Microbiome digest, October 22, 2014

Microbes in the mouth of patients with heart disease, bile and gall bladder microbiome of pigs, precisely restoring resistance to Clostridium difficile infection, and networks between fungi and plants. And don’t forget the solar eclipse tomorrow PM for most of the US.

Human oral microbiome

Microbial Diversity Similarities in Periodontal Pockets and Atheromatous Plaques of Cardiovascular Disease Patients – Wagner Serra e Silva Filho – PLOS ONE

“Subgingival biofilm and coronary balloons used in percutaneous transluminal coronary angioplasty were collected from 18 subjects presenting with generalized moderate to severe periodontitis and OCAA. DNA was extracted and the gene 16S was amplified, cloned and sequenced.”

Human gut microbiome

Dietary Patterns Differently Associate with Inflammation and Gut Microbiota in Overweight and Obese Subjects – Ling Chun Kong – PLOS ONE

“We aimed to characterize dietary patterns in overweight and obese subjects and evaluate the different dietary patterns in relation to metabolic and inflammatory variables as well as gut microbiota.”

Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men – Anne Salonen – ISME Journal

“Here we report a comprehensive and deep microbiota analysis of 14 obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSPs) and a weight-loss (WL) diet.”

Animal models of microbiome research

* Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

“..we determine that Clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium, is associated with resistance to C. difficile infection and, upon administration, enhances resistance to infection in a secondary bile acid dependent fashion.”

* Changes in the Bacterial Microbiota in Gut, Blood, and Lungs following Acute LPS Instillation into Mice Lungs – Marc A. Sze – PLOS ONE

“Bacterial microbiota of the bronchoalveolar lavage fluid, blood, and cecum were determined using 454 pyrotag sequencing and quantitative polymerase chain reaction (qPCR) at 4 through 168 hours post-instillation.”

Specific Microbiome Changes in a Mouse Model of Parenteral Nutrition Associated Liver Injury and Intestinal Inflammation – J. Kirk Harris – PLOS ONE

“Microbiome analysis in the PNALI mouse identified specific alterations within colonic microbiota associated with PNALI and further association of these communities with the lipid composition of the PN solution. “

Animal microbiome

Characterization of the bile and gall bladder microbiota of healthy pigs – Esther Jiménez – Microbiology Open

“We have studied, by culture-dependent techniques and a 16S rRNA gene-based analysis, the microbiota present in the bile, gall bladder mucus, and biopsies of healthy sows”

Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia – Petra Videnska – PLOS ONE

“In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. “

Plant microbiome

* Assembly of complex plant–fungus networks – Hirokazu Toju – Nature Communications

“The examined symbiotic network of a temperate forest in Japan includes 33 plant species and 387 functionally and phylogenetically diverse fungal taxa, and the overall network architecture differs fundamentally from that of other ecological networks. “

Soils and sediments

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 (MetalEurop: 3218 mg Zn kg−1; 913 mg Pb kg−1) were compared by shotgun metaproteogenomics. “

Bioinformatics / metabolomics

* Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment – A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses – Diogo M. O. Ogawa – PLOS ONE

“We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. “

Estimating coverage in metagenomic data sets and why it matters – Luis M Rodriguez-R and Konstantinos T Konstantinidis – ISME Journal

“We demonstrate here how available solutions can determine the level of sequencing coverage obtained by metagenomic data sets and thus, guide their robust analysis and comparison.”

Immunology

* Fall issue of Stanford Medicine reports on the immune system’s balancing act

“If you want to understand the human immune system, try studying humans — not mice, urges Mark Davis, PhD, in a special report on the immune system in the new issue of Stanford Medicine magazine.”

Bik’s Picks

Genome sequence of a 45,000-year-old modern human from western Siberia – Qiaomei Fu – Nature

“the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. “

Sky spectacle: Partial solar eclipse coming Thursday – USA Today

“In the afternoon, a partial solar eclipse — where the moon covers a part of the sun — will be visible across much of the USA, barring any pesky clouds that could block the show.”

Go Giants! The Science of Baseball – Exploratorium

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Microbiome digest, October 8, 2014

Blogging from our yearly retreat in Santa Cruz, California: Rethinking Enterotypes, Wolbachia phylogenomics,  hydrothermal vents, and the influence of salamanders on soil microbiome.

Human Microbiome General

Genes & cells: Body microbes make useful molecules: Human microbiome produces thousands of drug candidates – Tina Hesman Saey – Science News

Human Gut Microbiome

Rethinking “Enterotypes” – Dan Knights – Cell Host and Microbe

“However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.”

