Tag Archives: birds

Non-human microbiome digest, October 6, 2014

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Microbiomes of cats with diabetes, vaginas of ewes and cows, chickens, hoopoes, Drosophila, sponges, plants, and subways.

Mammal Microbiome

* Faecal Microbiota of Cats with Insulin-Treated Diabetes Mellitus – Erin T. Bell – PLOS ONE

“Faecal samples were collected from insulin-treated diabetic and non-diabetic cats, and Illumina sequencing of the 16S rRNA gene and quantitative PCR were performed on each sample. “

* Characterization of the vaginal microbiota of ewes and cows reveals a unique microbiota with low levels of lactobacilli and near-neutral pH – JD Swartz, M Lachman, K Westveer, T O’Neill, T Geary – Frontiers in Veterinary Science

“We amplified and sequenced the V3-V4 region of the 16S ribosomal RNA contents yielding a total of 907,667 high-quality reads. “

Avian microbiome

* The chicken gastrointestinal microbiome – Brian B. Oakley – FEMS Microbiology Letters

“In this mini-review, we provide an overview of the current state of knowledge of the chicken GI microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition.”

Environmental Factors Shape the Community of Symbionts in the Hoopoe Uropygial Gland More than Genetic Factors – Magdalena Ruiz-Rodríguez – Applied and Environmental Microbiology

“By disentangling the diversity of bacterial strains from the uropygium of hoopoes (Upupa epops) due to genetic relatedness or to a common environment, we explored the importance of horizontal (from the environment) and vertical (from parents) acquisition of antimicrobial-producing symbionts in this species.”

Insect Microbiome

Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster – John M. Chaston – mBio

“Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls.”

Invertebrate microbiome

* Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review – Cristiane C. P. Hardoim and Rodrigo Costa – Marine Drugs

“The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. “

Plant microbiome

Microbial genome-enabled insights into plant–microorganism interactions – David Guttman, Alice C. McHardy & Paul Schulze-Lefert – Nature Reviews Genetics

“… culture-independent community profiling methods, coupled with metagenomic and metatranscriptomic studies, have provided the first insights into the emerging field of research on plant-associated microbial communities.”

Soil microbiome

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland – Antje Gittel – Frontiers in Microbiology

“We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities.”

Water microbiome

Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake – Esther A. Gies – Applied and Environmental Microbiology

“Here we describe diversity, abundance, and cooccurrence patterns of uncultivated microbial communities inhabiting the permanently stratified waters of meromictic Sakinaw Lake, British Columbia, Canada, using 454 sequencing of the small-subunit rRNA gene with three-domain resolution.”

Microbiome of the built environment

* Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. “

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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 11, 2014

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Microbiomes of Eurasian Magpie, mosquitoes, ticks, 218 insect species, sponges, plants, and olives.

Bird microbiome

Effect of Incubation on Bacterial Communities of Eggshells in a Temperate Bird, the Eurasian Magpie (Pica pica) – Won Young Lee – PLOS ONE

“In this study, we employed culture-independent methods, quantitative PCR and 16S rRNA gene pyrosequencing, to elucidate the effect of incubation on the bacterial abundance and bacterial community composition on the eggshells of the Eurasian Magpie (Pica pica).”

Arthropod microbiome

Native microbiome impedes vertical transmission of Wolbachia in Anopheles mosquitoes
Grant L. Hughes – PNAS USA

“We show the native microbiota of Anopheles impede vertical transmission of Wolbachia. Antibiotic microbiome perturbation enables Wolbachia transmission in two Anopheles species.”

Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens – Yongjin Qiu – PLOS ONE

“Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. “

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host – Ji-Hyun Yun – Applied and Environmental Microbiology

In this study, we comprehensively characterized insect-associated gut bacteria of 305 individuals belonging to 218 species in 21 taxonomic orders, using 454 pyrosequencing of 16S rRNA genes.

