Microbiome digest, November 5, 2014

Bioinformatic tools for tree building and metagenomics, microbiome of iPads in hospitals, and stool samples from indigenous cultures.
Human clinical microbiome

MetaGeniE: Characterizing Human Clinical Samples Using Deep Metagenomic Sequencing – Arun Rawat – PLOS ONE

“We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes.”

Human gut microbiome

Human Fecal Microbiome–Based Biomarkers for Colorectal Cancer – Vilvapathy Narayanan – Cancer Prevention Research

“A recent study by Zackular and colleagues… provides an important way forward here in showing that specific analysis of multiple aspects of the microbiome composition in toto provides reliable detection of both precancerous and cancerous lesions. “

Plant microbiome

Covalently linked hopanoid-lipid A improves outer-membrane resistance of a Bradyrhizobium symbiont of legumes – Alba Silipo – Nature Communications

“Here we demonstrate that a photosynthetic Bradyrhizobium strain, symbiont of Aeschynomene legumes, synthesizes a unique LPS bearing a hopanoid covalently attached to lipid A.”

Microbiome of the built environment

* Surface Microbiology of the iPad Tablet Computer and the Potential to Serve as a Fomite in Both Inpatient Practice Settings as Well as Outside of the Hospital Environment – Elizabeth B. Hirsch – PLOS ONE

“Thirty iPads belonging to faculty with a variety of practice settings were sampled to determine the presence and quantity of clinically-relevant organisms.”

Bioinformatic tools

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation – Kalliopi Trachana – PLOS ONE

“Therefore, we constructed high quality “gold standard” orthologous groups that can serve as a benchmark set for orthology inference in bacterial species.”

Towards more accurate ancestral protein genotype–phenotype reconstructions with the use of species tree-aware gene trees – Mathieu Groussin – Molecular Biology and Evolution

“Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer and loss (DTL) of genes statistically increases ASR accuracy.”

IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies – Lam-Tung Nguyen – Molecular Biology and Evolution

“We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented.”

Sampling and DNA extraction techniques

Nasal Screening for MRSA: Different Swabs – Different Results! – Philipp Warnke – PLOS ONE

“This study investigates the performance of different swab-types in nasal MRSA-screening by utilizing a unique artificial nose model to provide realistic and standardized screening conditions.”

Microbes in the news

Les Dethlefsen from our lab did an excellent “AMA” (ask me anything) on Reddit/Science today, on the human gut microbiota. Read the questions and Les’ answers here.

* Fecal Matters: A Stepping Stool to Understanding Indigenous Cultures – Daniella Lowenberg – PLOS Blogs

“Suspecting that this excrement is rich in biological clues, a group of researchers conducted experiments to investigate fecal microbiomes and published a study in PLOS ONE detailing insights into the diets and lifestyles of two ancient indigenous cultures of Puerto Rico”

Quantifying the Microbiome and the State of Crowd Science with Jessica Richman (1h Podcast) – The Quantified Body

“…we have an excellent guest today to bring us up to date on all this. Jessica Richman, is CEO and co-founder of uBiome.”

* If you think your city subway only consists of smelly disgruntled commuters, think again… – Marcus Leung – MicroBEnet

“Have you ever wondered what microbes are around you when you take public transport? Personally, I think about it every day during my two-hour subway commute to and from our lab here in Hong Kong.”

Science, publishing, and career

Metascience could rescue the ‘replication crisis’ – Jonathan W. Schooler – Nature

“Metascience, the science of science, uses rigorous methods to examine how scientific practices influence the validity of scientific conclusions. “

Interactive notebooks: Sharing the code – Helen Shen – Nature

“The free IPython notebook makes data analysis easier to record, understand and reproduce.”

Column: It takes time and a team to win grants – Ingrid Eisenstadter – Nature

“All our applicants are people who were bright enough to get PhDs and MDs, but the proposals we receive tend to share the same flaws, whether they come from recent graduates or from researchers with years of experience.”

Elsevier bad for your h-index? – Ferniglab

“The negotiations between the Dutch universities and Elsevier have foundered…., which means that from 1 January 2015, Dutch researchers will no longer have access to Elsevier journals.”

