Microbiome digest, October 15, 2014

A seminar this Friday with Pat Schloss, but without HMP girl, aspartame and gut microbiome in a rat model, bacteria in arsenic contaminated soil, and inter-kingdom horizontal gene transfer.

Human oral microbiome

General Immune Status and Oral Microbiology in Patients with Different Forms of Periodontitis and Healthy Control Subjects – Jana Schmidt – PLOS ONE

“Subgingival plaque samples were taken from each individual and immediately cultivated for microbiological examination.”

Pregnancy and birth

* The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

“Ascending bacterial infection is implicated in about 40–50% of preterm births. “

Animal models of microbiome research

* Low-Dose Aspartame Consumption Differentially Affects Gut Microbiota-Host Metabolic Interactions in the Diet-Induced Obese Rat – Marie S. A. Palmnäs – PLOS ONE

“Serum metabolomics analysis revealed aspartame to be rapidly metabolized and to be associated with elevations in the short chain fatty acid propionate, a bacterial end product and highly gluconeogenic substrate, potentially explaining its negative affects on insulin tolerance. “

Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep – T. Ma – Journal of Animal Physiology and Animal Nutrition

“Two experiments were conducted to evaluate the effect of resveratrol on methanogenesis and microbial flora in Dorper × thin-tailed Han cross-bred ewes. “

Soil microbiome

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate – Romain L Barnard – ISME Journal

“Here, we investigated the effects of extending winter rainfall into the normally dry summer period on soil microbial response to a controlled rewetting event”

Surface binding and intracellular uptake of arsenic in bacteria isolated from arsenic contaminated site – Neha Vishnoi, Sonal Dixit, D.P. Singh – Ecological Engineering

“The present study deals with the surface binding and uptake of arsenic (As) in two bacterial strains (Bacillus subtilis and Paenibacillus macerans) isolated from the As contaminated soil.”

Water microbiome

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden – Michael Forth – ISME Journal

“We used molecular ecologic methods to study changes in bacterial community structure in response to the oxygenation in the Byfjord. “

Food microbiology

Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing – Haiyan Xu – Journal of the Science of Food and Agriculture

“The bacterial and fungal community diversity in 22 home-made yoghurt samples was analyzed by pyrosequencing. “

CRISPRs, phages, viruses

In Hopes Of Fixing Faulty Genes, One Scientist Starts With The Basics – Joe Palca – NPR Morning Edition

“That’s certainly true for Jennifer Doudna. She hasn’t won a Nobel Prize, but many are whispering that she’s in line to win one for her work on something called CRISPR/Cas9 — a tool for editing genes.”

Bioinformatics and metagenomics

* Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria – Alejandro Caro-Quintero and Konstantinos T Konstantinidis – ISME Journal

“Here, we devised a novel bioinformatic pipeline, which minimized the effect of over-representation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. “

* Origins of major archaeal clades correspond to gene acquisitions from bacteria
Shijulal Nelson-Sathi – Nature

“To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes.”

Evidence of Carbon Fixation Pathway in a Bacterium from Candidate Phylum SBR1093 Revealed with Genomic Analysis – Zhiping Wang – PLOS ONE

“A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. “

Metagenomic Approach Reveals Variation of Microbes with Arsenic and Antimony Metabolism Genes from Highly Contaminated Soil – Jinming Luo – PLOS ONE

“Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb.”

More microbiology

* The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota! – Judge Starling

“The molecular revelation based on orthologous ribosomal RNA sequences that prokaryotes are separable into two basic taxa—archaebacteria and eubacteria, and that these two taxa are approximately equidistant from eukaryotes, prompted Woese et al. (1990) to come up with a tripartite taxonomy of all life forms.”

Adhesion as a weapon in microbial competition – Jonas Schluter – ISME Journal

“We test the predictions of our model using the enteric pathogen Vibrio cholerae, which produces an extracellular matrix important for biofilm formation. “

Microbes in the news:

* Google Hangout on Friday: MicroSeminar: A new way of doing conferences – Pat Schloss

“You will not see HMP Girl, no quotes of specious statistics, no mention of obscure disease, and no venturing into the weeds of bioinformatics. I will be describing unpublished experiments from the lab where we have taken various sources of microorganisms and used them to colonize mice that lack their own microbiota.”