Fecal Bacterial Community Changes Associated with Isoflavone Metabolites in Postmenopausal Women after Soy Bar Consumption – Cindy H. Nakatsu – PLOS ONE

“Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. “

Insect microbiome

Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic – Michael Gerth  – Nature Communications

“Here we present the first comprehensive phylogenomic analysis of Wolbachia supergroup relationships based on new whole-genome-shotgun data.”

Coral microbiome

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean – Christina A. Kellogg – PLOS ONE

“Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. “

Soil Microbiome

Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska – Luis N. Morgado – Global Change Biology

“We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra.”

A metagenomics-based approach to the top-down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest – Donald M. Walker – Ecology and Evolution

“From each sample, DNA was extracted, fungal-specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU).”

Water microbiome

Evolutionary Strategies of Viruses, Bacteria and Archaea in Hydrothermal Vent Ecosystems Revealed through Metagenomics – Rika E Anderson – PLOS ONE

“Here, we explore the evolutionary strategies of both microorganisms and viruses in hydrothermal systems through comparative analysis of a cellular and viral metagenome, “

Metabolomics

Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine – Brianna B. Williams – -Cell Host and Microbe

“Using a combination of genetics, biochemistry, and crystallography, we identify and characterize two phylogenetically distinct enzymes found in the human microbiome that decarboxylate tryptophan to form the β-arylamine neurotransmitter

Techniques

Selective Microbial Genomic DNA Isolation Using Restriction Endonucleases – Helen E. Barnes – PLOS ONE

“Using synthetic genome mixtures, we demonstrate 80% recovery of Escherichia coli genomic DNA even when only femtogram quantities are spiked into 10 µg of human DNA background.”

 More Microbiology

Pseudomonas aeruginosa eradicates Staphylococcus aureus by manipulating the host immunity – Erwan Pernet – Nature Communications

“Our results indicate that a bacterium can eradicate another bacterium by manipulating the host immunity.”

Preparation and evaluation of low-calorie functional ice cream containing inulin, lactulose and Bifidobacterium lactis  – Majid Hashemi- International Journal of Dairy Technology

“This study was aimed to investigate the effects of replacing 5% fat and sugar by inulin and lactulose, respectively, on the survival of Bifidobacterium lactis and physicochemical and sensorial characteristics of the ice cream. “

Microbes in the News

Second Genome, Mayo Clinic team up to explore the microbiome – Stephanie M. Lee – SF Gate

“Second Genome will identify up to eight conditions in which the microbiome potentially plays a role, and the Mayo Clinic will provide human clinical samples for patients with those diseases.”

 Oral health affects overall health – PhillyTrib

“The evidence shows that an infection from periodontitis, or gum disease, can put you at risk for other serious conditions like heart disease, stroke and more.”

Safety Bees: Bacteria From Bees Used To Fight Infections – The Ledger

 “A group of 13 lactic-acid bacteria found in fresh honey from the honey stomach of bees could be the key to bringing an old folk remedy into modern science”

Bik’s Picks  

How dinosaurs divided their meals at the Jurassic dinner table – Science Daily

“How the largest animals to have ever walked on Earth fed, and how this allowed them to live alongside one another in prehistoric ecosystems, is the subject of new research.”

Imitation, Genetic Lineages, and Time Influenced the Morphological Evolution of the Violin – Daniel H. Chitwood – PLOS ONE

“Here, I provide an analysis of morphological evolution in the violin family, sampling the body shapes of over 9,000 instruments over 400 years of history.”

Cat Watch 2014: What’s it like being a cat? – BBC

“Cats are at a crucial point in their evolutionary journey as they transform from solitary hunters to domestic pets, a study by the BBC and the Royal Veterinary College has revealed.”
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Animal microbiome digest, September 16, 2014

Microbiomes of baby elephants, baby macaques, cows, mice, honey bees, oysters, Panama forest trees, yoghurt, air, beer, and clothes. We also learn that oregano has no effect on piglet microbiome. Just in case you wondered.

Mammal microbiome

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes – Nele Ilmberger – PLOS ONE

“A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal.”

Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems – Amir Ardeshir – Science Translational Medicine

“We show that breast-fed and bottle-fed infant rhesus macaques develop markedly different immune systems, which remain different 6 months after weaning when the animals begin receiving identical diets.”

Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil – Sharon Ann Huws – Microbial Biotechnology

“Microbiome pyrosequences showed that 50% of the bacterial genera were core to all diets (found at least once under each dietary intervention)”

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification – Parmar N.R. – Journal of Molecular Microbiology and Biotechnology

“Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing.”

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).”

The Use of Restriction Fragment Length Polymorphism and Fluorescence in Situ Hybridization to Investigate Microbiota of Piglets after Feeding Oregano – Katrin Stelter – Food and Nutrition Sciences

“The results showed no significant changes in microbiota in response to oregano. “

Insect microbiome

Buzz off, that’s my bee! – Gemma Langridge – Nature Reviews Microbiology

“These newly sequenced bee gut symbionts have revealed multiple genes that are candidates for determining host specificity. “

Hidden Diversity in Honey Bee Gut Symbionts Detected by Single-Cell Genomics – Philipp Engel – PLOS Genetics

“In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. “

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing – Ailin Wang – PLOS ONE

“We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax.”

Invertebrate microbiome

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection – Ana Lokmer and Karl Mathias Wegner – ISME Journal

“We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. “

Plant microbiome

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest – Steven W. Kembel – PNAS

“In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. “

Litter decomposition and soil microbial community composition in three Korean pine (Pinus koraiensis) forests along an altitudinal gradient – Yong Zhou – Plant and Soil

“Single- and mixed-species litter decomposition rates were determined by the litterbag method and soil microbial community composition was characterized by PLFAs.”

Soil microbiome

Pyrosequencing assessment of rhizosphere fungal communities from a soybean field – Akifumi Sugiyama – Canadian Journal of Microbiology

“This study utilized 454 pyrosequencing to analyze rhizosphere fungal communities during soybean growth.”

Water microbiome

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years – Jacob A Cram – ISME Journal

“Biodiversity appeared to be driven partially by exchange of microbes between depths and was highest when communities were changing slowly over time.”

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – Martin Eriksson – PeerJ PrePrints

“Pollution-Induced Community Tolerance (PICT) was observed for algae and cyanobacteria at 100 nM TCS and higher.”

Review: Master recyclers: features and functions of bacteria associated with phytoplankton blooms – Alison Buchan – Nature Reviews Microbiology

“In this Review, we discuss the central role that these bacteria have in transforming phytoplankton-derived organic matter and thus in biogeochemical nutrient cycling.”

Built environment microbiome

Diversity and dynamics of the indoor air microbiome in an urban subway network – Marcus H. Y. Leung – Applied and Environmental Microbiology

“Targeting the 16S rDNA V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those seen associated on skin.”

Microbial Odor Profile of Polyester and cotton clothes after a fitness session – Chris Callewaert – Applied and Environmental Microbiology

“A dissimilar bacterial growth was found in cotton versus synthetic clothing textiles. Micrococci were isolated in almost all synthetic shirts and were detected almost solely on synthetic shirts by means of DGGE fingerprinting. “

Food microbiology

Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling’? – Gabriele Berg – Microbial Biotechnology

“Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. “

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

“The bacterial and fungal community diversity of 22 home-made yoghurt samples from Zhaosu and Tekesi counties of Xinjiang in China were analyzed with pyrosequencing. “

Victory, life-sciences firm team up to detect bacteria that can spoil beer’s taste – Diane Mastrull – Philly.com

“The list is long of the perfect accompaniments to beer: hot dogs, pizza, peanuts, and pretzels, to name just a few. Most definitely not on that list: pediococcus and lactobacillus. Consider them beer buzzkills.”

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Human microbiome digest, September 16, 2014

Still catching up after my vacation, but almost there!

Some general microbiome reviews, using saliva to track human evolution, probiotics that actually change the microbiome, and several animal model studies.

 

General microbiome reviews

Which is more important for classifying microbial communities: who’s there or what they can do? – Zhenjiang Xu – ISME Journal

“… might we not instead expect that function would be substantially more important for classifying biologically meaningful groups of samples than who is providing those functions? “

Microbiome analysis – from technical advances to biological relevance – Michelle I. Smith – F1000Prime Reports

“Here, we introduce techniques that go beyond identifying the taxa present within a sample and examine the biological function of the microbiome or the host-microbiome interaction.”

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity – Melania E. Cristescu – Trends in Ecology & Evolution

“DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. “

Human oral microbiome

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies – Karsten Henne – BMC Evolutionary Biology

“By focussing on the house-keeping gene gdh .., on the virulence gene gtf .. of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations.’

Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis – M. N. Zakaria – International Endodontic Journal

“Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. “

The Adenoid Microbiome in Recurrent Acute Otitis Media and Obstructive Sleep Apnea – Carolyn P. Ojano-Dirain – Otolaryngology – Head and Neck Surgery

“Microbes are present on all adenoid specimens, however, the microbial profile differs between recurrent AOM and OSA.”

Human gut microbiome

Susceptibility to Campylobacter Infection Is Associated with the Species Composition of the Human Fecal Microbiota – Johan Dicksved – mBio

“Here we address this by prospectively studying the gut microbiota composition before, during, and after natural Campylobacter infection in exposed poultry abattoir workers.”

Eukaryote Culturomics of the Gut Reveals New Species – Nina Gouba, Didier Raoult, Michel Drancourt – PLOS ONE

“We further explored this repertoire using PCR-sequencing and culture in seven individuals living in four tropical countries. A total of 41 microeukaryotes including 38 different fungal species and three protists were detected. “

Review: Decade in review—gut microbiota: The gut microbiota era marches on – Francisco Guarner – Nature Reviews Gastroenterology & Hepatology

“Research on the gut microbial communities harboured in the human gut is progressing rapidly owing to the availability of novel and reliable tools for analysis.”

Modulation of Fecal Clostridiales Bacteria and Butyrate by Probiotic Intervention with Lactobacillus paracasei DG Varies among Healthy Adults – Chiara Ferrario – Journal of Nutrition

“High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota in healthy adults (23–55 y old) of both sexes, before and after 4 wk of daily consumption of a capsule containing at least 24 billion viable Lactobacillus paracasei DG cells”

Review: The gut microbiota, bacterial metabolites and colorectal cancer – Petra Louis, Georgina L. Hold & Harry J. Flint – Nature Reviews Microbiology

“In this Review, we discuss the relationship between diet, microbial metabolism and CRC and argue that the cumulative effects of microbial metabolites should be considered in order to better predict and prevent cancer progression.”

Changes of the human gut microbiome induced by a fermented milk product – Patrick Veiga – Nature Scientific Reports

“Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.”

Gut Microbiome and Multiple Sclerosis – Pavan Bhargava, Ellen M. Mowry – Current Neurology and Neuroscience Reports

“We examine the different sources of information linking the gut microbiota to multiple sclerosis and examine the future avenues for utilizing the knowledge of the gut microbiome to potentially treat and prevent multiple sclerosis.”

Microbial Modulation of Insulin Sensitivity – Muhammad Tanweer Khan, Max Nieuwdorp, Fredrik Bäckhed – Cell Metabolism

“The gut microbiota has emerged as an integral factor that impacts host metabolism and has been suggested to play a vital role in metabolic diseases such as obesity, insulin resistance, type 2 diabetes, and cardiovascular disease.”

Gut Microbial Community Structure and Complications After Kidney Transplantation: A Pilot Study – Lee, John R – Transplantation

“We characterized bacterial composition by polymerase chain reaction amplification of the 16S rRNA V4-V5 variable region and deep sequencing using the Illumina MiSeq platform.’

Human genital microbiome

Association between cigarette smoking and the vaginal microbiota: a pilot study – Rebecca M Brotman – BMC Infectious Diseases

“Smokers had a lower proportion of vaginal Lactobacillus spp. compared to non-smokers.”

Pregnancy and birth

Human Breast Milk – The Magic In The Microbiome – Science20

“Ma et al (2014 submitted manuscript) recently postulated that the opportunistic pathogen such as Staphylococcus aureus, which has been confirmed to exist in the human milk microbiome, is normally suppressed by a network of beneficial bacteria coexisted in the breast milk microbiome, but may become source of infectious mastitis when the host environment permits.”

Animal models of human microbiome research

Antibiotic Treatment of Pregnant Non-Obese Diabetic Mice Leads to Altered Gut Microbiota and Intestinal Immunological Changes in the Offspring – N. Tormo-Badia – Scandinavian Journal of Immunology

“we found a differential clustering of gut microbiota in the offspring from NOD mothers treated with antibiotics during gestation compared with offspring from control mothers.”

Shifts in microbiota species and fermentation products in a dietary model enriched in fat and sucrose – U. Etxeberria – Beneficial Microbes

“The aim of the present study was to identify gut microbiota dysbiosis and associated metabolic changes produced in male Wistar rats fed a HFS diet for 6 weeks and compare it with the basal microbial composition.”