Sexy molecules! Comedian Megan Amram talks ‘Science… for Her!’ (Q&A) – Amanda Kooser -CNET

“”Parks and Recreation” writer Megan Amram offers up a “raunchy, crazy” textbook full of carbon dating, physics as nail art and kale.”

Bik’s Picks

YouTube video: Brian Cox visits the world’s biggest vacuum chamber – Human Universe: Episode 4 Preview – BBC Two

“…what happens when a bowling ball and a feather are dropped together under the conditions of outer space (vacuum – EB).”

Study in paradise: Stanford professors turn Hawaii into a living science classroom – Bjorn Carey – Stanford News

“Students in the School of Earth Science’s Wrigley Field Program in Hawaii spend the quarter measuring vegetation, coral reefs and volcanoes to understand the dynamics of one of the planet’s most interesting ecosystems.”

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Microbiome digest, September 22, 2014

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Temporal stability of the microbiomes of 85 adults, bacteria in breast milk, vaginal microbiome during pregnancy, water microbiomes, and Bik’s Picks.

Human microbiome general

Temporal variability is a personalized feature of the human microbiome – Gilberto E Flores – PeerJ PrePrints

“Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over three months.”

Pregnancy and birth

It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant – Lars Bode – Advances in Nutrition

“This article is a summary of the symposium “It’s Alive: Microbes and Cells in Human Milk and Their Potential Benefits to Mother and Infant” held 29 April 2014 at the ASN Scientific Sessions and Annual Meeting at Experimental Biology 2014 in San Diego, CA.”

Microorganisms in the Female Genital Tract during Pregnancy: Tolerance versus Pathogenesis – Bruna de Andrade Ramos – American Journal of Reproductive Immunology

“We review the state of knowledge of microbe–host interactions in gestational tissues and highlight mechanisms that promote tolerance or pathogenesis.”

Determinants and pattern of care seeking for preterm newborns in a rural Bangladeshi cohort – Rashed Shah – BMC Health Services Research

“Only one-fifth (19.7%) of preterm newborns were taken to seek either preventive or curative health care.”

Human oral microbiome

Microbial signature profiles of periodontally healthy and diseased patients – Talita Gomes Baêta Lourenço – Journal of Clinical Periodontology

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

Human gut microbiome

Review: Modulation of the Gut Microbiota by Nutrients with Prebiotic and Probiotic Properties – Céline Druart – Advances in Nutrition

“In this review, we describe how changes in the composition and/or activity of the gut microbiota by administration of nutrients with probiotic or prebiotic properties can modulate host gene expression and metabolism and thereby positively influence host adipose tissue development and related metabolic disorders.”

Mammal microbiome

Resistance to Antibiotics of Clinical Relevance in the Fecal Microbiota of Mexican Wildlife – Jurgi Cristóbal-Azkarate – PLOS ONE

“Here, we used culture and molecular methods to assess ATBR in bacteria in fecal samples from howler monkeys, spider monkeys, tapirs and felids living freely in two regions of the Mexican state of Veracruz under different degrees of human influence.“

Bird microbiome

Do feather-degrading bacteria actually degrade feather colour? No significant effects of plumage microbiome modifications on feather colouration in wild great tits – Staffan Jacob – Naturwissenschaften

“Here, we tested whether (i) keratinolytic microorganisms can degrade feathers in vivo and thus modify the colour of feathers during the nesting period and (ii) whether feather microorganisms have a long-term effect on the investment in colouration of newly moulted feathers.”

Plant microbiome

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize – David Johnston-Monje – BMC Plant Biology

“The impact of these soil swaps on founder bacterial endophyte communities was tested using 16S-rDNA profiling, culturing and microbial trait phenotyping.“

Microbiota in Wheat Roots, Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems – Leszek Lenc – Journal of Phytopathology

“The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. “

Soil microbiome

Bacterial and Archaeal Communities in Bleached Mottles of Tropical Podzols –
K. J. Silva, P. Vidal-Torrado, M. R. Lambais – Microbial Ecology

“In this study, we examined the bacterial and archaeal communities along three Brazilian coastal podzol profiles, as well as in bleached mottles and their immediate vicinity, using 16S rRNA gene profiling.”

