Microbiome digest, October 13, 2014

Preterm infant gut microbiome, fecal transplants, microbes in space, and microbiome of 8 different fish species.

Pregnancy and birth

* Development of the preterm infant gut microbiome: a research priority – Maureen W Groer (Jack Gilbert lab) – Microbiome

“This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant.”

Fluorescence in situ hybridization for identification of microorganisms in acute chorioamnionitis – D. Schmiedel – Clinical Microbiology and Infection

“Using a diagnostic fluorescence in situ hybridization probe panel, we visualized Staphylococcus aureus and Streptococcus mitis group in two cases of acute chorioamnionitis. “

The Role of Mycoplasma and Ureaplasma in Adverse Pregnancy Outcomes – Amy P. Murtha – Obstetrics and Gynecology Clinics of North America

* Impact Of Lifestyle On The Gut Microbiota Of Healthy Infants And Their Mothers – The Aladdin Birth Cohort – Helena Marell Hesla – FEMS Microbiology Ecology

“Samples collected from infants at ages six days, three weeks, two months and six months and from their mothers before and after delivery, respectively, were analyzed using 454-pyrosequencing.”

Human gut microbiome

* Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection – Ilan Youngster – JAMA

“Self-ranked health scores improved significantly on a scale of 1 to 10 from a median of 5  for overall health and 4.5  for gastrointestinal-specific health on the day prior to FMT to 8 after FMT administration for both overall and gastrointestinal health (P = .001).”

* Impact of Experimental Hookworm Infection on the Human Gut Microbiota – Cinzia Cantacessi – Journal of Infectious Diseases

“We used 16S rRNA gene amplification and pyrosequencing to characterize, for the first time to our knowledge, the differences in composition and relative abundance of fecal microbial communities in human subjects prior to and following experimental infection with the blood-feeding intestinal hookworm, Necator americanus. “

Genomics of schizophrenia: time to consider the gut microbiome? – T G Dinan – Molecular Psychiatry

“To date, this vast quantity of DNA has been largely ignored in schizophrenia research.”

Animal microbiome

Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits – Jinjin Li – Journal of Applied Microbiology

“The V1 to V3 regions of 16S rRNA gene were analyzed by highthroughput sequencing (454 platform) to compare the gut microbiota of different fish species. “

Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured – Richard O’Rorke – Environmental Microbiology

“we collected 102 snail fecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. “

Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus) – Amber R Paulson – BMC Microbiology

“We characterized the bacterial symbionts of Megastigmus (Hymenoptera: Torymidae), a lineage of seed-parasitic chalcid wasps, with the goal of identifying microbes that might play an important role in aiding development within seeds, including supplementing insect nutrition or manipulating host trees.“

Bioreactor microbiome

Biofouling and Microbial Communities in Membrane Distillation and Reverse Osmosis – Katherine R. Zodrow – Environmental Science & Technology

“Phylogenetic analysis using next-generation sequencing of 16S ribosomal DNA showed significant shifts in the microbial communities. “

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture – Amy A Boaro – FEMS Microbiology Ecology

“16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment.”

Environmental microbiome

Effects of Bioavailable Heavy Metal Species, Arsenic, and Acid Drainage from Mine Tailings on a Microbial Community Sampled Along a Pollution Gradient in a Freshwater Ecosystem – Togwell A. Jackson – Geomicrobiology Journal

“Ribosomal ribonucleic acid, fatty acid, and phospholipid analyses, along with assays of CO2 production, denitrification, and enzyme activities, were performed to characterise the microflora; and environmental conditions were defined by various physicochemical analyses, including determination of bioavailable metal species. “

The role of macrobiota in structuring microbial communities along rocky shores – Catherine A Pfister​, Jack A Gilbert, Sean M Gibbons – PeerJ

“At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton.”

Microbes in (simulated) space

The development and succession of microbial communities in 90-day Bioregenerative Life Support Experiment in the Lunar Palace 1 – Yi Sun – 40th COSPAR Scientific Assembly

“In this study, the development and succession of the microbial communities of air, water system, plant system, and key facilities surfaces in Lunar Palace 1 were continuously monitored and analyzed by using plate counting method and molecular biological method during the 90-day experiment.”

