Microbiome digest, August 28, 2014

Cool new study today by Jack Gilbert on the bacteria living in our homes, what happens to you microbiome after you die, (gut) microbiome and respiratory diseases, lots of water studies, and Bik’s Picks.

General  human microbiome 

* Your death microbiome could catch your killer – Anna Williams – NewScientist

“These “friendly” bacteria adhere to the lining of the gut and keep the microbial villains at bay by outcompeting them. After we die, however, our gut flora have a party.“

Human respiratory microbiome

The Microbiome and the Lung – Lijia Cui – Annals of the American Thoracic Society

“In this review, we provide an overview of the basics of microbiome studies.”

Microbiome Diversity and Asthma and Allergy Risk – Antje Legatzki – Current Allergy and Asthma Reports

“In this review, we will discuss the available literature concerning the human microbiota and asthma and allergy development and occurrence. “

Gut microbiome

You waited for it: The journal Helicobacter has a Helicobacter special!
Gastric and Enterohepatic Helicobacters other than Helicobacter pylori
Armelle Ménard – Helicobacter

“Several studies highlighted the virulence of non-H. pylori species including H. cinaedi in humans and hyperlipidemic mice or H. macacae in geriatric rhesus monkeys with intestinal adenocarcinoma. “

Pregnancy and birth

Systemic Inflammation in the Extremely Low Gestational Age Newborn Following Maternal Genitourinary Infections – Raina N. Fichorova – American Journal of Reproductive Immunology

“Mothers of 914 infants born before 28th gestation week reported cervical/vaginal infection (CVI), and/or urine/bladder/kidney infection (UTI), or neither. Inflammation proteins measured in baby’s blood”

Animal models of microbiome research

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats – Ren, Zhigang – Transplantation

“cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR.”

Microbiology of the built environment

* Longitudinal analysis of microbial interaction between humans and the indoor environment – Simon Lax – Science

“Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. “

* Sloan Microbiology of the Built Environment Data Analysis Workshop (secrets of QIIME, VAMPS and QIITA) January 6-7, 2015 – Jonathan Eisen – MicroBEnet

“to learn hands-on how to use these tools on their own data, to perform meta-analyses that combine built environment datasets“

Water microbiome

Microbial weeds in hypersaline habitats: the enigma of the weed-like Haloferax mediterranei – Aharon Oren and John E. Hallsworth – FEMS Microbiology Letters

“Here, we discuss the enigma of the less abundant Haloferax mediterranei, an archaeon that grows faster than any other, comparable extreme halophile.”

Bacterial profiling in brine samples of the Emalahleni Water Reclamation Plant, South Africa, using 454-pyrosequencing method – Sudharshan Sekar – FEMS Microbiology Letters

“A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. “

The role of dispersal mode and habitat specialisation in metacommunity structuring of aquatic macroinvertebrates in isolated spring fens – Vanda Rádková – Freshwater Biology

“We applied two species categorisations, common/rare and generalists/specialists, to disentangle the roles of dispersal capacity and habitat specialisation.”

Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary – Jiwen Liu – FEMS Microbiology Ecology

“Using 454 pyrosequencing, the present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. “

Soil microbiome

The Effects of Radiation Pollution on the Population Diversities and Metabolic Characteristics of Soil Microorganisms – Meiying Gu – Water, Air, & Soil Pollution

“Microbial diversities were determined by using methods of cultured isolates and carbon source utilization on Biolog EcoPlate™. “

Bik’s Picks

A chocolate habit in ancient North America – Michael Bawaya – Science

“the findings suggest regular trade in cacao—and movements of the people who imbued it with significance—between ancient Mesoamericans and their northern neighbors, says Dorothy Washburn, an archaeologist at the University of Pennsylvania Museum of Archaeology and Anthropology “

Babies may be good at remembering, and forgetting – Laura Sanders – Science News

“over 20 percent of 5-year-olds and 8- to 9-year olds recounted events from their first year, some from the very first months of life.”

How the zebrafish gets its stripes: Uncovering how beautiful color patterns can develop in animals – Science Daily

Three major pigment cell types, black cells, reflective silvery cells, and yellow cells emerge during growth in the skin of the tiny juvenile fish and arrange as a multi-layered mosaic to compose the characteristic color pattern. “

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Human microbiome, July 29

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

Skin microbiome

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

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

Gastric microbiome

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

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

Pregnancy and Birth

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 

Animal models of human microbiome and disease

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

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

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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 microbiome and science, July 8

Metabolic networks, CRISPR induced immunity, and influence of extraction methods and primers on microbiome analysis. Plus some smallpox in the Lost&Found, and a big citation scandal in SAGE journals.

Microbial ecology / metabolomics

Screen Shot 2014-07-08 at 10.07.56 PMIdentifying All Moiety Conservation Laws in Genome-Scale Metabolic Networks – Andrea De Martino – PLOS ONE

“ Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism.”

