in the news.

Metabolomics and proteomics

Turning up the heat on biofilms – Christina Tobin Kåhrström – Nature Reviews Microbiology

“This study used tandem mass tag (TMT)-based proteomics to measure protein expression in acid mine drainage biofilms at 40 °C, 43 °C and 46 °C. “

Identification of a human neonatal immune-metabolic network associated with bacterial infection – Claire L. Smith – Nature Communications

“Here, a system-level investigation of neonatal systemic responses to infection shows a surprisingly strong but unbalanced homeostatic immune response; developing an elevated set-point of myeloid regulatory signalling and sugar-lipid metabolism with concomitant inhibition of lymphoid responses. “

Secondary metabolite gene expression and interplay of bacterial functions in a tropical freshwater cyanobacterial bloom – Kevin Penn – ISME Journal

“To characterize microbial activities in a cyanoHAB, transcripts from a eutrophic freshwater reservoir in Singapore were sequenced for six samples collected over one day-night period.”

Microbial Ecology

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems
Ryan J. Williams – Frontiers in Microbiology

“To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. “

Fluvial network organization imprints on microbial co-occurrence networks – Stefanie Widder – PNAS USA

“We combined co-occurrence analyses of biofilms based on next-generation sequencing with a probabilistic hydrological model, and showed how fragementation of microbial co-occurrence networks change across stream networks. “

Bioinformatics

Equivalent input produces different output in the UniFrac significance test – Jeffrey R Long – BMC Bioinformatics

“UniFrac produces different outputs for these equivalent forms of the same input tree.”

More microbes

PNAS has an upcoming 100th Anniversary Special Feature on Vaccines. Here is the introduction: Vaccines: Science, health, longevity, and wealth – Rino Rappuoli – PNAS

“The special issue of the centenary of PNAS provides an opportunity to review the his- tory of vaccines, the most exciting features of vaccine science, and to contemplate the future. “

Microbes in the news

Gut Check: Exploring your Microbiome – University of Colorado Boulder course

“Join us on a guided tour of the human gut and its microscopic inhabitants. “

* The ‘Whoville’ in Your Gut: Your Microbiome – Raphael Kellman – Everyday Health

“Just as Horton’s neighbors could not “see” the tiny residents of Whoville, most of us are unaware of the microscopic world within us. “

Your Gut Bacteria Want You to Eat a Cupcake – Julie Beck – The Atlantic

“But a recent review published in BioEssays suggests that these bacteria might be a little too big for their britches, bossing their hosts around and demanding certain kinds of foods. “

* Diversify Your Microbiome by Rock Climbing Indoors – Embriette Hyde – MicroBEnet

“Though I don’t feel as though the findings in the study are earth shattering, they do illustrate an important point-the built environments that we inhabit each and every day-whether they are our houses, workplaces, or gyms-are perfect places for sharing microbes of all sorts-both environmental and human-associated. “

Sea Smells By The Sea Shore – Benjamin Wolfe – PopSci.com

“A microbiologist explores the distinctive odors of a day at the beach”

Bik’s Picks

Effect of soccer shoe upper on ball behaviour in curve kicks – Hideyuki Ishii – Nature Scientific Reports

“In this study, by using a finite element simulation, we investigated the factors that affect ball behaviour immediately after impact in a curve kick. Five experienced male university soccer players performed one curve kick. “‘

Illegal killing for ivory drives global decline in African elephants – George Wittemyer – PNAS USA

“…to our knowledge we provide the first detailed assessment of African elephant illegal killing rates at population, regional, and continental scales. “

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Microbiome digest, August 17, 2014

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Childhood undernutrition and the gut microbiome, hibernating ground squirrels, Sphagnum, nematodes, and forensic discrimination of soils.

Human gut microbiome

An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome – Tahmeed Ahmed – Annals of the New York Academy of Sciences

“This paper summarizes work on mechanisms underlying the varied manifestations of childhood undernutrition and discusses current gaps in knowledge and challenges to our understanding of undernutrition and infection/immunity throughout the human life cycle, focusing on early childhood growth. ”

Animal microbiome

Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defense in the gut of 13-lined ground squirrels – Kimberly A. Dill-McFarland – Molecular Ecology

“We used 16S rRNA pyrosequencing and cecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels.”