Water microbiome

Microplastic is an abundant and distinct microbial habitat in an urban river – Amanda McCormick – Environmental Science & Technology

“Results from high-throughput sequencing showed that bacterial assemblages colonizing microplastic within the river were less diverse and were significantly different in taxonomic composition compared to those from the water column and suspended organic matter.”

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity – Masanori Fujimoto – PLOS ONE

“The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry.”

Microbial diversity of the Soldhar hot spring, India, assessed by analyzing 16S rRNA and protein-coding genes – Avinash Sharma – Annals of Microbiology

“Bacterial diversity of the Soldhar hot spring, located in the Chamoli district of Uttarakhand, India, was investigated using a clone library, denaturing gradient gel electrophoresis (DGGE) and functional genes.”

Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types – Zuzana Urbanová and Jiří Bárta – FEMS Microbial Ecology

“Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. “

A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing – Thangavelu Boopathi – Polar Biology

“In this study, freshwater microeukaryotes in an Arctic reservoir at Ny-Ǻlesund (Svalbard, Norway) were studied using the hypervariable V1–V3 small subunit rRNA and 454 pyrosequencing.”

Built Environment

Urban microbiomes and urban ecology: How do microbes in the built environment affect human sustainability in cities? – Gary M. King – Journal of Microbiology

“I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems”

Phages and viruses

Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution – Elyse Stachler and Kyle Bibby – Environmental Science & Technology

“Here, 86 publically available metagenomes were surveyed to determine the presence and abundance of crAssphage in various environments, and to identify its utility for source tracking of human fecal pollution.”

Microbes in the news

Understanding the Microbiome and Its Impact on Human Health – Kristine Nally – HCPLive

“Instant polling at an educational session of the 2014 American Academy of Pain Management annual clinical meeting in Phoenix, AZ, revealed that only 40 percent of the approximately 350-person audience was “familiar” with the concept of a microbiome.”

Mining the microbiome for medicines – Set a thief… – The Economist

“Antibiotics are not the only things Dr Donia’s technique might turn up, for the bugs in the human microbiome spit out all sorts of other chemicals that could potentially be put to use as drugs.”

Techniques

Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr and Elhanan Borenstein – MicroBEnet

“We therefore set out to develop a set of ‘best practices’ for our lab for metagenomic sequence annotation and to prove (or disprove) quantitatively that such direct functional annotation of short reads provides a valid functional representation of the sample.”

Science and publishing

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

“The power of anonymous comments—and the liability of those who make them—is at the heart of a possible legal battle embroiling PubPeer, an online forum launched in October 2012 for anonymous, postpublication peer review.”

Time to Raise the Profile of Women and Minorities in Science – Brian Welle and Megan Smith – Scientific American

“Along these lines, over the past few years, we discovered some pretty ugly news about our beloved Google Doodles. “

Bik’s Picks

Immune system of newborn babies stronger than previously thought – Science Daily

“Contrary to what was previously thought, newborn immune T cells may have the ability to trigger an inflammatory response to bacteria, according to a new study.”

The Preservation Of Lonesome George – Sarah Fecht – PopSci.com

“Decades after the last giant tortoise was thought to have disappeared from the island of Pinta in the Galapagos, Lonesome George turned up in 1971 and became a conservation icon.”

 Great white sharks partly to blame for otter recovery stall – Peter Fimrite – SF Gate

“Most scientists agree that the number of animals, which are also known as southern sea otters, should be increasing, but hungry predators and a lack of food may be limiting their growth.”

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Non-human microbiome, August 25, 2014

Microbiotas of pigs, two fish species in the same pond, coral-algal associations, hypersaline soil, and marine eukaryotes.

Mammal microbiome

The influence of host’s genetics on the gut microbiota composition in pigs and its links with immunity traits – J. Estellé – Proceedings, 10th World Congress of Genetics Applied to Livestock Production

“A cohort of 60-days old piglets was assessed for fecal microbiota composition by pyrosequencing of the 16S rDNA. “

Fish microbiome

* Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond? – Xuemei Li – Journal of Applied Microbiology

“After 30-days of rearing the intestinal microbiota of the two fish species were assessed by pyrosequencing of 16S rRNA genes”

Insect microbiome

Microbial Associates of the Vine Mealybug Planococcus ficus (Hemiptera: Pseudococcidae) under Different Rearing Conditions – Lilach Iasur-Kruh – Microbial Ecology

“To examine the possible role of microbial symbionts in virus transmission, the archaeal, bacterial, and fungal microbiota of field and laboratory P. ficus were characterized using molecular and classical microbiological methods. “

Coral microbiome

* The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral–algal associations – John E. Parkinson and Iliana B. Baums – Frontiers in Microbiology

“Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. “

Soil microbiome

Salinity-induced differences in soil microbial communities around the hypersaline Lake Urmia – Mohsen Barin – Soil Research

“We tested the hypotheses that salinity reduces microbial biomasses and change the structure of the microbial community.”