Emergent

Emergent Biosynthetic Capacity in Simple Microbial Communities – Hsuan-Chao Chiu – PLOS Computational Biology

“We specifically focus on detecting emergent biosynthetic capacity – instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. “

DIET ArchaeaDirect Interspecies Electron Transfer between Geobacter metallireducens and Methanosarcina barkeri – Amelia-Elena Rotaru – Applied and Environmental Microbiology

“M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. “

Optimal defenseOptimal Defense Strategies in an Idealized Microbial Food Web under Trade-Off between Competition and Defense – Selina Våge – PLOS ONE

“ Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist.”

Microbial detection

Screen Shot 2014-07-08 at 10.13.13 PMHuman Herpes Viruses Are Associated with Classic Fever of Unknown Origin (FUO) in Beijing Patients – Weimin Zhou – PLOS ONE

“HHVs are associated with Chinese patients (especially for children) with classic FUO. Our study adds perspective to the aetiological and clinical characteristics of classic FUO in beijing patients.”

Phages and viruses

Screen Shot 2014-07-08 at 10.13.31 PMCRISPR-Induced Distributed Immunity in Microbial Populations – Lauren M. Childs – PLOS ONE

“We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities.”

Techniques

Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems – Perrine Cruaud – Applied and Environmental Microbiology

“Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples.”

Dengue

Sanofi’s dengue vaccine first to complete phase 3 – Gunjan Sinha – Nature Biotechnology

“Banking on approval, Sanofi has already started production, a move some have described as a “huge gamble” in light of the vaccine’s disappointing results from earlier studies, says Mark Clark, a pharmaceuticals analyst at Deutsche Bank in London.”

Microbes in the News

Found: Forgotten Vials of Smallpox – Maryn McKenna – Wired.com (also see CDC Media Statement)

“Workers clearing out an old storage room on the Bethesda, Md. campus of the National Institutes of Health have found a forgotten box of vials that contain smallpox.”

The Bacteria That Got Spread Throughout The US By Military Testing – Esther Inglis-Arkell – IO9

“Have you ever heard of serratia marcescens bacteria? Today they are a cause of hospital infections. In the 1960s, they were secretly sprayed across Washington, San Francisco, and New York.”

Manage Your Microbes – Laura Stec – Palo Alto Online

“I’ve been researching this wonderful advance in science for Manage Your Microbes, a cook class at Belmont Library on July 29th. “

Science, Publishing, and Career

SAGE Publications busts “peer review and citation ring,” 60 papers retracted – Retraction Watch

SAGE announces the retraction of 60 articles implicated in a peer review and citation ring at the Journal of Vibration and Control (JVC). “

13 Subtle Ways Women Are Treated Differently At Work – Jenna Goudreau – Business Insider

“Both men and women hold these views but often don’t even realize it. “It’s hard to fight this,” says Rivers, but awareness is key.

Dr. Bik’s Picks

Combining colour and temperature: A blue object is more likely to be judged as warm than a red object – Hsin-Ni Ho – Nature Scientific Reports

“It is commonly believed that reddish colour induces warm feelings while bluish colour induces cold feelings. We, however, demonstrate an opposite effect when the temperature information is acquired by direct touch.”

MandarinSequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication – G Albert Wu – Nature Biotechnology

“Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. “

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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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Human microbiome, June 17

Gut bacteria swapping DNA segments, what happens after a fecal transplant, intestinal archaea, and more.

Gut microbiome

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut – Michael J. Coyne – mBio

“Using seven coresident Bacteroidales species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity.”

Recovery of the Gut Microbiome following Fecal Microbiota Transplantation – Anna M. Seekatz – mBio

“Here we investigated changes in the fecal microbiota structure following FMT in patients with recurrent C. difficile infection, and imputed a hypothetical functional profile based on the 16S rRNA profile using a predictive metagenomic tool.”

The Intestinal Archaea Methanosphaera stadtmanae and Methanobrevibacter smithii Activate Human Dendritic Cells – Corinna Bang – PLOS ONE

“Taken together, our findings strongly argue that the archaeal gut inhabitants M. stadtmanae and M. smithii are specifically recognized by the human innate immune system. “

Microbiota and Metabolome Associated with Immunoglobulin A Nephropathy (IgAN) –
Maria De Angelis – PLOS ONE

“This study aimed at investigating the fecal microbiota, and the fecal and urinary metabolome of non progressor (NP) and progressor (P) patients with immunoglobulin A nephropathy (IgAN). “

Respiratory microbiome

Impact of Experimental Human Pneumococcal Carriage on Nasopharyngeal Bacterial Densities in Healthy Adults – Joshua R. Shak – PLOS ONE

“These data on bacterial associations are the first to be reported surrounding experimental human pneumococcal colonization and show that co-colonizing effects are likely subtle rather than absolute.”

Vaginal microbiome

Diversity and stability of cultured vaginal lactobacilli in pregnant women from a multi-ethnic urban UK population – S.M. Husain – Journal of Applied Microbiology

“Self-collected vaginal swabs at 13 and 20 weeks gestation were obtained from women attending for routine antenatal care and cultured for lactobacilli.”

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