The viability of native microbial communities in martian environment (model) – Vorobyova, Elena – 40th COSPAR Scientific Assembly

“It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ.”

Food microbiology

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine – Joanita Sulaiman – Frontiers in Microbiology

“Whole genome shotgun (WGS) method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida.”

Transcriptomics/metagenomics

Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities – Leyden Fernandez – BMC Genomics

“We have here characterized and analyzed the metaregulome of three different environments, as well as their impact in the adaptation to particular variable physico-chemical conditions. “

Other microbiology

Inverse Correlation Between Helicobacter pylori Colonization and Obesity in a Cohort of Inner City Children – Hanh D. Vo – Helicobacter

“Our findings in a North American cohort are in agreement with studies from Asia and Europe suggesting that H. pylori infection decreases the prevalence of obesity in children.”

Microbes in the news

* Podcast: Your Home, Your Bacteria – Science Friday

“Jack Gilbert… is trying to develop a better understanding of the way people, bacteria, and the environment around them interact, from the kitchen floor to the greater Chicago area.”

Landmark Crohn’s Microbiome Study Yields Important Findings – David Wild – GastroEndoNews

“The association suggests that there is a potential link between the presence of these microbes and the serologic biomarkers, but that needs to be determined in future studies,” said Dr. Xavier, who presented the study at Digestive Disease Week 2014”

Is that how the capsules will look like? Good news: You can take your fecal transplants orally – Rachel Feltman – Washington Post

“In a study published Saturday in the Journal of the American Medical Association, researchers report that the same success rate can be reached by processing the healthy excrement into capsules and administering the pills by mouth.“

Probiotics on the brain: A growing number of scientists now believe that gut bacteria can influence mental health – Elizabeth Gehrman – Boston Globe

“Whenever someone says there’s an impossibility in medicine,” says Williams, “they end up being corrected in a few years.”

Unravelling the link between gut bacteria and horse health – University of Surrey

“Researchers at the University of Surrey, in collaboration with colleagues from Reading and Liverpool universities, have been awarded £100,000 funding by Petplan Charitable Trust… to create a laboratory model of the horse’s hindgut.”

The Second Brain: Gut Bacteria Control Human Behavior to Get the Best Nutrients – David Gutierrez – Epoch Times

“Bacteria within the gut are manipulative,” researcher Carlo Maley, PhD, said. “There is a diversity of interests represented in the microbiome, some aligned with our own dietary goals, and others not.”

Science, publishing, career

Sometimes My Job Seems Like a Secret – Amy Davidson – Speaking Of Research

“You are going to hell.” “You are a horrible person.” “We cannot be friends anymore.”

Sell yourself: Adding substance to your personal statement – Brian Rybarczyk – Science Careers at Science Magazine

“Obtaining feedback on your personal statement (or any piece of writing) can be intimidating, but feedback is essential for creating a polished and readable document.”

Bik’s Picks

Why Orange Juice Tastes Disgusting After You Brush Your Teeth: Finally, an answer – Sarah Fecht – Popular Science

“In a handy video, the American Chemical Society has explained why orange juice (and food in general) tastes like soap after you brush your teeth. “

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Non-human microbiome digest, September 29, 2014

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Microbiome of house mice, rumen, fish species in the same pond, sponges and corals, coastal sediments, and mycobacteria and amoeba in drinking water.

Mammal microbiome

Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing – Jakub Kreisinger – Molecular Ecology

“Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus)”

Study of methanogen communities associated with different rumen protozoal populations – Alejandro Belanche – FEMS Microbiology Ecology

“Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. “

Microbial profiles of liquid and solid fraction associated biomaterial in buffalo rumen fed green and dry roughage diets by tagged 16S rRNA gene pyrosequencing – K. M. Singh – Molecular Biology Reports

“The rumen bacterial composition of both liquid and solid fraction was surveyed using pyrosequencing of the 16S rRNA gene.”