‘Grapes of Wrath’: Stomping out grape disease one vineyard at a time – Phys.org

“A Rochester Institute of Technology scientist and an RIT alumnus are close to completing the genetic blueprint, or microbiome, of grape crown gall tumor disease—the bane of vineyards worldwide. ”

Redefining Human: The Microbiome Documentary Series – Root House Studio – Kickstarter

“We know science documentaries can be painfully boring, so Redefining Human will use a variety of new techniques to turn this complex science into an informative and entertaining documentary series.”

What’s in my microbiome? – Richard Sprague

“To find out what’s in my microbiome now, I bought a $400 kit from the San Francisco company uBiome. “

Science, publishing and career

* Rise of the Rest: The Growing Impact of Non-Elite Journals – Anurag Acharya – Google / Arxiv

“Our analysis indicates that the number of top-1000 papers published in non-elite journals for the representative subject category went from 149 in 1995 to 245 in 2013, a growth of 64%.”

Review rewards – Welcome efforts are being made to recognize academics who give up their time to peer review – Nature Editorial

“A welcome movement is under way to publicly register and recognize the hitherto invisible efforts of referees.”

Overqualified or underqualified? – Carrie Arnold – Science

“As unemployment stretched from weeks into months, Milstein decided that her Ph.D. was working against her. “

 

Satire: Facebook Offers To Freeze Female Employee’s Newborn Children – The Onion

“Women deserve to have the option to postpone motherhood until they feel fully prepared, which is why Facebook will also cover the cryonic facility’s annual maintenance costs for as many years as our employees feel they need. “

Bik’s Picks

360-Degree View of the Tomato – Anna Azvolinsky – The Scientist

“Researchers have sequenced 360 varieties of the tomato plant to create a comprehensive map of the evolution of the fruit from its wild form to the modern varieties. “

Extinct giant kangaroos didn’t hop, they walked – Andy Coghlan – New Scientist

“They had faces like rabbits and some were 2 metres tall. But now it seems that an extinct giant kangaroo didn’t hop – it walked.“

 

Chimpanzees have favorite ‘tool set’ for hunting staple food of army ants – Science Daily

“New research shows that chimpanzees search for the right tools from a key plant species when preparing to ‘ant dip’ — a crafty technique enabling them to feast on army ants without getting bitten. “

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General microbiology and science digest, September 16, 2014

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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Microbiome digest, August 15, 2014

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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Microbiome digest, July 23

Just one post today. Invading oral bacteria found in liver cirrhosis patients guts, obesity, biofilms and dispersal, motile and electric bacteria, dengue, and Weird Al Yankovic.

General microbiome

Screen Shot 2014-07-23 at 7.12.37 PMRadio show: City Visions: Exploring the Human Microbiome

“City Visions host David Onek explores these questions and more with Bay Area leading researchers Katie Pollard of the Gladstone Institutes, Susan Lynch of UCSF, and Peter diLaura of Second Genome.”

Human gut microbiome

Nan Qin Nature GutAlterations of the human gut microbiome in liver cirrhosis – Nan Qin – Nature

“Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals… Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. “

Lancet DiabetesObesity, inflammation, and the gut microbiota – Amanda J Cox – The Lancet Diabetes & Endocrinology

“In this Review, we provide evidence supporting perturbation of the intestinal microbiota and changes in intestinal permeability as potential triggers of inflammation in obesity.”

ParasitesOpinion: (Self-) infections with parasites: re-interpretations for the present
Julius Lukeš – Trends in Parasitology

“Here, we critically review cases in which humans were deliberately infected with parasites. Moreover, we summarize the contribution of (self-) infections and propose protist and helminth candidates, chosen on the basis of several criteria, to test as possible therapy for selected human diseases.”

General Microbiology

Screen Shot 2014-07-23 at 7.14.29 PMDispersed cells represent a distinct stage in the transition from bacterial biofilm to planktonic lifestyles – Song Lin Chua – Nature Communications

“Here we use single-nucleotide resolution transcriptomic analysis to show that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells. “

Screen Shot 2014-07-23 at 7.15.00 PMBrownian motion? – Bacteria swim with bodies and flagella – Kevin Stacey – Brown University

“Using a new technique to track the swimming motion of a single bacterium, researchers have discovered that the movement of the bacterium’s body — not just thrust from the flagellum — allow movement through fluids.”