Sponge microbiome

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge – Ren-Mao Tian – Environmental Microbiology

“Here, we present and analyze the first genome of sponge-associated SOB using a recently developed metagenomic binning strategy”

Plant microbiome

Foliage Friendships (behind paywall) – Peter Andrey Smith – Scientific American

“Microbial communities on a plant’s roots, stems and leaves may improve crop growth”

Effects of Fusarium oxysporum on rhizosphere microbial communities of two cucumber genotypes with contrasting Fusarium wilt resistance under hydroponic condition – Ju Ding – European Journal of Plant Pathology

“PCR-DGGE analysis of 16S rDNA fragments indicated that following FO inoculation, significant changes in the bacterial structure isolated from the root surfaces of susceptible plants were observed, such as an increased diversity index, a decreased evenness index, and the occurrence of several types of bacteria that decomposed organic substances.”

Food microbiology

Open-refrigerated retail display case temperature profile and its impact on product quality and microbiota of stored baby spinach – Liping Kou – Food Control

“All bags were immediately loaded in the display cases and the overall visual quality, tissue electrolyte leakage, total aerobic mesophilic bacteria and psychrotrophic bacteria were evaluated for each bag. “

Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production – Xi Zhang – Bioresouce Technology

“The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. “

Genetic diversity and dynamics of bacterial and yeast strains associated to Spanish-style green table-olive fermentations in large manufacturing companies – Helena Lucena-Padrós – International Journal of Food Microbiology

“We have genotyped a total of 1045 microbial isolates obtained along the fermentation time of Spanish-style green table olives from the fermentation yards (patios) of two large manufacturing companies in the province of Sevilla, south of Spain.”

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Non-human microbiome, July 17

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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

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Microbiomes of frogs, kakapo birds, and very hot water springs. And a special on Ed DeLong.

Cow microbiome

RumenRumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains – Bareket Dassa – PLOS ONE

“Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen”

Reptile microbiome

Occurrence, Diversity, and Host Association of Intestinal Campylobacter, Arcobacter, and Helicobacter in Reptiles – Maarten J. Gilbert – PLOS ONE

“Based on PCR, Campylobacter, Arcobacter, and Helicobacter were detected in 69.3% of the reptiles; 82.5% of the chelonians, 63.8% of the lizards, and 58.0% of the snakes were positive for one or more of these genera.”

Amphibian microbiome

Frog taggingTagging Frogs with Passive Integrated Transponders Causes Disruption of the Cutaneous Bacterial Community and Proliferation of Opportunistic Fungi – Rachael E. Antwis – Applied and Environmental Microbiology

“We find that PIT tagging causes a major disruption to the bacterial community associated with the skin of frogs (∼12-fold increase in abundance), as well as a concurrent proliferation in resident fungi (up to ∼200-fold increase).”

Bird microbiome

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo – David W. Waite – Applied and Environmental Microbiology

“Amplicon pyrosequencing revealed a juvenile fecal microbiota enriched with particular lactic acid bacteria compared to the microbiota of adults, although the overall community structure did not differ significantly among kakapos of different ages. “

Multilocus Sequence Typing Confirms Wild Birds as the Source of a Campylobacter Outbreak Associated with the Consumption of Raw Peas – Patrick S. L. Kwan – Applied and Environmental Microbiology

“Novel STs clustered closely with isolates typically associated with wild birds and the environment but distinct from lineages commonly seen in human infections. “

 

Sponge microbiome

SpongeIn Situ Natural Product Discovery via an Artificial Marine Sponge – James J. La Clair – PLOS ONE

“Retrieving this artificial sponge from a tropical ecosystem after deployment for 320 hours afforded three actin–targeting jasplakinolide depsipeptides that had been discovered two decades earlier using traditional sponge specimen collection and isolation procedures.”

 

Water microbiology

Profile of Edward DeLong – Paul Gabrielsen – PNAS

“DeLong has learned that studying a reservoir of life as large and diverse as the ocean can lead to unexpected discoveries. “We’re continually being surprised,” he says.”