Bacterial Community Composition and Fermentation Patterns in the Rumen of Sika Deer (Cervus nippon) Fed Three Different Diets – Zhipeng Li – Microbial Ecology

“The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design.”

Fish microbiome

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

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

Tending a complex microbiota requires major immune complexity – Keaton Stagaman – Molecular Ecology

“In this issue of Molecular Ecology, Bolnick et al. (2014a) sample the gut microbial community from 150 genetically diverse stickleback isolated from a single lake”

Insect microbiome

The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand – Nicola M. Reid – FEMS Microbiology Ecology

“We identified core bacterial taxa involved in gut processes through combined DNA- and RNA (cDNA)-based pyrosequencing analysis of the 16S nucleotide sequence from five S. ruficeps colonies.”

Genetic groups and endosymbiotic microbiota of the Bemisia tabaci species complex in Japanese agricultural sites – A. Fujiwara – Journal of Applied Entomology

“Use of the cleaved amplified polymorphic sequence technique and mitochondrial cytochrome oxidase subunit I gene sequencing detected five genetic groups”

Sponge and Coral microbiome

Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges – Cole G. Easson and Robert W. Thacker – Frontiers in Microbiology

“As part of the Earth Microbiome Project, we surveyed the microbiomes associated with 20 species of tropical marine sponges collected over a narrow geographic range.”

* Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora – Kimberley A. Lema – Molecular Ecology

“Using an amplicon pyrosequencing approach, the diversity of both nitrogen-fixing bacteria and of bacterial communities overall was assessed through analysis of nifH and 16S rRNA genes, respectively. “

Biogeography rather than association with cyanobacteria structures symbiotic microbial communities in the marine sponge Petrosia ficiformis  – Ilia Burgsdorf – Forntiers in Microbiology

“16S rRNA gene tag pyrosequencing data of the microbial communities revealed that Chloroflexi, Gammaproteobacteria and Acidobacteria dominated the bacterial communities of all sponges analyzed. “

Soil and sediments microbiome

Interactive effects of C, N and P fertilization on soil microbial community structure and function in an Amazonian rain forest – Nicolas Fanin – Functional Ecology

“Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. “

The long-term adaptation of bacterial communities in metal-contaminated sediments. A metaproteogenomic study – David C. Gillan – Environmental Microbiology

“Two freshwater sites, Férin and MetalEurop, differing by one order of magnitude in metal levels .. were compared by shotgun metaproteogenomics.”

Effect of plankton-derived organic matter on the microbial community of coastal marine sediments – Paula Carpintero de Moraes – Journal of Experimental Marine Biology and Ecology

“Analyses of molecular fingerprints of bacterial communities by denaturing gel gradient electrophoresis (DGGE) showed differences in bacterial community composition between both treatments and control just after algae addition. “

Rapid bacterial colonization of low-density polyethylene microplastics in coastal sediment microcosms – Jesse P Harrison – BMC Microbiology

“Sequencing of cloned 16S rRNA genes demonstrated that these communities were dominated after 14 days by the genera Arcobacter and Colwellia “

Water microbiome

Picky, hungry eaters in the cold: persistent substrate selectivity among polar pelagic microbial communities – Andrew D. Steen and Carol Arnosti – Frontiers in Microbiology

“The purpose of this study was to investigate potential factors preventing hydrolysis of pullulan in Svalbard fjord waters. “

Saltwater intrusion history shapes the response of bacterial communities upon rehydration – Tiffanie M. Nelson – Science of The Total Environment

“Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. “

Diversity of marine microbes in a changing Mediterranean Sea – Gian Marco Luna – Rendiconti Lincei

“This review aims at summarizing the knowledge on microbial diversity in the basin, by focusing on prokaryotes (bacteria and archaea) in pelagic and benthic habitats. “

First evidence of amoebae – mycobacteria association in drinking water network – Vincent Delafont – Environmental Science & Technology

“Direct Sanger sequencing as well as pyrosequencing of environmental isolates demonstrated the frequent association of mycobacteria and FLA”

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Non-human microbiome, August 26, 2014

Microbiomes of rabbits, exercising mice, fish, bees, beetles, forest soil after a hurricane (a simulated one!), water, and – why not – the whole world.