Water microbiome

Microbial Community Response to Chlorine Conversion in a Chloraminated Drinking Water Distribution System – Hong Wang – Environmental Science & Technology

“Although high throughput sequencing of 16S rRNA genes revealed a distinct community shift and higher diversity index during the chlorine burn, it steadily returned towards a condition more similar to pre-burn than burn stage.”

Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes – Vera G. Fonseca – Global Ecology and Biogeography

“Here, we ask: (1) if the macroecology of meiobenthic communities is explained mainly by dispersal constraints or by environmental conditions; and (2) if levels of meiofaunal diversity surpass existing estimates based on morphological taxonomy.”

Microbiology of the Built Environment

* A disturbing trend – casual and reckless use of antimicrobial agents in building materials – Jonathan Eisen – MicroBEnet

“So they put in flooring that apparently was impregnated with some sort of antibacterial agent and they have no evidence that it works. “

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Microbiome digest, August 7, 2014

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

Human mouth microbiome

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

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

Human gut microbiome

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

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

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

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

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

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

 

Human microbiome after death

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

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

Animal models of human microbiome

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

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

Dog microbiome

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

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

Fish microbiome

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

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

Insect microbiome

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

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

Plant microbiome

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

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

Soil and water microbiome

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

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

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

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

Microbiome of the built environment

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

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

Metagenomics

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

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

Microbes in the News

The Quantified Microbiome Self – Carl Zimmer – National Geographic

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

Science and Career

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

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

Bik’s Picks

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

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

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

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

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

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

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

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

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Non-human microbiome, July 17

Microbiomes of sparrows, stinkbugs, corals, grapevine, and archeological stones.

Bird microbiome

Screen Shot 2014-07-17 at 5.14.56 PMGut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis – Leticia Mirón – Metagenomics

“This study is the first description of the diversity of bacteria along the whole intestine of a wild bird (Passer domesticus). Pyrosequencing of the 16S rRNA gene unveiled a high bacterial diversity, distributed in 11 bacterial phyla. “

Insect microbiome

StinkybugsSymbiont polyphyly, co-evolution, and necessity in pentatomid stinkbugs from Costa Rica – Kalia S. I. Bistolas – Frontiers in Microbiology

“The gut microbiota of 13 micro-allopatric tropical pentatomid species, from a Costa Rican lowland rainforest, was characterized and compared with insect and host plant phylogenies.”

Coral microbiome

CoralsReview: A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum – Chuya Shinzato – Frontiers in Microbiology

“Here we review recent genomic data derived from the scleractinian coral, Acropora digitifera, and the endosymbiotic dinoflagellate, Symbiodinium minutum. “

Plant microbiome

Screen Shot 2014-07-17 at 5.15.23 PMPyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere – Sohail Yousaf – Frontiers in Microbiology

“We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). “

Built Environment microbiome

Screen Shot 2014-07-17 at 5.15.49 PM 1Biological nanosilver particles for the protection of archaeological stones against microbial colonization – Ashraf M M Essa – International Biodeterioration & Biodegradation

“The stones treated with silicon polymer loaded with AgNPs showed an elevated antimicrobial potentiality against A. niger and S. parvullus.”

Water microbiome

Screen Shot 2014-07-17 at 5.16.30 PM16S rDNA-based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization – Marie Ragon – Frontiers in Microbiology

“To explore the diversity of these two distant cyanobacterial lineages representing two different patterns of intracellular calcification, we designed specific primers against their 16S rRNA genes and looked for their occurrence in a wide variety of samples. “

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Non-human microbiome digest, July 3

Parasites, effect of antibiotics in pigs, microbiome of birds, Drosophila, microbiome of plant crops, Hawai’i waters, and bacteria to preserve stone monuments.