NewScientistBacteria that don’t need to eat: Meet the electric life forms that live on pure energy – Catherine Brahic – New Scientist

“Unlike any other living thing on Earth, electric bacteria use energy in its purest form – naked electricity in the shape of electrons harvested from rocks and metals. “

NatureCell communication: Stop the microbial chatter – Vivien Marx – Nature

“Bacteria can coat everything from thermal springs to teeth. Researchers are looking for antibiotics that can subvert the signalling that the microbes use to carve their niche.”

Dengue

Screen Shot 2014-07-23 at 7.19.32 PMSafety, immunogenicity and efficacy of a recombinant tetravalent dengue vaccine: A meta-analysis of randomized trials – Vivaldo G. da Costa – Vaccine

“..we conducted a meta-analysis to determine a more precise estimate of the overall parameters of safety, immunogenicity and efficacy of CYD-TDV. A data search was conducted in the PubMed, Medline, Cochrane Central Register of Controlled Trials and SciELO databases with defined selection criteria.”

Screen Shot 2014-07-23 at 7.19.57 PMKinome siRNA screen identifies novel cell-type specific dengue host target genes – Yong-Jun Kwon – Antiviral Research

“To identify novel human host cell targets important for dengue virus infection and replication, an image-based high-throughput siRNA assay screening of a human kinome siRNA library was conducted using human hepatocyte cell line Huh7 infected with a recent dengue serotype 2 virus isolate BR DEN2 01-01.”

Dr. Bik’s Picks

Bat polarizationA functional role of the sky’s polarization pattern for orientation in the greater mouse-eared bat – Stefan Greif – Nature Communications

“Here we demonstrate that the female greater mouse-eared bat (Myotis myotis) uses polarization cues at sunset to calibrate a magnetic compass, which is subsequently used for orientation during a homing experiment. “

Screen Shot 2014-07-23 at 7.20.54 PMScience and politics: Hello, Governor – Virginia Gewin – Nature

“When California’s governor enlisted the aid of two palaeoecologists, their careers took an unusual turn.”

Screen Shot 2014-07-23 at 7.21.49 PMYouTube distraction: Foil – Weird Al Yankovic music video

“fungal rot, bacterial formation, microbes, enzymes, mould and oxidation”

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Human microbiome digest, July 21

Today we have articles on two microbiome pioneers: Rob Knight and Jeffrey Gordon, as well as papers on periodontitis, eczema, Crohn’s disease, and Helicobacter.

General microbiome

The effects of the microbiota on the host immune system – Jacek Karczewski – Autoimmunity

“This review is focused on host–microbiota interactions, specifically on influence of bacterial-derived signals on immune cell function and the mechanisms by which these signals modulate the development and progression of inflammatory and autoimmune diseases.”

Imposition of encapsulated non-indigenous probiotics into intestine may disturbs human core microbiome – Abolfazl Barzegari – Frontiers in Microbiology

“We envision that the lack of survivability of some of the probiotic candidates within such hostile milieu of GIT may negatively affect the coevolving process of bacteria in human host and hence impact the endpoint health promotion goals.”

40 under 40: Rob Knight – Cell

“Some dead scientists who I would have loved to have had the opportunity to work with include Carl Woese, Richard Feynman, Francis Crick, Erwin Chargaff, Sewall Wright, Benjamin Franklin, Antonie van Leeuwenhoek, Robert Boyle, Eratosthenes, and Lucretius. These lists are intended to be illustrative rather than exhaustive; according to my NSF Conflict of Interest form I have written grants or papers with about 750 people, all of whom I admire.”

Jeffrey I. Gordon, M.D., Will Receive Pitt’s Dickson Prize at Science 2014—Sustain It! – University of Pittsburgh

“A scientist who has explored how the tens of trillions of microbes that live in the gastrointestinal tract and their genes influence human physiology, metabolism and nutritional status will receive the University of Pittsburgh’s 2014 Dickson Prize in Medicine.”

Oral microbiome

Quantitative analysis of classical and new putative periodontal pathogens in subgingival biofilm: a case–control study – N. N. Al-hebshi – Journal of Periodontal Research

“Pooled subgingival biofilm samples were obtained from 40 patients with chronic periodontitis and 40 healthy controls. Taqman q-PCR assays were used to determine the absolute and relative counts of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Parvimonas micra, Filifactor alocis, oral Synergistetes and oral TM7s. “

Skin microbiome

Review: Microbiota in Healthy Skin and in Atopic Eczema – Giuseppe Baviera – BioMed Research International

“This review also highlights recent observations on the importance of innate immune systems and the relationship with normal skin microflora for the maintenance of healthy skin.”

