Category Archives: More Microbes

Microbiome digest, September 23, 2014

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I don’t have much time tonight, so I’ll keep it short.

Pregnancy and birth

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women – Yi-E Huang- Microbial Ecology

Impact of Feeding and Medical Practices on the Development of Necrotizing Enterocolitis – Brian L. Montenegro, Camilia R. Martin – Current Pediatrics Reports

Human respiratory microbiome

Expanding Our Understanding of Respiratory Microbiota in Cystic Fibrosis – John J. LiPuma – Annals of the American Thoracic Society

Microbiota in the throat and risk factors of laryngeal carcinoma – Hongli Gong – Applied and Environmental Microbiology

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

The Overarching Influence of the Gut Microbiome on End-Organ Function: The Role of Live Probiotic Cultures – Luis Vitetta – Pharmaceuticals

Excretion of host DNA in feces is associated with risk of Clostridium difficile infection –  Caroline Vincent – Journal of Immunology Research

Animal and in vitro studies of human microbiome

Effect of Oral Administration of Metronidazole or Prednisolone on Fecal Microbiota in Dogs – Hirotaka Igarashi – PLOS ONE

Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
Hannah Lees – PLOS ONE

A comparative evaluation of prebiotic oligosaccharides using in vitro cultures of infant fecal microbiome – J Stiverson – Applied and Environmental Microbiology

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs – Crystal L. Levesque – PLOS ONE

Mammal microbiome

Fecal microbial diversity and putative function in captive western lowland gorillas (Gorilla gorilla gorilla), common chimpanzees (Pan troglodytes), Hamadryas baboons (Papio hamadryas), and binturongs (Arctictis binturong) – Erin A. McKenney – Integrative Zoology

Pathogenic Eukaryotes in Gut Microbiota of Western Lowland Gorillas as Revealed by Molecular Survey – Ibrahim Hamad – Scientific Reports

Insect microbiome

Routes of acquisition of the gut microbiota of Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

Sponge microbiome

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12427/abstract

Plant microbiome

Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars – Márton Szoboszlay – Soil Biology and Biochemistry

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria – Pilar Martínez-Hidalgo – Scientific Reports

Effects of Clonal Integration on Microbial Community Composition and Processes in the Rhizosphere of the Stoloniferous Herb Glechoma longituba (Nakai) Kuprian – Ningfei Lei – PLOS ONE

Soil type dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

Soil microbiome

Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils – Keisuke Obase – FEMS Microbiology Ecology

Food microbiology

Dynamic changes of the microbial communities during the preparation of traditional Tibetan Qula cheese – Bei Zhang – Dairy Science & Technology

Metabolomics / Functional metagenomics

Identification of Aminoglycoside and β-Lactam Resistance Genes from within an Infant Gut Functional Metagenomic Library – Fiona Fouhy – PLOS ONE

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

Aleksandr Milshteyn, Jessica S. Schneider, Sean F. Brady – Chemistry & Biology

Commensally sourced antibiotics – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of dietary polydextrose fiber on the human gut metabolome – Santosh Lamichhane – Journal of Agricultural and Food Chemistry

Preserving the earth’s microbes for drug discovery in the future – Ranjith N. Kumavath and Satyanarayana S.V – Journal of Microbiology and Microbial Research

Microbial Ecology

PNAS has a special issue this week on Biogeography (with the Panama forest trees paper by Jessica Green): The emergence and promise of functional biogeography – Cyrille Violle – PNAS

Active invasion of bacteria into living fungal cells – Nadine Moebius – eLife

Microbes in the news

Microbiome: You are never alone – John A Goldman – Atlanta Medicine

Seeking the Sweet Spot, from Mouth to Microbiome – David Katz – Huffington Post

New evidence suggests long-term relationships with bacteria begins before we’re born – Norbert Berzog and David Niesel – Galveston County Daily News

MIT Developing Ship-Repairing Bacteria – World Maritime News

Science and publishing

Anonymous peer-review comments may spark legal battle – Kelly Servick – Science

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General microbiology and science digest, September 16, 2014

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Detection of microbes in tissues, a magnet to pull out bacteria from blood, temperature stability of samples, enriching for rare microbial community members, bioinformatics tools for microbiome research, and Bik’s Picks.
Microbial detection

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues – Don A. Baldwin – mBio

“the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. “

More microbes

Review: Physical stress and bacterial colonization – Michael Otto – FEMS Microbiology Reviews

“This review will give an overview over the mechanisms human bacterial colonizers have to withstand physical stresses with a focus on bacterial adhesion.”

Techniques

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles – Jun Hang – Microbiome

“Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis.”

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalisation methods – Dragana Gagic – Molecular Ecology Resources

“The synthetic metagenome was fractionated and thermally re-natured, allowing the most abundant sequences to hybridise. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease (DSN).”

Bioinformatics

A better sequence-read simulator program for metagenomics – Stephen Johnson – BMC Bioinformatics

“We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions.”