Diversity of Bacteria Carried by Pinewood Nematode in USA and Phylogenetic Comparison with Isolates from Other Countries – Diogo Neves Proença – PLOS ONE

“The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. “

Plant microbiome

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions – Anastasia Bragina – Molecular Ecology

“We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation.”

Soil microbiome

Random Whole Metagenomic Sequencing for Forensic Discrimination of Soils – Anastasia S. Khodakova – PLOS ONE

“Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles”

Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production – Takashi Narihiro – PLOS ONE

“In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). “

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda? – Peter O Alele – PLOS ONE

“Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. “

Soil-Borne Microbial Functional Structure across Different Land Uses – Eiko E. Kuramae – The Scientific World Journal

“In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio.”

Water microbiome

Temperature response of denitrification and anammox rates and microbial community structure in Arctic fjord sediments – Andy Canion – Environmental Microbiology

“Community structure in intact sediments and slurry incubations was determined using Illumina MiSeq SSU rRNA gene sequencing.”

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems – Marianne Simon – Environmental Microbiology

“We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm-size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France.”

Metagenomics

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” – Brian P. Hedlund- Extremophiles

“Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems.”

Metabolomics

Metabolic Modelling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells Reveals Substrate Limitations in Electrical Current Generation – Nadeera Jayasinghe – Biotechnology Journal

“The goal of this work is to develop a model that integrates genome-scale metabolic models with the model of biofilm environment. “

Bioinformatics

Rarefaction and extrapolation of phylogenetic diversity – Anne Chao – Methods in Ecology and Evolution

“We develop in this paper the “PD accumulation curve” (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness.”

Microbes in the news

Can’t Stick to That Diet? Blame Your Gut Bacteria – Nolan Feeney – Time

“The gut microbiome, the collection of all the microbes in our digestive tracts, may influence our food choices and behavior, suggests a new study that recently appeared in the journal BioEssays.”

How Clean Is Your Produce? Testing Fruit For Bacteria – WFMyNews2.com

“Ellis took samples of the fruits one by one and placed the samples on a petri dish. She then washed some of the lettuce and repeated the testing procedure on both the head of lettuce and the pre-washed bag of lettuce, in 72-hours the results were in.”

Bik’s Picks

9/11 dust cloud may have caused widespread pregnancy issues – ScienceDaily

“Pregnant women living near the World Trade Center during the 9/11 attacks experienced negative birth outcomes, according to a new paper.”

Volunteers on the scent of science with whale carcass – Peter Fimrite – SF Gate

“If there’s anything as enjoyable to Dan Sudran as sawing through the stinking blubber of a whale carcass and extracting bones from the gooey tissues, it would be showing the results to children.”

Alaska’s Shrinking Glaciers Seen from Space – Kelly Dickerson – LiveScience

“Compared with a vintage satellite photo of the region, an image taken from space last year reveals just how much the glaciers have shrunk over the past 26 years.”

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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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General microbiology and science, August 14

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

Metabolomics

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

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

Transcriptomics

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

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

More microbiology

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

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

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

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

Techniques

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

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

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

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

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

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

Science, Publishing, Career

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

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

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

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

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

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

Science of inclusion – Holly McDede – SFBG.com

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

Bik’s Picks

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

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

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

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

Newborns’ genetic code sends infection distress signal – Science Daily

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

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Microbiome digest, August 4, 2014

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Relief in a pressing problem, microbes at high altitude, and microbiome in cystic fibrosis.

Human gut microbiome

So glad this one finally came out!  Structural changes in the gut microbiome of constipated patients – Lixin Zhu – Physiological Genomics

“A cross-sectional pilot study was performed to compare stool microbial composition of 8 constipated patients and 14 non-constipated controls using 16S rRNA gene pyrosequencing.”

Microbiota and diabetes: an evolving relationship – Herbert Tilg, Alexander R Moschen – Gut

“A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism.”