Parasites and microbiome

Cooperation and conflict in host manipulation: interactions among macro-parasites and micro-organisms – Frank Cézilly – Frontiers in Microbiology

“Here, we review the empirical evidence in favor of the existence of synergistic or antagonistic interactions between co-occurring parasites, and highlight the neglected role of micro-organisms. “

holobiontHolobiont–Holobiont Interactions: Redefining Host–Parasite Interactions – Nolwenn Marie Dheilly – PLOS Pathogens

“It has been established in different model species that immune system maturation requires the presence of mutualistic bacteria”

Marine mammal microbiome

Screen shot 2014-07-03 at 04.24PM, Jul 03Intestinal helminth fauna of striped dolphins (Stenella coeruleoalba) in the western Mediterranean: No effects of host body length, age and sex – Paula Mateu – Marine Mammal Science

“The intestine of 52 (28 males and 24 females) striped dolphins (Stenella coeruleoalba) from western Mediterranean waters was examined for helminths. Animals were found stranded along the Spanish coasts during the morbillivirus epizootic in 1990.”

Pig microbiome

Screen shot 2014-07-03 at 03.17PM, Jul 03Carbadox has both temporary and lasting effects on the swine gut microbiota – Torey Looft – Frontiers in Microbiology

“Carbadox is an in-feed antibiotic that is widely used in swine production to prevent dysentery and to improve feed efficiency. The goal of this study was to characterize the effects of carbadox and its withdrawal on the swine gut microbiota. ”

Screen shot 2014-07-03 at 03.18PM, Jul 03Learning from agriculture: understanding low-dose antimicrobials as drivers of resistome expansion – Yaqi You – Frontiers in Microbiology

“Unconfined storage or land deposition of a large volume of animal waste causes its wide contact with the environment and drives the expansion of the environmental resistome through mobilome facilitated horizontal genet (sic, EB) transfer. “

Bird microbiome

Screen shot 2014-07-03 at 03.18PM, Jul 03Interspecific variations in the faecal microbiota of Procellariiform seabirds – Meagan L. Dewar – FEMS Microbiology Ecology

“Examining the faecal microbiota of three Procellariiform species (short-tailed shearwater, common diving petrel and fairy prion) provided a unique opportunity to not only characterise the gastrointestinal (GI) microbial composition of seabirds but to also examine the influence of stomach oils on the microbial community.”

Insect microbiome

Drosophila modelTransient adult microbiota, gut homeostasis and longevity: Novel insights from the Drosophila model – Berra Erkosar, Francois Leulier – FEBS Letters

“In the last decade, Drosophila has emerged as a useful model to study host–microbiota interactions, creating an active research field with prolific publications.”

Plant microbiome

Screen shot 2014-07-03 at 03.21PM, Jul 03Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance – Devin Coleman-Derr – Frontiers in Microbiology

“In recent years, studies have attempted to identify microbial symbionts capable of conferring the same stress-tolerance to their plant hosts, and new developments in genomic technologies have greatly facilitated such research. “

Screen shot 2014-07-03 at 03.21PM, Jul 03Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants – Catherine A. Gehring – Frontiers in Microbiology

“We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa.”

Screen shot 2014-07-03 at 03.22PM, Jul 03Nitrogen-fixing Rhizobium-legume symbiosis: are polyploidy and host peptide-governed symbiont differentiation general principles of endosymbiosis? – Gergely Maróti- Frontiers in Microbiology

“This review focuses on symbiotic plant cell development and terminal bacteroid differentiation and demonstrates the crucial roles of symbiotic peptides”

Screen shot 2014-07-03 at 03.22PM, Jul 03Disparate origins of Bradyrhizobium symbionts for invasive populations of Cytisus scoparius (Leguminosae) in North America – Kevin Horn – FEMS Microbiology Ecology

“To identify the geographic origin of nodule bacteria associated with invasion of the European legume Cytisus scoparius in the United States, isolates from 15 sites in six states were compared to > 200 Bradyrhizobium strains from indigenous legumes in the U.S., Mexico, Europe (six countries), Morocco, and Australia. “

Food microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic – Marilynn R. Fairfax – Frontiers in Microbiology

“Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals.”