Gene finding in metatranscriptomic sequences – Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang – BMC Bioinformatics

“In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences.”

Data analysis for 16S microbial profiling from different benchtop sequencing platforms
Victor S. Pylro – Journal of Microbiological Methods

“Satisfactory results were obtained in those pipelines that applied a chimera-filtering step.”

Metagenome fragment classification based on multiple motif-occurrence profiles – Naoki Matsushita – PeerJ

“we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence.”

Revolutionizing prokaryotic systematics through next-generation sequencing – Vartul Sangal – Methods in Microbiology

“In this chapter, we have provided a brief summary of recent advances in sequencing technologies and easy to use bioinformatic tools to analyse sequence data, with a focus on prokaryotic biology. “

Microbes in the news

A Lesson in Language – McAlarnen, Lindsey A. – Academic Medicine

“while I expected a challenge working with human microbiome expert Dr. Rob Knight, I never expected to be as lost as I was that first morning.”

An extracorporeal blood-cleansing device for sepsis therapy – Joo H Kang – Nature Medicine

“Magnets pull the opsonin-bound pathogens and toxins from the blood; the cleansed blood is then returned back to the individual. “

Science and career

Too Few University Jobs For America’s Young Scientists – Richard Harris – NPR Morning Edition

“Imagine a job where about half of all the work is being done by people who are in training. That’s, in fact, what happens in the world of biological and medical research.”

Diversity in Science: Where Are the Data? – Fred Guterl – Scientific American

“Global figures on diversity in the science and engineering workforce are hard to come by, but what we know is not flattering”

 

Bik’s Picks

Jack the Ripper, more poison at NIH, Rosetta & the comet – Tabitha M. Powledge – PLOS Blogs

“Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.”

Human faces are so variable because we evolved to look unique – ScienceDaily

“The amazing variety of human faces — far greater than that of most other animals — is the result of evolutionary pressure to make each of us unique and easily recognizable”

Joanne Chang Brings the Sweet Science of Sugar to Harvard – Leah Blumenthal – Eater.com

“Harvard University’s annual Science & Cooking public lecture series brings chefs from around the world to lecture on the intersection of science and cooking.”

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General microbiology and science, September 15, 2014

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

Microbial Ecology

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

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

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

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

Metabolomics

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

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

Techniques

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

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

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

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

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

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

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

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

Bioinformatics

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

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

Viruses and Phages

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

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

More Microbes

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

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

Bacteria in the news

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

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

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

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

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

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

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

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

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

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

Scientific publishing

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

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

The digital toolbox – Nature Editorial

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

Scientific career

There is life after academia – Nature Editorial

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

Bik’s Picks

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

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

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

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

On the Other Hand – Bob Grant – The Scientist

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

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General microbiology and science, August 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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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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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 18, 2014

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Mushroom microbiome, mice fed T7 phages, and uBiome got some money.

Plant microbiome

Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing – M. Kim – Journal of Applied Microbiology

“The bacterial communities in soil samples collected from inside, beneath and outside the T. matsutake fairy ring were investigated using barcoded pyrosequencing. “

Rhizospheric fungal community structure of a Bt brinjal and a near isogenic variety – A.K. Singh – Journal of Applied Microbiology

“..this study concludes that genetic modification of brinjal crop has minor effect on the fungal community.”

Phages and viruses

Observation of inflammatory responses in mice orally fed with bacteriophage T7 – K. Park – Journal of Applied Microbiology

“A histopathological analysis of tissue samples from the stomach, small intestine and colon revealed no significant pathological change.”

Microbes in the news

GW High students to name bacterium – Maria Hernandez – Pacific Sunday News

“Students from George Washington High School got the opportunity to name a bacterium that was discovered during a historic underwater expedition to the Mariana Trench, which was led by filmmaker James Cameron in 2012.”

uBiome Raises $4.5M From Angel Investors, Andreessen Horowitz To Crowdsource Microbiome Research – Julian Chokkattu – Techcrunch

“uBiome also has the largest private dataset of human microbiome samples in the world, giving participants a quick way to compare what’s in their microbiome to a large group.”

Bik’s Picks

All Things Considered podcast (3 min): Often On The Move, Restless Elephants Are Tough To Count — And Keep Safe – Gregory Warner – NPR

“The reason elephants are so hard to protect is the same that makes them so hard to count: They roam — exceptionally far.”

Mapping Cell Fate Conversion via CellNet, a Network Biology Tool – Kevin Mayer – GenEngNews

“The differentiation of engineered stem cells may be imagined as a subway journey, where the genetic equivalents of missing a transfer or getting off at the wrong stop can take your stem cells far off course.”

Camouflage sheet inspired by octopus – Jonathan Webb – BBC Science

“Based on the camouflage abilities of octopuses and cuttlefish, engineers in the US have built a flexible material that changes colour to match its surroundings.”