Harnessing the Intestinal Microbiome for Optimal Therapeutic Immunomodulation – S. Viaud – Cancer Research

“gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively.”

Specific genetic and microbial signature associated with paediatric ileal Crohn’s disease -Isobel Leake – Nature Reviews Gastroenterology & Hepatology

“An increase in DUOX2 expression was associated with an expansion of Proteobacteria across all forms of IBD, whereas downregulation of APOA1 expression in association with depletion of certain Firmicutes and Bacteroidetes taxa was found to be specific for Crohn’s disease.”

Skin and wounds microbiome

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research – Brendan Hodkinson and Elizabeth Grice – Advances in Wound Care

“The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing.”

Human respiratory microbiome

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota – Perry S Brown – Annals ATS

“After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial rRNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.”

Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj – Samir Benkouiten – Emerging Infectious Diseases

“One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.”

Fish microbiome

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae – Christos Giatsis – PLOS ONE

“Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. “

Soil microbiome

FEMS Microbiology Ecology has a special issue on Polar and Alpine Microbiology with many papers on microbiomes of ice and soil. Here is the Editorial:
Polar and alpine microbiology in a changing world – John C. Priscu – FEMS Microbiology Ecology

“By virtue of their relatively rapid growth rates and metabolic diversity, we can expect microorganisms to be the first responders to fluctuating climatic conditions.”

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau – Jun-Tao Wang – Microbial Ecology

“Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation.”

Water microbiome

Satellite remote sensing data can be used to model marine microbial metabolite turnover – Peter E Larsen – ISME Journal

“We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters”

Microbial Ecology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function – Joseph E. Knelman and Diana R. Nemergut – Frontiers Microbiology

“Can differences in community assembly alter the relationship between biodiversity and ecosystem function?”

Probiotics

Lactobacillus rhamnosus GG suspected infection in a newborn with intrauterine growth restriction – I. Sadowska-Krawczenko – Beneficial Microbes

“Genotyping with the rep-PCR and AFLP methods confirmed the 100% genetic similarity for both the strain isolated from patient blood and the probiotic product.”

Can Eating Probiotic Yogurt Help Lower Your High Blood Pressure? – Susmita Baral – Wall St Cheat Sheet

“Now, a new study (published Monday in the journal Hypertension) has found another added benefit of probiotics — it may reduce high blood pressure.”

Microbes in the News

Your garden hose: a potential health risk due to Legionella spp. growth facilitated by free-living amoebae – Jacqueline Marie Thomas – Environmental Science & Technology

“Here we present data on FLA and Legionella spp. detected in water and biofilm of two garden hose types over 18 months. “

Truth about your toothbrush – Anne Agbaje – Bussiness Day Online

“You don’t store your plates and glasses by the toilet, so why would you want to place your toothbrush there?” McCombs says. “It’s just common sense to store your toothbrush as far away from the toilet as possible.”

Metabolomics

Fecal volatile organic compounds: a novel, cheaper method of diagnosing inflammatory bowel disease? – Chris SJ Probert – Expert Review of Clinical Immunology

“…this article will focus specifically on the fecal VOC metabolome and its potential role in identifying a novel diagnostic method for IBD.”

Review: Emerging mass spectrometry techniques for the direct analysis of microbial colonies – Jinshu Fang, Pieter C Dorrestein – Current Opinion in Microbiology

“In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies.”

Techniques

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing – Jennifer J. Mosher – Journal of Microbiological Methods

“With accurate read lengths of > 1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples.”

 

Bik’s Picks

The Secret to a Tattoo’s Permanence: The Immune System – Olga Khazan – The Atlantic

“We rarely stop and think about the science of tattoos. In fact, some people don’t even stop and think before getting tattooed.”

 

Mathematical equation to predict happiness: Doesn’t depend on how well things go, but on whether things are better than expected – Science Daily

“The happiness of over 18,000 people worldwide has been predicted by a mathematical equation, with results showing that moment-to-moment happiness reflects not just how well things are going, but whether things are going better than expected.”

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