Gastric microbiome

Microbial Profile of the Stomach: Comparison between Normal Mucosa and Cancer Tissue in the Same Patient – Incheol Seo – Journal of Bacteriology and Virology

“In this study, we identified differences in the microbial communities between gastric cancer and normal gastric mucosa by comparing the microbiomes of tissues from the same patients. The clustering analysis results showed different bacterial communities between normal gastric mucosa and gastric cancer.”

Motility and Chemotaxis Mediate the Preferential Colonization of Gastric Injury Sites by Helicobacter pylori – Eitaro Aihara – PLOS Pathogens

“Using anesthetized mice in which we have induced microscopic damage to the stomach surface, we find that H. pylori is able to rapidly detect and navigate towards this damage site. Within minutes, bacterial accumulation slows repair of the damage.”

Gut microbiome

Metabolic Modeling of Common Escherichia coli Strains in Human Gut Microbiome
Yue-Dong Gao – BioMed Research International

“we investigated the E. coli strains in human gut microbiome using deep sequencing data and reconstructed genome-wide metabolic networks for the three most common E. coli strains, including E. coli HS, UTI89, and CFT073. “

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease [PDF] – Sumathi Sankaran Walters – Symbiosis

“Fecal samples were obtained from patients with Crohn’s disease in a pilot diet crossover trial comparing the effects of a specific carbohydrate diet (SCD) versus a low residue diet (LRD) on the composition and complexity of the gut microbiota and resolution of IBD symptoms. The gut microbiota composition was assessed using a high-density DNA microarray PhyloChip “

Review: Managing the manager: Gut microbes, stem cells and metabolism
M. Serino – Diabetes & Metabolism

“The LPS-sensitive cell types can be seen within bone marrow-derived cells (BMC), which are involved in the development of inflammation in the adipose tissue of obese and type 2 diabetic mice. “

 

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General microbiology and science, July 17

Detection of microbes in clinical samples, phages living in viruses, and archaea in biofilms.

Microbial detection in clinical samples

Metagenomic analysis of a sample from a patient with respiratory tract infection reveals the presence of a γ-papillomavirus – Marta Canuti – Frontiers in Microbiology

“We therefore concluded that the detected γ-papillomavirus is unlikely to be the causative agent of the respiratory complaints and its presence in the nose of the patient is not related to the disease.”

Detection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Are Quantitative Bacterial Wound Cultures Useful? – George Kallstrom – Journal of Clinical Microbiology

“This minireview briefly summarizes the clinical microbiology of wound cultures, with an emphasis on the history and utility (or lack thereof) of the quantitative wound culture.”

Phages and viruses

The origins of giant viruses, virophages and their relatives in host genomes – Aris Katzourakis and Amr Aswad – BMC Biology

“These viruses, together with the transposon-related virophages that infect them, pose a number of questions about their evolutionary origins that need to be considered in the light of the complex entanglement between host, virus and virophage genomes.”

Antibiotics

Antibiotics promote aggregation within aquatic bacterial communities – Gianluca Corno – Frontiers in Microbiology

“In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses.”

Biofilms and Archaea

Biofilm formation of mucosa-associated methanoarchaeal strains – Corinna Bang – Frontiers in Microbiology

“Here, the ability of three methanoarchaeal strains, Methanobrevibacter smithii and Methanosphaera stadtmanae, which form part of the human gut microbiota, and the Methanosarcina mazei strain Gö1 to grow on different surfaces and form biofilms was investigated. “

Microbial ecology

Persistence in the shadow of killers – Robert M. Sinclair – Frontiers in Microbiology

“What we show is that coexistence is not only possible, but that it is possible even if the absolute fitness advantage of the sensitive strain over the killer strain is arbitrarily small. We do this by performing a specifically targeted mathematical analysis on our model, rather than via simulations.”

General microbiology

Editorial: Bioterrorism: myth or reality? – G. Greub and M. P. Grobusch – Clinical Microbiology and Infection

Dr. Bik’s Picks

Today I can only cry for the people onboard flight MH17.

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General microbiology and science, July 14

Rectal swabs instead of stool samples, faster way of finding orthologs, and intelligence in bacteria.