Handling Temperature Bursts Reaching 464°C: Different Microbial Strategies in the Sisters Peak Hydrothermal Chimney – Mirjam Perner – Applied and Environmental Microbiology

“The SP metagenome reveals considerable differences in the taxonomic composition from those of other hydrothermal vent and subsurface samples; these could be better explained by temperature than by other available abiotic parameters. “

Methanotrophic bacteria in warm geothermal spring sediments identified using stable isotope probing – Christine E. Sharp – FEMS Microbiology Ecology

“Quantitative (q)PCR of pmoA genes identified the position of the heavy (13C-labelled) DNA fractions in density gradients, and 16S rRNA gene pyrotag sequencing of the heavy fractions was performed to identify the active methanotrophs.”

Bacterial and archaeal communities in long-term contaminated surface and subsurface soil evaluated through co-extracted RNA and DNA – Anu Mikkonen – FEMS Microbiology Ecology

“Soil RNA and DNA were co-extracted along a contamination gradient at a landfarming field with aged crude oil contamination to investigate pollution-dependent differences in 16S rRNA and rRNA gene pools”

rpoD Gene Pyrosequencing for the Assessment of Pseudomonas Diversity in a Water Sample from the Woluwe River – David Sánchez – Applied and Environmental Microbiology

“Culture-independent methods consisted of cloning and pyrosequencing of a Pseudomonas rpoD amplicon from total DNA extracted from the same sample and amplified with selective rpoD gene primers. “

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.”

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Non-human microbiome, July 7

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Microbiomes of buffalo’s, chickens on melatonin, and acid mine drainages.

Buffalo microbiome

Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis – Bhaskar Reddy – Molecular Biology Reports

“We analyzed the metagenomes of buffalo rumen in the liquid and solid phase of the rumen biomaterial from river buffalo adapted to varying proportion of concentrate to green or dry roughages, using high-throughput sequencing to know the occurrence of antibiotics resistance genes, genetic exchange between bacterial population and environmental reservoirs.”

Chicken microbiome

Exogenous melatonin improves growth performance, intestinal microbiota, and morphology in temporarily feed restricted broilers – A. Akbarian – Livestock Science

“An increment in ileal Lactobacillus counts was found in MFR group compared to CON (P<0.05). No significant differences were noticed in microbial counts of cecum among treatments.”

Insect microbiome

Homeostasis between gut-associated microorganisms and the immune system in Drosophila – Hyejin You – Current Opinion in Immunology

“A deeper understanding of the role of uracil in Drosophila immunity will provide additional insight into the molecular mechanisms underlying host–microbe symbiosis and dysbiosis.”

Water and other microbiology

Inter-species interconnections in acid mine drainage microbial communities
Luis R. Comolli and Jillian F. Banfield – Frontiers in Microbiology

“Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. “

Biogeochemical activity of microbial biofilms in the water column overlying uranium mine tailings – V.F. Bondici – Journal of Applied Microbiology

“To describe microbial diversity, biofilm composition and biogeochemical potential within biofilms in the water overlying uranium tailings characterized by high pH, high metal concentration and low permeability.”

Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture – Beate Kraft – Environmental Microbiology

“In this study, a heterotrophic denitrifying community from sediments of a marine intertidal flat active in nitrogen cycling was selected in a chemostat and monitored over a period of 50 days.”

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Non-human microbiome digest, July 3

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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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Human and other microbiomes, July 2

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Fungi in the mouth, microbiome in celiac disease, viruses in bats, fecal microbiota of penguins, and bacteria in water and concrete.

Human oral microbiome

Screen Shot 2014-07-02 at 10.35.22 PMMolecular Analysis of Fungal Populations in Patients with Oral Candidiasis Using Internal Transcribed Spacer Region – Shinsuke Ieda – PLOS ONE

“In this study we examined the fungal flora in patients with oral candidiasis and investigated changes in the flora after antifungal treatment using length heterogeneity-polymerization chain reaction (LH-PCR) analysis of ITS regions.”

Human respiratory microbiome

Screen Shot 2014-07-02 at 10.35.47 PMLetter: No Clinical Association of Live Attenuated Influenza Virus with Nasal Carriage of Bacteria or Acute Otitis Media – Kathleen L. Coelingh, Robert B. Belshe – mBio

“We write this note to clarify the article “Live Attenuated Influenza Vaccine Enhances Colonization of Streptococcus pneumoniae and Staphylococcus aureus in Mice” by Mina et al. (1) in order that patients or clinicians not misinterpret the study’s clinical relevance.”