Mammal microbiome 

* Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy – Christine Bäuerl – PLOS ONE

“Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR.”

Effect of Intestinal Microbiota on Exercise Performance in Mice – Hsu, Yi-Ju – Journal of Strength & Conditioning Research

“We investigated the association of intestinal bacteria and exercise performance in specific pathogen-free (SPF), germ-free (GF), and Bacteroides fragilis (BF) gnotobiotic mice.”

Fish microbiome

Non invasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches – Taiga Asakura – PeerJPrePrints

“We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments.”

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing – Tongtong Li – Microbial Ecology

“In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. “

Insect microbiome

* Microbial Communities of Three Sympatric Australian Stingless Bee Species – Sara D. Leonhardt – PLOS ONE

“Here, we characterized the microbiota of three Australian stingless bee species (Apidae: Meliponini) of two phylogenetically distant genera (Tetragonula and Austroplebeia). “

Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis – Matteo Montagna – Insect Science

“The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs).”

Invertebrate microbiome

Antioxidant Activity of Bacteria Associated with the Marine Sponge Tedania anhelans – Dhivya Balakrishnan – Indian Journal of Microbiology

In the present study, several Bacillus sp. with just 97 % similarity with its closest match in Gen Bank were isolated, and found to show free radical scavenging activity”

Soil and sediment microbiome

Effects of a simulated hurricane disturbance on forest floor microbial communities – Sharon A. Cantrell – Forest Ecology and Management

“We studied the independent and interactive hurricane effects of canopy openness and debris deposition on the relative abundance and diversity of microorganisms in soil and leaf litter using ester link fatty acids methyl esters (EL-FAME) analysis, and terminal restriction fragment length polymorphism (TRFLP) profile.”

Spatiotemporal changes in arbuscular mycorrhizal fungal communities under different nitrogen inputs over a 5-year period in intensive agricultural ecosystems on the North China Plain – Wei Liu – FEMS Microbiology Ecology

“Terminal restriction fragment length polymorphism and clone sequencing were used to analyse the AMF community. “

A Long-Term Cultivation of an Anaerobic Methane-Oxidizing Microbial Community from Deep-Sea Methane-Seep Sediment Using a Continuous-Flow Bioreactor – Masataka Aoki – PLOS ONE

“Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor.”

Water microbiome

Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models – Sangwon Lee – PLOS ONE

“…using PhyloChip 16S-rRNA-gene targeting microarrays, we compared the compositions of sampled communities to those of inocula propagated in the laboratory in simulated wastewater conditionally amended with various carbon sources”

* Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa) – Rosine E. Tiodjio – Nature Scientific Reports

“Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. “

Comparative survey of bacterial and archaeal communities in high arsenic shallow aquifers using 454 pyrosequencing and traditional methods – Ping Li – Ecotoxicology

“A survey of bacterial and archaeal community structure was carried out in 10 shallow tube wells in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia by 16S rRNA gene based two-step nested PCR-DGGE, clone libraries and 454 pyrosequencing. “

* Biogeographic Congruency among Bacterial Communities from Terrestrial Sulfidic Springs – Brendan Headd – Frontiers in Microbiology

“Complementary Sanger sequencing and 454 pyrosequencing of 16S rRNA genes retrieved five proteobacterial classes, and Bacteroidetes, Chlorobi, Chloroflexi, and Firmicutes phyla from all springs, which suggested the potential for a core sulfidic spring microbiome. “

The whole world microbiome

* The Earth Microbiome project: successes and aspirations – Jack A Gilbert, Janet K Jansson, and Rob Knight – BMC Biology

“ ‘Knight and Gilbert literally talk about sampling the entire planet. It is ludicrous and not feasible – yet they are doing it’”

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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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Microbiome digest, August 4, 2014

Relief in a pressing problem, microbes at high altitude, and microbiome in cystic fibrosis.