Bioinformatics

Screen shot 2014-07-14 at 06.24PM, Jul 14Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss? – Natalie Ward, Gabriel Moreno-Hagelsieb – PLOS ONE

“Since sequence comparison can be time consuming, we decided to compare the number and quality of RBHs detected using algorithms that run in a fraction of the time as BLAST. We tested BLAT, LAST and UBLAST.”

Sampling techniques

Screen shot 2014-07-14 at 06.24PM, Jul 14ectal Swabs for Analysis of the Intestinal Microbiota – Andries E. Budding – PLOS ONE

“In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota.”

Screen shot 2014-07-14 at 06.25PM, Jul 14Some Are More Equal – A Comparative Study on Swab Uptake and Release of Bacterial Suspensions – Philipp Warnke – PLOS ONE

“Highest amount of CFU release was detected for the MWE Dryswab in the unrestricted setting for both S. aureus and S. epidermidis with 1544 CFU and 553 CFU, respectively, lowest release for the Sarstedt neutral swab with 32 CFU and 17 CFU, respectively (p<0.001).”

Antibiotics, resistance, biofilms

Screen shot 2014-07-14 at 06.26PM, Jul 14Beta-Lactam Antibiotics Stimulate Biofilm Formation in Non-Typeable Haemophilus influenzae by Up-Regulating Carbohydrate Metabolism – Siva Wu – PLOS ONE

“When exposed to sub-inhibitory concentrations of beta-lactam antibiotics NTHi strains produced tightly packed biofilms with decreased numbers of culturable bacteria but increased biomass.”

General microbiology

Screen shot 2014-07-14 at 12.23PM, Jul 14Macromolecular networks and intelligence in microorganisms – Hans V. Westerhoff – Frontiers in Microbiology

“Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected.”

Screen shot 2014-07-14 at 06.26PM, Jul 14 1The syndemics of childhood diarrhoea: A biosocial perspective on efforts to combat global inequities in diarrhoea-related morbidity and mortality – Nicola Bulled – Global Public Health

“Drawing from available literature, this paper uses syndemic theory to explore the role of adverse biosocial interactions in increasing the total disease burden of enteric infections in low-resources populations and assesses the limitations of recent global calls to action.”

Bacteria in the news

Screen shot 2014-07-14 at 06.19PM, Jul 14We Are Our Bacteria – Jane E. Brody – New York Times (illustration by Ken Orvidas)

“We may think of ourselves as just human, but we’re really a mass of microorganisms housed in a human shell.”

Screen shot 2014-07-14 at 06.27PM, Jul 14#BacteriaHysteria : Gross! Lots of bacteria found on new swimsuits – Jane Weaver – Today Health

“The removable liner in women’s swimsuits that is meant to protect the fabric from our cooties isn’t really protective after all, according to a microbe researcher. “

Screen shot 2014-07-14 at 06.28PM, Jul 14Milford hospital enlists robots in war against infections – Mary MacDonald – Boston Globe

“The robots, made by Xenex Disinfection Services, use an intense flash of ultraviolet light to fight the bacteria, viruses, fungi, and other micro-organisms that traditional cleaning methods can miss, according to the hospital’s infection control staff.”

Screen shot 2014-07-14 at 06.29PM, Jul 14CDC Cracks Down on Labs After Anthrax, Bird Flu Scares – Jonel Aleccia – NBC News

“Dr. Tom Frieden, director of the Centers for Disease Control and Prevention, on Friday announced an immediate moratorium on all shipments of biological materials from CDC biosecurity level 3 and level 4 labs until problems are addressed.”

Marine Mammals

Screen shot 2014-07-14 at 06.29PM, Jul 14 1How Dolphins’ Genetics Could Help Find Answers Into Mysterious Animal Die-Off – Sascha Cordner – WFSU

“A discovery into dolphin genetics may have brought research scientists one step closer to finding out the source of a mysterious animal die-off last year in the troubled Indian River Lagoon.”

Science and publishing

Screen shot 2014-07-14 at 12.45PM, Jul 14Retractions are coming thick and fast: it’s time for publishers to act – Adam Marcus and Ivan Oransky – The Guardian

Another encouraging development is the rise of post-publication peer review, which has been made possible in recent years by the availability of papers online. Contributors to PubPeer, for example, have found signs of flawed or falsified results, leading to papers being retracted.”