Human gut microbiome

Review: Screen Shot 2014-07-02 at 10.16.45 PMIntestinal Microbiota and Probiotics in Celiac Disease – Luís Fernando de Sousa Moraes – Clinical Microbiology Reviews

“This review aims to discuss the characteristics of the microbiota in CD subjects and the use of probiotics as a novel therapy for CD. “

Bat microbiome

Screen Shot 2014-07-02 at 10.36.24 PMBat Distribution Size or Shape as Determinant of Viral Richness in African Bats – Gaël D. Maganga – PLOS ONE

“We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. “

Bird microbiome

Screen Shot 2014-07-02 at 10.36.58 PMInfluence of Fasting during Moult on the Faecal Microbiota of Penguins – Meagan L. Dewar – PLOS ONE

“Therefore, the present study aimed to examine the microbial composition and diversity of the GI microbiota of fasting little (Eudyptula minor) and king penguins (Aptenodytes patagonicus) penguins during early and late moult.”

Invertebrate microbiome

Screen Shot 2014-07-02 at 10.37.27 PMBacterial Community Composition in the Gut Content and Ambient Sediment of Sea Cucumber Apostichopus japonicus Revealed by 16S rRNA Gene Pyrosequencing – Fei Gao – PLOS ONE

“The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. “

Plant microbiome

Screen Shot 2014-07-02 at 10.37.55 PMSelecting Microbial Strains from Pine Tree Resin: Biotechnological Applications from a Terpene World – Cristina Vilanova – PLOS ONE

“The taxonomic and functional diversity of the cultivated, resin-tolerant fraction of the whole microbiota were unveiled by high-throughput sequencing, which resulted in the detection of more than 40 bacterial genera among the terpene-degrading microorganisms, and a range of genes involved in the degradation of different terpene families.”

Water and concrete microbiology

Screen Shot 2014-07-02 at 10.38.23 PMCoupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species – Alexander J. Probst – PLOS ONE

“Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current.”

Screen Shot 2014-07-02 at 10.38.41 PMMicrobial Quality and Phylogenetic Diversity of Fresh Rainwater and Tropical Freshwater Reservoir – Rajni Kaushik – PLOS ONE

“The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. “

Screen Shot 2014-07-02 at 10.29.38 PMBacteria and concrete-a love-hate relationship – Embriette Hyde

“Sometimes bacteria appear to harm concrete, sometimes they appear to help it.”

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General microbiome digest, July 1

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Diet and gut microbiome (again), Campylobacter in chicken is not a commensal, microbiomes of fish, insects, corals, plant, and hospitals, and women in science.

Human gut microbiome

Screen shot 2014-07-01 at 06.07PM, Jul 01Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health – T Kelder – Nutrition & Diabetes

“We assessed fecal microbiota composition and host response patterns of metabolic and inflammatory markers in 10 apparently healthy men subjected to a high-fat high-caloric diet (HFHC, 1300 kcal/day extra) for 4 weeks. “

Pregnancy and birth

Screen shot 2014-07-01 at 06.08PM, Jul 01 1Gestational Age and Age at Sampling Influence Metabolic Profiles in Premature Infants
Reese H. Clark – Pediatrics

“Metabolic profiles (15 amino acids and 35 acylcarnitines) were obtained by using standard newborn techniques on infants born between 23 and 31 completed weeks of gestation.”

Screen shot 2014-07-01 at 06.08PM, Jul 01Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing – Jason M. Knight – Nature Scientific Reports

“we have developed a novel, noninvasive, molecular approach that utilizes next generation RNA sequencing on stool samples containing intact epithelial cells for the purpose of quantifying intestinal gene expression.”

Screen shot 2014-07-01 at 06.09PM, Jul 01Cesarean Section and Rate of Subsequent Stillbirth, Miscarriage, and Ectopic Pregnancy: A Danish Register-Based Cohort Study – Sinéad M. O’Neill – PLOS Medicine

“This study found that cesarean section is associated with a small increased rate of subsequent stillbirth and ectopic pregnancy.”