The short chain fatty acids, butyrate and propionate, have differential effects on the motility of the guinea pig colon – Norm R. Hurst – Neurogastroenterology & Motility

“We hypothesized that the effect of SCFAs on colonic motility varies with chain length and aimed to determine the effects of SCFAs on propagating and non-propagating contractions of guinea pig proximal and distal colon.”

Small Bowel Resection Induces Long-Term Changes in the Enteric Microbiota of Mice – J. Sommovilla – Journal of Gastrointestinal Surgery

Bowel resection induces long-term changes in the microbial community of the murine ileum, but not at more distal sites of the gastrointestinal tract. “

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Microbiome Digest, August 22, 2014

The microbiome of the human eye,  chronic lung diseases, ticks, trout, the air in wineries, and Bik’s Picks. Have a good weekend!
Pregnancy and birth

The human microbiome and the great obstetrical syndromes, a new frontier in maternal fetal medicine – Ido Solt – Best Practice & Research Clinical Obstetrics & Gynaecology

“The transmission of maternal microbiomes to the neonate, according to vaginal delivery or cesarean section, is shown to affect health from birth to adulthood.”

Human skin microbiome

Considerations in Understanding the Ocular Surface Microbiome – Michael E. Zegans – American Journal of Ophthalmology

“In ophthalmology, the question naturally arises as to whether or not the ocular surface, like other mucous membrane surfaces, has a resident microbiota, and, if so, what role it plays in ocular surface physiology. This question has provoked much debate over many years. “

Human respiratory microbiome
* The role of the microbiome in exacerbations of chronic lung diseases – Robert P Dickson – The Lancet

“We propose that exacerbations are occasions of respiratory tract dysbiosis—a disorder of the respiratory tract microbial ecosystem with negative effects on host biology.”

Human gut microbiome

* Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates – Erica D. Sonnenburg, Justin L. Sonnenburg – Cell Metabolism

“The low-MAC Western diet results in poor production of gut microbiota-generated short-chain fatty acids (SCFAs), which attenuate inflammation through a variety of mechanisms in mouse models. “

Human vaginal microbiome

Rectal Lactobacillus Species and Their Influence on the Vaginal Microflora: A Model of Male-to-Female Transsexual Women – Ljubomir Petricevic – The Journal of Sexual Medicine

“We undertook this observational study to characterize the Lactobacillus species present in the neovagina and rectum of male-to-female transsexual women and to determine the degree of neovaginal-rectal co-colonization in order to gain a better understanding of the potential role of the gut as a reservoir for genital lactobacilli.”

Animal models of microbiome research

Perinatal antibiotic-induced shifts in gut microbiota have differential effects on inflammatory lung diseases – Shannon L. Russell – Journal of Allergy and Clinical Immunology

“Disease severity was assessed by measuring lung inflammation, pathology, cytokine responses, and serum antibodies. Microbial community analyses were performed on stool samples via 16S ribosomal RNA pyrosequencing and correlations between disease severity and specific bacterial taxa were identified.”

Animal microbiome

The composition and transmission of microbiome in hard tick, Ixodes persulcatus, during blood meal – Xue-Chao Zhang – Ticks and Tick-borne Diseases

“By 16S rRNA Illumina sequencing, we investigated the microbiome of I. persulcatus and assessed the variation of the microbiome before and after blood feeding.”

Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss) – Hans-Christian Ingerslev – Fish & Shellfish Immunology

“This study investigated the influence of the rainbow trout (Oncorhynchus mykiss) commensal intestinal microbiota in connection to an experimental Yersina ruckeri infection, the causative agent of enteric redmouth disease.”

Food microbiology

* Microbial communities in air and wine of a winery at two consecutive vintages – Fátima Pérez-Martín – International Journal of Food Microbiology

“The microbial composition was determined by using both a culture-dependent method and a culture-independent method, PCR-denaturing gradient gel electrophoresis (PCR-DGGE).”

Metabolomics

* Microbial catabolism of procyanidins by human gut microbiota – Keqin Ou – Molecular Nutrition & Food Research

“The objective of this study was to identify and quantify the microbial metabolites of procyanidins after anaerobic fermentation with human microbiota.”

Bioinformatics

* Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model – Andries J. van Tonder – PLOS Computational Biology

“The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. “

* Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads – Rogan Carr, Elhanan Borenstein – PLOS ONE

“Overall, our findings provide a first comprehensive evaluation of the capabilities and limitations of functional metagenomic annotation, providing crucial goal-specific best-practice guidelines to inform future metagenomic research.”