Stone microbiology

Screen shot 2014-07-03 at 03.24PM, Jul 03 1Application of calcifying bacteria for remediation of stones and cultural heritages – Navdeep Kaur Dhami – Frontiers in Microbiology

“The present review emphasizes about different causative agents leading to deterioration and application of microbially induced calcium carbonate precipitation as a novel and potential technology for dealing with these problems. “

Soil microbiology

Screen shot 2014-07-03 at 03.25PM, Jul 03Volatile-mediated interactions between phylogenetically different soil bacteria
Paolina Garbeva – Frontiers in Microbiology

“Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. “

Screen shot 2014-07-03 at 03.27PM, Jul 03Land-use influences the distribution and activity of high affinity CO-oxidizing bacteria associated to type I-coxL genotype in soil – Liliana Quiza – Frontiers in Microbiology

“The main objective of this study was to assess the impact of land-use and soil properties on coxL gene diversity and identify molecular indicators for the soil uptake of atmospheric CO.”

Screen shot 2014-07-03 at 03.26PM, Jul 03Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia
Yong-Liang Chen – FEMS Microbiology Ecology

“… we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. “

Water microbiology

Screen shot 2014-07-03 at 03.27PM, Jul 03Biogeography of planktonic and benthic cyanobacteria in coastal waters of the Big Island, Hawai’i – Samuel D. Chamberlain – FEMS Microbiology Ecology

“To understand the patterns of cyanobacterial biogeography in relation to coastal environmental factors, we examined the diversity of planktonic and benthic cyanobacteria at 12 sites along the west coast of Hawaii’s Big Island.”

Screen shot 2014-07-03 at 03.29PM, Jul 03Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments – François Thomas – Frontiers in Microbiology

“We combined next-generation amplicon sequencing of 16S rDNA and rRNA libraries with phylogenetic analyses of marker genes for two S-oxidation pathways (soxB and rdsrAB). Gene and transcript numbers of soxB and rdsrAB phylotypes were quantified simultaneously, using newly designed (RT)-qPCR assays.”

Screen shot 2014-07-03 at 03.28PM, Jul 03Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities – Luisa Delgado-Serrano – FEMS Microbiology Ecology

“In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03Occurrence and activity of anammox bacteria in surface sediments of the southern North Sea – Nicole J. Bale – FEMS Microbiology Ecology

“The presence of anammox bacteria was established through the detection of specific phosphocholine-monoether ladderane lipids, 16S rRNA gene, and hydrazine synthase (hzsA) genes. “

Screen shot 2014-07-03 at 03.29PM, Jul 03 1Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools – Tanja Shabarova – FEMS Microbiology Ecology

“Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes.”

Screen shot 2014-07-03 at 03.30PM, Jul 03Abundance, diversity and seasonal dynamics of predatory bacteria in aquaculture zero discharge systems – Prem P. Kandel – FEMS Microbiology Ecology

“The dynamics of populations belonging to the obligate predators Bdellovibrio and like organisms (BALOs) were analyzed in freshwater and saline ZDS over a 7-month period using QPCR targeting the Bdellovibrionaceae, and the Bacteriovorax and Bacteriolyticum genera in the Bacteriovoracaeae”

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Non-human microbiome, June 30

Primate vaginal microbiome, birds painting eggs with bacteria, MHC and microbiota in fish, onions and tomato, bacteria on the beach, and (#BacteriaHysteria alert) “fecal veneer on climbing walls”.

Primate microbiome (also see Human digest)

Screen Shot 2014-06-30 at 11.23.32 PMPrimate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance – Suleyman Yildirim – ISME J (uncorrected proof, link to Chapman Research)

“Our results indicated that all primates exhibited host-specific vaginal microbiota and that humans were distinct from other primates in both microbiome composition and extent of diversity”

Bird microbiome

Screen Shot 2014-06-30 at 11.43.49 PMSpecial structures of hoopoe eggshells enhance the adhesion of symbiont-carrying uropygial secretion that increase hatching success – Manuel Martín-Vivaldi – Journal of Animal Ecology

“The findings of specialized crypts on the eggshells of hoopoes, and of video-recorded females smearing secretion containing symbiotic bacteria at a high density onto the eggshells strongly support a link between secretion and bacteria on eggs. “

and:  The Bird That Paints Its Eggs With Bacteria – Ed Yong – National Geographic

“Now, they’ve found evidence that these birds use the same bacteria to protect their young before they’re even born. By filming nesting females, they confirmed that the birds actively paint their eggs with their uropygial secretions.”