Dr. Bik’s Picks

Screen shot 2014-07-14 at 06.34PM, Jul 14Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease – Britt-Sabina Petersen – BMC Genomics

“We present a thorough genetic characterization of the sequenced individuals but detected no consistent differences within the twin pairs. “

Screen shot 2014-07-14 at 06.32PM, Jul 14How much science is there in new Planet of the Apes film? – Paul Rincon – BBC Science

“The latest instalment in the Planet of the Apes film franchise opens in the US on Friday. The rubber masks of the 60s and 70s films have been discarded in favour of motion capture suits and CGI. But how much did science inform the new movie’s portrayal of our close relatives?”

Screen shot 2014-07-14 at 06.31PM, Jul 14Domestication syndrome: White patches, baby faces and tameness explained by mild neural crest deficits – Science Daily

“Compared to their wild ancestors, domestic species are more tame, and they also tend to display a suite of other characteristic features, including floppier ears, patches of white fur, and more juvenile faces with smaller jaws.”

 

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General microbiome and science, June 30

Monday is always a busy day, so lots of papers today. Phages, CRISPRs, antibiotic resistance, probiotics, archaea, biofilms and a Goldilocks planet.

Antibiotics and resistance

Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes – JR Huddleston – Infection and Drug Resistance

“This review aims to give an overview of the major horizontal transfer mechanisms and their evolution and then demonstrate the human lower gastrointestinal tract as an environment in which horizontal gene transfer of resistance determinants occurs.”

Screen shot 2014-06-30 at 06.47PM, Jun 30Bacterial persisters: formation, eradication, and experimental systems
Sophie Helaine, Elisabeth Kugelberg – Trends in Microbiology

“Toxin–antitoxin (TA) modules have an important role in the formation of persisters and several studies show that they can form in response to different triggers.”

Screen shot 2014-06-30 at 06.48PM, Jun 30Antibiotic Treatment Suppresses Rotavirus Infection and Enhances Specific Humoral Immunity – Robin Uchiyama – Journal of Infectious Diseases

“Microbiota ablation resulted in reduced rotavirus infection/diarrhea and a more durable rotavirus antibody response, suggesting that antibiotic administration before rotavirus vaccination could raise low seroconversion rates that correlate with the vaccine’s inefficacy in developing regions.”

And:  Antibiotics Help Control Rotavirus Infections and Enhance Antirotaviral Immunity: Are You Serious? – Luther A. Bartelt and Richard L. Guerrant – Journal of Infectious Diseases

“Yes, we must understand intriguing new findings; but no, we are far from serious about widespread use of antimicrobials with routine immunizations.”

Screen shot 2014-06-30 at 06.44PM, Jun 30Transferrin Iron Starvation Therapy for Lethal Bacterial and Fungal Infections – Lin Lin – Journal of Infectious Diseases

“These results provide proof of principle that bacterial infections can be treated in vivo by attacking host targets (ie, trace metal availability) rather than microbial targets.”

Bacterial detection in blood and other sites

Screen shot 2014-06-30 at 06.45PM, Jun 30Identification of pathogens from blood culture bottles in spiked and clinical samples using matrix-assisted laser desorption ionization time-of-flight mass-spectrometry analysis – Simone Konnerth – BMC Research Notes

“MALDI-TOF MS using the SARAMIS database was applied to 37 spiked blood culture samples. Identification rates of spiked samples were as follows: The species level was determined in 16 of 21 (76.2%) Gram negative bacteria and in 11 of 13 (84.6%) Gram positive bacteria. “

Infection and host response

Type I and III Interferon Production in Response to RNA Viruses – Elizabeth Reid and Bryan Charleston – Journal of Interferon & Cytokine Research

“There are now many examples of RNA viruses inducing type I and type III IFNs, and although these IFNs act through different receptors, in many systems studied, they induce a similar spectrum of genes. “

CRISPRs

Screen shot 2014-06-30 at 06.50PM, Jun 30Review: Adapting to new threats: the generation of memory by CRISPR-Cas immune systems – Robert Heler – Molecular Microbiology

“Recent studies have begun to elucidate the genetic requirements for adaptation and have demonstrated that rather than being a stochastic process, the selection of new spacers is influenced by several factors. We review here our current knowledge of the CRISPR adaptation mechanism”

Screen shot 2014-06-30 at 06.53PM, Jun 30The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus – Jason Carte – Molecular Microbiology

“Our findings indicate that multiple CRISPR-Cas systems can function independently in crRNA biogenesis within a given organism – an important consideration in engineering coexisting CRISPR-Cas pathways”

Viruses and phages

Screen shot 2014-06-30 at 06.53PM, Jun 30Exploiting gut bacteriophages for human health – Marion Dalmasso – Trends in Microbiology

“We emphasise the complexity and individuality of the phageome, and the link to the health state of the host. We highlight the practical applications of bacteriophages in medicine and in the food chain.”