Human gut microbiome

So glad this one finally came out!  Structural changes in the gut microbiome of constipated patients – Lixin Zhu – Physiological Genomics

“A cross-sectional pilot study was performed to compare stool microbial composition of 8 constipated patients and 14 non-constipated controls using 16S rRNA gene pyrosequencing.”

Microbiota and diabetes: an evolving relationship – Herbert Tilg, Alexander R Moschen – Gut

“A further hint towards an association between microbiota and T2D has been derived from studies in pregnancy showing that major gut microbial shifts occurring during pregnancy affect host metabolism.”

Harnessing the Intestinal Microbiome for Optimal Therapeutic Immunomodulation – S. Viaud – Cancer Research

“gut commensals, through lipopolysaccharide and other bacterial components, switch the tumor microenvironment, in particular the redox equilibrium and the TNF production of intratumoral myeloid cells during therapies with platinum salts or intratumoral TLR9 agonists combined with systemic anti-IL10R Ab respectively.”

Specific genetic and microbial signature associated with paediatric ileal Crohn’s disease -Isobel Leake – Nature Reviews Gastroenterology & Hepatology

“An increase in DUOX2 expression was associated with an expansion of Proteobacteria across all forms of IBD, whereas downregulation of APOA1 expression in association with depletion of certain Firmicutes and Bacteroidetes taxa was found to be specific for Crohn’s disease.”

Skin and wounds microbiome

Next-Generation Sequencing: A Review of Technologies and Tools for Wound Microbiome Research – Brendan Hodkinson and Elizabeth Grice – Advances in Wound Care

“The purpose of this review is to outline the current platforms, their applications, and the steps necessary to undertake microbiome studies using next-generation sequencing.”

Human respiratory microbiome

Directly Sampling the Lung of a Young Child with Cystic Fibrosis Reveals Diverse Microbiota – Perry S Brown – Annals ATS

“After pathologic examination verified that this child’s lung tissue reflected CF lung disease, we used bacterial rRNA gene pyrosequencing and computational phylogenetic analysis to identify the microbiota in serial sections of the tissue.”

Respiratory Viruses and Bacteria among Pilgrims during the 2013 Hajj – Samir Benkouiten – Emerging Infectious Diseases

“One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.”

Fish microbiome

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae – Christos Giatsis – PLOS ONE

“Our results showed that variation in gut microbiota between replicate tanks was not significantly higher than within tank variation, suggesting that there is no tank effect on water and gut microbiota. “

Soil microbiome

FEMS Microbiology Ecology has a special issue on Polar and Alpine Microbiology with many papers on microbiomes of ice and soil. Here is the Editorial:
Polar and alpine microbiology in a changing world – John C. Priscu – FEMS Microbiology Ecology

“By virtue of their relatively rapid growth rates and metabolic diversity, we can expect microorganisms to be the first responders to fluctuating climatic conditions.”

Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau – Jun-Tao Wang – Microbial Ecology

“Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation.”

Water microbiome

Satellite remote sensing data can be used to model marine microbial metabolite turnover – Peter E Larsen – ISME Journal

“We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters”

Microbial Ecology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function – Joseph E. Knelman and Diana R. Nemergut – Frontiers Microbiology

“Can differences in community assembly alter the relationship between biodiversity and ecosystem function?”

Probiotics

Lactobacillus rhamnosus GG suspected infection in a newborn with intrauterine growth restriction – I. Sadowska-Krawczenko – Beneficial Microbes

“Genotyping with the rep-PCR and AFLP methods confirmed the 100% genetic similarity for both the strain isolated from patient blood and the probiotic product.”

Can Eating Probiotic Yogurt Help Lower Your High Blood Pressure? – Susmita Baral – Wall St Cheat Sheet

“Now, a new study (published Monday in the journal Hypertension) has found another added benefit of probiotics — it may reduce high blood pressure.”