Bird microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01Campylobacter jejuni Is Not Merely a Commensal in Commercial Broiler Chickens and Affects Bird Welfare – Suzanne Humphrey – mBio

“Through experimental infection of four commercial breeds of broiler chickens, we show that breed has a significant effect on C. jejuni infection and the immune response of the animals, although these factors have limited impact on the number of bacteria in chicken ceca. “

Fish microbiome

Screen shot 2014-07-01 at 06.10PM, Jul 01 1Quorum quenching bacteria Bacillus sp. QSI-1 protect zebrafish (Danio rerio) from Aeromonas hydrophila infection – Weihua Chu – Nature Scientific Reports

“In this study, the effect of Bacillus sp. QSI-1 as an efficient quorum quencher on virulence factors production and biofilm formation of fish pathogen Aeromonas hydrophila was investigated. ”

Insect microbiome

Screen shot 2014-07-01 at 06.11PM, Jul 01Evolutionary origin of insect–Wolbachia nutritional mutualism – Naruo Nikoh – PNAS

“In the bedbug’s Wolbachia genome, we identified a gene cluster encoding the complete synthetic pathway for biotin (vitamin B7), which is not present in other Wolbachia genomes and is presumably acquired via lateral transfer from a coinfecting endosymbiont. “

Corals and sponges microbiome

Screen shot 2014-07-01 at 06.12PM, Jul 01Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors – Linda W. Kelly – PNAS

“The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. “

Plant microbiome

Screen shot 2014-07-01 at 06.13PM, Jul 01The role of sulfur and phosphorus mobilizing bacteria in biochar induced growth promotion of Lolium perenne – A Fox – FEMS Microbiology Ecology

“16S rRNA gene based rhizobacteria community analysis revealed a significant biochar treatment effect. Abundance of nematodes feeding on bacteria was also significantly increased in the biochar treatments.”

Functional diversification within bacterial lineages promotes wide functional overlapping between taxonomic groups in a Mediterranean soil forest – J Curiel Yuste – FEMS Microbiology Ecology

“We investigated the relationship between taxonomy and functioning of soil bacterial communities in soils from a Mediterranean Holm-oak forest using a high throughput DNA pyrosequencing technique. “

Soil, sewage and sludge microbiome

Screen shot 2014-07-01 at 06.15PM, Jul 01Response of soil-associated microbial communities to intrusion of coal mine-derived acid mine drainage – Justin S Brantner and John M Senko – Environmental Science & Technology

” Evaluation of pyrosequencing-derived 16S rRNA gene sequences recovered from incubations revealed the development of microbial community characteristics that were similar to those of the mature iron mound sediment. “

Transformation Products and Human Metabolites of Triclocarban and Triclosan in Sewage Sludge Across the United States – Benny F. G. Pycke – Environmental Science & Technology

“Here, we report on the levels of eight transformation products, human metabolites, and manufacturing byproducts of TCC and TCS in raw and treated sewage sludge.”

Built Environment Microbiome

Screen shot 2014-07-01 at 06.14PM, Jul 01Rethinking Sterile: The Hospital Microbiome – Carrie Arnold – Environ Health Perspect

“Gilbert, an environmental microbiologist at Argonne National Laboratory, and his platoon of graduate students, postdocs, and research assistants descended on the hospital several times each day, even before it opened to the public. Armed with cotton swabs, they focused their efforts on the floors devoted to surgery and oncology. “

Bioinformatics

Screen shot 2014-07-01 at 06.15PM, Jul 01 1A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples – Samia N. Naccache – Genome Research

“Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. “

Metagenomics

Metagenomic scaffolds enable combinatorial lignin transformation
Cameron R. Strachan – PNAS

“In this study, we devised a previously unidentified biosensor responsive to lignin transformation products. We used this biosensor in a functional screen to recover metagenomic scaffolds sourced from coal bed bacterial communities. “

Arsenic metabolism

Sealing rice field boundaries in Bangladesh: a pilot study demonstrates reductions in water use, arsenic loading to field soils, and methane emissions from irrigation water – Rebecca B Neumann – Environmental Science & Technology

“Irrigation of rice fields in Bangladesh with arsenic-contaminated and methane-rich groundwater loads arsenic into field soils and releases methane into the atmosphere. We tested the water-savings potential of sealing field bunds (raised boundaries around field edges) as a way to mitigate these negative outcomes.”