Screen shot 2014-06-30 at 06.52PM, Jun 30Environmental bacteriophages : viruses of microbes in aquatic ecosystems – Télesphore Sime – Ngando – Frontiers in Microbiology

“The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.”

Archaea

Screen shot 2014-06-30 at 06.55PM, Jun 30Taxonomic database and cut-off value for processing mcrA gene 454 pyrosequencing data by MOTHUR – Sizhong Yang – Journal of Microbiological Methods

“The functional mcrA gene of methanogens can generate phylogeny as congruent as the 16S rRNA gene phylogeny. “

Screen shot 2014-06-30 at 06.59PM, Jun 30Biofilm formation of mucosa-associated methanoarchaeal strains
Corinna Bang – Frontiers in Microbiology

“Here, the ability of three methanoarchaeal strains, Methanobrevibacter smithii and Methanosphaera stadtmanae, which form part of the human gut microbiota, and the Methanosarcina mazei strain Gö1 to grow on different surfaces and form biofilms was investigated.”

Biofilms (see also Archaea above and Probiotics below)

Screen shot 2014-06-30 at 07.02PM, Jun 30Development of an in vitro periodontal biofilm model for assessing antimicrobial and host modulatory effects of bioactive molecules
Emma Millhouse – BMC Oral Health

Multi-species biofilms were either treated with either molecule, or alternatively epithelial cells were treated with these prior to biofilm co-culture. Biofilm composition was evaluated and inflammatory responses quantified at a transcriptional and protein level.

Probiotics

Screen shot 2014-06-30 at 06.43PM, Jun 30Review: Enumeration of probiotic strains: Review of culture-dependent and alternative techniques to quantify viable bacteria – Catherine Davis – Journal of Microbiological Methods

“Consensus on an operational definition of viability and systematic efforts to validate these alternative techniques ultimately will strengthen the accuracy and reliability of probiotic strain enumeration.”

Inhibitory effect of Lactobacillus salivarius on Streptococcus mutans biofilm formation
Chien-Chen Wu – Molecular Oral Microbiology

“We analyzed 64 L. salivarius strains and found that two, K35 and K43, significantly inhibited S. mutans biofilm formation with inhibitory activities more pronounced than those of Lactobacillus rhamnosus GG (LGG), a prototypical probiotic that shows anti-caries activity.

General taxonomy and phylogeny

Screen shot 2014-06-30 at 07.04PM, Jun 30Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA) – S Dray – Molecular Ecology Resources

“In this work, we extend DPCoA to integrate the information of external variables measured on communities. The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and(or) remove the effect of confounding factors. “

Screen shot 2014-06-30 at 06.43PM, Jun 30Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms – Surajit Das – Journal of Microbiological Methods

“In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques.”

Metabolomics

Screen shot 2014-06-30 at 07.01PM, Jun 30Nutrient sharing in the microbial world – Erica C. Seth and Michiko E. Taga – Frontiers in Microbiology

“Cofactor cross-feeding can contribute to both the health and nutrition of a host organism, the virulence and persistence of pathogens, and the composition and function of environmental communities. “

Metagenomics

Combination of Metagenomics and Culture Based Methods to Study the Interaction Between Ochratoxin A and Gut Microbiota – Mingzhang Guo – Toxicological Sciences

“Changes in functional genes of gut microbiota including signal transduction, carbohydrate transport, transposase, amino acid transport system and mismatch repair were observed.”

Chromosomal organization

NuChart-II: a graph-based approach for the analysis and interpretation of Hi-C data (PDF) – Fabio Tordini – Proceedings of the CIBB 2014

“NuChart-II is a highly optimized implementation of a previous prototype package developed in R, in which the graph-based representation of Hi-C data was tested, but that also showed inevitable problems of scalability while working genome-wide on large datasets.”

Science and education

Screen shot 2014-06-30 at 06.58PM, Jun 30Starting small: using microbiology to foster scientific literacy
Amy F. Savage, Brooke A. Jude – Trends in Microbiology

“In order to achieve scientific literacy for all students, Bard College recently implemented Citizen Science, a common January course for all first-year students. Structured around the question ‘how do we reduce the global burden of disease?’, this course uses microbiological tools to develop an understanding of potential answers.”