Fish microbiology

Screen Shot 2014-06-30 at 11.45.12 PMMajor Histocompatibility Complex class II polymorphism influences gut microbiota composition and diversity – Daniel I. Bolnick – Molecular Ecology

“Here, we show that MHC II polymorphism is associated with among-individual variation in gut microbiota within a single wild vertebrate population of a small fish, the threespine stickleback. “

Insect microbiome

WolbachiaThe Coevolutionary Period of Wolbachia pipientis Infecting Drosophila ananassae and its Impact on the Evolution of the Host Germline Stem Cell Regulating Genes – Jae Young Choi and Charles F. Aquadro – Molecular Biology and Evolution

“Phylogenetic analysis of D. ananassae mitochondrial DNA and W. pipientis DNA sequence diversity revealed the current W. pipientis infection is not recent. In addition, we examined the population genetics and molecular evolution of several Germline Stem Cell (GSC) regulating genes of D. ananassae”

Plant microbiome

Screen Shot 2014-06-30 at 11.43.01 PMIdentification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene – Jean M. Bonasera – Journal of Microbiological Methods

“We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.”

Occurrence and distribution of tomato seed-borne mycoflora in Saudi Arabia and its correlation with the climatic variables – Abdulaziz A. Al-Askar – Microbial Biotechnology

“One hundred samples of tomato seeds were collected in 2011 and 2012 from tomato-cultivated fields in Saudi Arabia and screened for their seed-borne mycoflora. A total of 30 genera and 57 species of fungi were recovered from the collected seed samples using agar plate and deep-freezing blotter methods. “

WasabiManagement of Meloidogyne incognita on tomato with endophytic bacteria and fresh residue of Wasabia japonica – Guang-Ju Li – Journal of Applied Microbiology

“By in vitro bioassay, 53 NEB strains showing nematicidal efficacies of >50% against J2 of M. incognita were isolated from wasabi. Basing on 16S rRNA gene sequences, these NEB were identified into 18 species of 11 genera.”

Lichen and fungi

Screen Shot 2014-06-30 at 11.46.20 PMA single macrolichen constitutes hundreds of unrecognized species – Robert Lücking – PNAS

“This lichen was long believed to represent a single species, but after revising this number to 16 in two genera (Cora and Corella), here we show that at least 126 phylogenetically and morphologically distinct species are contained within this group, with statistical analysis predicting more than 400. “

Soil, sand, and slurry microbiome

The Ecological Controls on the Prevalence of Candidate Division TM7 in Polar Regions – Tristrom Winsley – Frontiers in Microbiology

“We correlated chemical, physical and biological parameters of each soil with the relative abundance of the two major classes of the phylum to deduce factors that influence the groups’ seemingly ubiquitous nature. “

Review: Present status of effect of microorganisms from sand beach on public
health – Emmanuel Velonakis – Journal of Coastal Life Medicine

“Relatively, recent epidemiological studies in the USA revealed positive correlation between time spent at the beach and gastroenteritis. New parameters such as wind blowing and beach users’ density are also introduced for discussion in association with the sand microbial load”

Crusts slurryMethanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts – Yun-Feng Duan – Journal of Applied Microbiology

“Microbial communities in four crusts from cattle and swine slurries were investigated using DGGE and tag-encoded amplicon pyrosequencing. All crusts had distinct compositions of bacteria and archaea.”

Water microbiology

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria
Vinayak Agarwal – Nature Chemical Biology

“Herein we report the discovery of a conserved biosynthetic gene cluster in marine bacteria responsible for the synthesis of widespread polybrominated aromatic compounds”

Environmental 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.”

Built Environment

I really dislike this title …
Screen Shot 2014-06-30 at 11.47.38 PMMicrobial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds – S. L. Bräuer – Current Microbiology

“In contrast to many other studies of built environments, the majority of microorganisms on holds were most closely related to microbes annotated as being recovered from environmental sources, such as soil, with human skin also representing an important source.”

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