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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 13, 2014

Posted on by

Nose, glycan, butyrate, microbes on plastics, seawater microbial mats, and plants with microbes.

Respiratory microbiome

The nasal cavity microbiota of healthy adults – Christine M Bassis, Alice L Tang, Vincent B Young and Melissa A Pynnonen – Microbiome

“In our initial analysis, we compared the bacterial communities of the nasal cavity and the oral cavity from ten of these subjects.”

Gut microbiome

Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations – Omer Eilam – mBio

“Based on GlyDeR, we found a clear connection between microbial glycan degradation and human diet, and we suggest a method for the rational design of novel prebiotics.”

Microbial-Derived Butyrate: An Oncometabolite or Tumor-Suppressive Metabolite? -Scott J. Bultman, Christian Jobin – Cell Host & Microbe

“Dietary factors, microbial composition, and metabolism are intimately intertwined into a complex network whose activities influence important intestinal functions”

Review: Collateral Damage: Microbiota-Derived Metabolites and Immune Function in the Antibiotic Era – Christopher A. Lopez – Cell Host & Microbe

“A disruption of gut-associated microbial communities by antibiotic treatment can result in a depletion of microbiota-derived metabolites, thereby enhancing pathogen susceptibility, impairing immune homeostasis, and contributing to the rise of certain chronic inflammatory diseases”

Animal model of microbiome

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids
Sabina Lukovac – mBio

“The aim of this study was to characterize effects of the microbiota on host epithelium using a novel ex vivo model based on mouse ileal organoids.”

Plant microbiome

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors – Thomas R. Williams, Maria L. Marco – mBio

“We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce.”

Fundamental Plant Chemicals Rooted in Bacteria – Jenna Iacurci – Nature World News

“A fundamental chemical pathway that all plants use to create the essential amino acid phenylalanine has now been traced to two groups of ancient bacteria, a new study reports.”

Water microbiome

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters – Sonja Oberbeckmann – FEMS Microbial Ecology

“Denaturing Gradient Gel Electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location, and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. “

Molecular Ecology of Microbial Mats – Henk Bolhuis – FEMS Microbial Ecology

“Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring and hypersaline).”

Microbes in the news

Wearable structure of bacteria references antique animal bone corsets

“in terms of the material, it is grown from acetobacter xylinum, a strain of bacteria that produces a microbial cellulose textile as it consumes glucose.”

Bik’s Picks

Google Maps Dives Underwater – Scientific American

“Google has taken its ‘street view’ maps to a whole new level—namely, the ocean’s depths. “

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General microbiology and science, August 12, 2014

Posted on by

Prokaryotic Essential Genes, 10 years of next-generation sequencing, a short podcast on the Hadza microbiome, and Ebola.

 

Metagenomics

Protein Localization Analysis of Essential Genes in Prokaryotes – Chong Peng & Feng Gao – Nature Scientific Reports

“Here, a comprehensive protein localization analysis of essential genes in 27 prokaryotes including 24 bacteria, 2 mycoplasmas and 1 archaeon has been performed. “

Techniques

Review: Ten years of next-generation sequencing technology – Erwin L. van Dijk – Trends in Genetics

“Here we provide an overview of the evolution of NGS and discuss the most significant improvements in sequencing technologies and library preparation protocols.”

More Microbiology

CISAC experts tackle public health & policy questions on Ebola – Beth Duff-Brown – Stanford University

“We ask CISAC biosecurity experts to answer several questions about Ebola and the public health concerns and policy implications. “

Rapid and reagentless detection of microbial contamination within meat utilizing a smartphone-based biosensor – Pei-Shih Liang – Nature Scientific Reports

“An 880 nm near infrared LED was irradiated perpendicular to the surface of ground beef, and the scatter signals at various angles were evaluated utilizing the gyro sensor and the digital camera of a smartphone.”

Academic Minute Podcast: Microbiota of the Hadza Tribe – Alyssa Crittenden, UNLV

“My colleagues and I have, for the first time, characterized the hunter-gatherer gut microbiome– working with a population of foragers in East Africa, the Hadza of Tanzania.”

Women in Science

Why are the media so obsessed with female scientists’ appearance? –  Alice Bell – The Guardian

“Yet another profile of Susan Greenfield feels the need to dwell on her ‘long, youthfully blond hair’. Why are the media so rubbish at covering women in science?”

Bik’s Picks

Under- and over-water halves of Gyrinidae beetle eyes harbor different corneal nanocoatings providing adaptation to the water and air environments – Artem Blagodatski – Nature Scientific Reports

“In this study we analyze the micro- and nanostructure of the split eyes of two Gyrinidae beetles genera, Gyrinus and Orectochilus. “

Antarctic midge’s genome is smallest in insects to date: Bare-bones genome is adaptation to deep freeze – Science Daily

“Scientists who sequenced the genome of the Antarctic midge suspect the genome’s small size — the smallest in insects described to date — can probably be explained by the midge’s adaptation to its extreme living environment.”

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