Microbes in the News

Your garden hose: a potential health risk due to Legionella spp. growth facilitated by free-living amoebae – Jacqueline Marie Thomas – Environmental Science & Technology

“Here we present data on FLA and Legionella spp. detected in water and biofilm of two garden hose types over 18 months. “

Truth about your toothbrush – Anne Agbaje – Bussiness Day Online

“You don’t store your plates and glasses by the toilet, so why would you want to place your toothbrush there?” McCombs says. “It’s just common sense to store your toothbrush as far away from the toilet as possible.”

Metabolomics

Fecal volatile organic compounds: a novel, cheaper method of diagnosing inflammatory bowel disease? – Chris SJ Probert – Expert Review of Clinical Immunology

“…this article will focus specifically on the fecal VOC metabolome and its potential role in identifying a novel diagnostic method for IBD.”

Review: Emerging mass spectrometry techniques for the direct analysis of microbial colonies – Jinshu Fang, Pieter C Dorrestein – Current Opinion in Microbiology

“In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies.”

Techniques

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing – Jennifer J. Mosher – Journal of Microbiological Methods

“With accurate read lengths of > 1400 base pairs, the PacBio system opens up the possibility of identifying microorganisms to the species level in environmental samples.”

 

Bik’s Picks

The Secret to a Tattoo’s Permanence: The Immune System – Olga Khazan – The Atlantic

“We rarely stop and think about the science of tattoos. In fact, some people don’t even stop and think before getting tattooed.”

 

Mathematical equation to predict happiness: Doesn’t depend on how well things go, but on whether things are better than expected – Science Daily

The happiness of over 18,000 people worldwide has been predicted by a mathematical equation, with results showing that moment-to-moment happiness reflects not just how well things are going, but whether things are going better than expected.”

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Non-human microbiome, July 29

Microbiomes of chickens with Marek’s disease, fish, fungus-growing termites, ticks, leeches, mosses, soil and acid mine drainage.

Chicken microbiome

Marek’s Disease Virus Influences the Core Gut Microbiome of the Chicken During the Early and Late Phases of Viral Replication – Sudeep Perumbakkam – FEMS Microbiology Ecology

“In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. “

Fish microbiome

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata) – Konstantinos A. Kormas – Microbiology Open

“There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. “

Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism? – Sébastien Boutin – PLOS ONE

“we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. “

Arthropod microbiome

Identifying the core microbial community in the gut of fungus-growing termites – Saria Otani – Molecular Ecology

“The objective of our study was to compare the intestinal bacterial communities of five genera (nine species) of fungus-growing termites to establish whether or not an ancestral core microbiota has been maintained and characterizes extant lineages. “

Characterization of the Bacterial Communities of Life Stages of Free Living Lone Star Ticks (Amblyomma americanum) – Amanda Jo Williams-Newkirk – PLOS ONE

“We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5–3.”

Leech microbiome

Hitchhiking of host biology by beneficial symbionts enhances transmission
Brittany M. Ott – Nature Scientific Reports

“we show that the A. veronii population within secretions originates from the host digestive tract and proliferates synchronously with shedding frequency, demonstrating the coupling of partner biology.”

Plant microbiome

Forestry impacts on the hidden fungal biodiversity associated with bryophytes – Marie L. Davey – FEMS Microbiology Ecology

“Shoots of Hylocomium splendens were collected in Picea abies dominated forests of different ages, and their associated fungal communities were surveyed by pyrosequencing of ITS2 amplicons. “

Soil microbiology

Review: Functional soil microbiome: Belowground solutions to an aboveground problem
Venkatachalam Laksmanan – Plant Physiology

“This update addresses the importance of the functional microbiome to identify phenotypes that may provide a sustainable and effective strategy to increase crop yield and food security.”

Microbial Diversity of a Mediterranean Soil and Its Changes after Biotransformed Dry Olive Residue Amendment – Jose A. Siles – PLOS ONE

“Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community.”

Water and drainage microbiome

Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and others drivers along an acid mine drainage – A. Volant – FEMS Microbiology Ecology

“biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and highthrouput sequencing.”

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