Localised Flux-Maxima of Arsenic, Lead and Iron around Root Apices in Flooded Lowland Rice – Paul Nicholas Williams – Environmental Science & Technology

“Here we use new diffusive gradients in thin-film (DGT)/planar optode sandwich sensors deployed in situ on rice roots to demonstrate a new geochemical niche of greatly enhanced As, Pb and Fe(II) mobilization into solution immediately adjacent to the root tips characterized by O2 enrichment and low pH. “

Dengue

Screen shot 2014-07-01 at 06.16PM, Jul 01Baicalin, a metabolite of baicalein with antiviral activity against dengue virus – Ehsan Moghaddam – Nature Scientific Reports

“Here, we examined the anti-DENV properties of baicalin in vitro, and described the inhibitory potentials of baicalin at different steps of DENV-2 (NGC strain) replication.”

Antibiotic resistance

Review: The expression of antibiotic resistance genes in antibiotic-producing bacteria – Stefanie Mak – Molecular Microbiology

“Antibiotic-producing bacteria encode antibiotic resistance genes that protect them from the biologically active molecules that they produce. The expression of these genes needs to occur in a timely manner: either in advance of or concomitantly with biosynthesis. It appears that there have been at least two general solutions to this problem. “

General microbiology

Screen shot 2014-07-01 at 06.20PM, Jul 01Bacterial sugar utilization gives rise to distinct single-cell behaviors – Taliman Afroz – Molecular Microbiology

“Here, we performed single-cell analyses to probe the behavior of representative pathways in the model bacterium Escherichia coli. “

Identification of essential Alphaproteobacterial genes reveals operational variability in conserved developmental and cell cycle systems – Patrick D. Curtis and Yves V. Brun – Molecular Microbiology

“These results show that while essential cell functions are conserved across varying genetic distance, much of a given organism’s essential gene pool is specific to that organism.”

Science and career

Screen shot 2014-07-01 at 06.22PM, Jul 01Elite male faculty in the life sciences employ fewer women – Jason M. Sheltzer and Joan C. Smith – PNAS

“To explore the current causes of women’s underrepresentation in biology, we collected publicly accessible data from university directories and faculty websites about the composition of biology laboratories at leading academic institutions in the United States. “

Screen shot 2014-07-01 at 06.01PM, Jul 01Americans Think We Have the World’s Best Colleges. We Don’t. – Kevin Carey – New York Times

“We see K-12 schools and colleges differently because we’re looking at two different yardsticks: the academic performance of the whole population of students in one case, the research performance of a small number of institutions in the other.”

Dr. Bik’s picks

Screen shot 2014-07-01 at 06.23PM, Jul 01Herbivore diet breadth mediates the cascading effects of carnivores in food webs – Michael S. Singer – PNAS

“Accounting for phylogenetic nonindependence of herbivores and plants, we show for the first time (to our knowledge) that dietary specialization of herbivore species is associated with reduced bird predation across an herbivore phylogeny, and that dietary specialization of herbivores increases the antipredator effects of camouflage and aposematism.”

Screen shot 2014-07-01 at 06.23PM, Jul 01 1Evolution of the ribosome at atomic resolution – Anton S. Petrov – PNAS

“Comparing eukaryotic and prokaryotic ribosomes allows us to identify 3D insertion fingerprints of the expansion segments. Similar fingerprints allow us to analyze the common core and detect ancestral expansion segments within it. “

Plastic mapPlastic debris in the open ocean – Andrés Cózar – PNAS

“In this work, we synthetize data collected across the world to provide a global map and a first-order approximation of the magnitude of the plastic pollution in surface waters of the open ocean.”

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Non-human microbiome, June 30

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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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