 

Dr. Bik’s Picks

Screen Shot 2014-07-01 at 12.06.17 AMBird brains: Public asked to look out for clever rooks – Victoria Gill – BBC News

“The British Trust for Ornithology (BTO) is asking the public to take part in a national survey of bird intelligence. From 1 July, the charity is asking people to submit video clips or descriptions of the behaviour or rooks – some of our cleverest garden birds.”

Screen Shot 2014-07-01 at 12.06.52 AMPotentially habitable Earth-like planet discovered; May have similar temperatures to our planet – Science Daily

“A potentially habitable Earth-like planet that is only 16 light years away has been discovered. The “super-Earth” planet, GJ 832 c, takes 16 days to orbit its red-dwarf star, GJ 832, and has a mass at least five times that of Earth.”

Screen Shot 2014-07-01 at 12.07.35 AMStudy Implicates Smog In Autism And Schizophrenia – Science 2.0

“A recent paper found that exposure to air pollution early in life produces harmful changes in the brains of mice, including an enlargement of part of the brain that is seen in humans who have autism and schizophrenia, and that led them to conclude that smog causes autism.”

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General microbiology and science, June 10

Transcription in 12 different human tissues, bacteria in arterial plaques, and hairs with anticancer activity.

Infection and Host Response

Genome wideGenome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues – Zhiyun Guo – Nature Scientific Reports

“Finally, we describe TSmiR (http://bioeng.swjtu.edu.cn/TSmiR), a novel and web-searchable database that houses interaction maps of TF-TS miRNA in 12 tissues.”

IntracellularIntracellular Bacteria Interfere with Dendritic Cell Functions: Role of the Type I Interferon Pathway – Laurent Gorvel – PLOS ONE

To analyze the mechanisms used by C. burnetiiand B. abortus to alter moDC activation, we performed microarray and found that C. burnetiiand B. abortus induced a specific signature consisting of TLR4TLR3STAT1 and interferon response genes.”

Screen Shot 2014-06-10 at 9.55.25 PMBacteria Present in Carotid Arterial Plaques Are Found as Biofilm Deposits Which May Contribute to Enhanced Risk of Plaque Rupture – Bernard B. Lanter – mBio

“In the current work, atherosclerotic carotid artery explants from 15 patients were all shown to test positive for the presence of eubacterial 16S rRNA genes”

Screen Shot 2014-06-10 at 10.01.00 PMRNA-seq: Impact of RNA degradation on transcript quantification – Irene Gallego Romero – BMC Biology

“We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data.”

Dengue virus

DengueSpatiotemporal Dynamics of DENV-2 Asian-American Genotype Lineages in the Americas – Daiana Mir – PLOS ONE

“Our study reveals that genetic diversity of DENV-2 AS/AM genotype circulating in the Americas mainly resulted from one single founder event and can be organized in at least four major lineages”

Phages, viruses, CRISPRs

Screen Shot 2014-06-10 at 9.53.22 PMCasposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity – Mart Krupovic – BMC Biology

“We describe a new superfamily of archaeal and bacterial mobile elements which we denote casposons because they encode Cas1 endonuclease, a key enzyme of the CRISPR-Cas adaptive immunity systems of archaea and bacteria. “

Dr. Bik’s Picks

GeckoHow do geckos climb? – Ann Le Good – BioMedCentral

“The answer, from the recent Royal Society conference on cell adhesion, is that their climbing mechanism depends on van der Waals forces (as well as friction and shear stress). “

This one is intriguing:
AnticancerAnticancer Properties of Peptide Fragments of Hair Proteins – Sergiusz Markowicz – PLOS ONE

“We found out that the mixtures of soluble peptides obtained from human hair inhibited the proliferation of human melanoma cells in vitro. Moreover, the hair-derived peptide mixtures also inhibited the proliferation of B lymphoma cells and urinary bladder cancer cells. “

EarthEarth is around 60 million years older than previously thought — and so is the moon, new research finds – Science Daily

The timing of the giant impact between Earth’s ancestor and a planet-sized body occurred around 40 million years after the start of solar system formation. This means that the final stage of Earth’s formation is around 60 million years older than previously thought, according to new research.”

 

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