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era
Andre J. Aberer – Molecular Biology and Evolution

“We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on datasets of arbitrary size.”

Microbes in the news

Behold 50 shades of Gross: A guide to Germaphobia! – Katherine Dahlhausen – MicroBEnet

“So logically, I began researching germaphobic practices. Some of them are just too good not to share! “

California Trees Nailed As The Source Of Mystery Infections – Nancy Shute – NPR

“”We had a good idea that the fungus was going to be associated with trees,” says Deborah Springer, a postdoctoral fellow at Duke University who studies C. gatti. “

Bik’s Picks

Pulling teeth from history: DNA from ancient teeth can help to yield information about our ancestors’ health, diet and diseases – Philip Hunter – EMBO Reports

“Teeth have proven to be an excellence source of ancient DNA. New analytical tools are helping to exploit this treasure trove to address questions about the link between diet and health, and the impact of historical epidemics with clear relevance for human health today.”

Ten Simple Rules of Live Tweeting at Scientific Conferences – Sean Ekins, Ethan O. Perlstein – PLOS Computational Biology

“Increasingly, some scientists are using Twitter as a vehicle to summarize presentations and posters at conferences in real time, which is defined as “live tweeting.””

Why the World Smells Different After It Rains – Behold, the wonders of petrichor.
Megan Garber – The Atlantic

In the video above, PBS’s Joe Hanson describes the biology that leads to petrichor.”

Scientist Mistakenly Does “Dry-Ice Bucket Challenge” – The Allium

Sad news has come to us today at The Allium, when we learned that scientist Dr. Liv Good, has mistakenly carried out a Dry-Ice Bucket challenge.”

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Microbiome digest, August 21, 2014

Ground squirrels, scallops, hypersaline water, and dead bodies.

Postmortem human microbiome

* Microbial communities associated with human decomposition and their potential use as postmortem clocks – Sheree J. Finley – International Journal of Legal Medicine

“the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.”

* Effects of Season and Host Physiological State on the Diversity, Density, and Activity of the Arctic Ground Squirrel Cecal Microbiota – Timothy J Stevenson – Applied and Environmental Microbiology

“We examined the seasonal changes of the cecal microbiota of captive arctic ground squirrels (Urocitellus parryii) by measuring microbial diversity and composition, total bacterial density and viability, and short-chain fatty acid concentrations at four sample periods (summer, torpor, interbout arousal, and posthibernation).”

Invertebrate microbiome

* IMMR abstract: Analysis of the scallop microbiota by means of 16S rRNA gene pyrosequencing – Aide Lasa – Frontiers in Microbiology

“In this study, we present the analysis of the microbiota associated to reared scallop gonads before and after spawning by pyrosequencing of the 16S rRNA gene. “

Soil microbiome

Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons – Viviane D. Rodrigues – Antonie van Leeuwenhoek

“In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. “

* Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil – Yao Pan – FEMS Microbiology Ecology

“Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. “

Water microbiome

The Santa Pola saltern as a model for studying the microbiota of hypersaline environments – Antonio Ventosa – Extremophiles

“Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. “

Food microbiology

Book: Microorganisms and Fermentation of Traditional Foods – Ramesh C. Ray, Montet Didier – CRC Press

Fungi

Reconstruction of the original mycoflora in pelleted feed by PCR-SSCP and qPCR – Samart Dorn-In – FEMS Microbiology Letters

“A fungal-specific primer pair ITS1/ITS5.8R was used to amplify fungal DNA; PCR products were processed for the PCR-SSCP method. In the resulting acrylamide gel, more than 85% of DNA bands of ground feeds were preserved after pelleting. “

 

From Dandruff to Deep-Sea Vents: Malassezia-like Fungi Are Ecologically Hyper-diverse – Anthony Amend – PLOS Pathogens

“As the dominant component of the mycobiota on human skin —both healthy and diseased [2] —the genus Malassezia has received a fair amount of attention. “

Microbes in the news

The Birth of Pathogens: How Bacteria Become Deadly – Brian Stallard – Nature World News

“Two new studies have revealed two very different ways bothersome bacteria strains can suddenly become deadly, evolving into difficult-to-rid pathogens that can threaten entire populations.” – belongs to a PNAS paper on Salmonella enterica, and a Nature Communications paper on Group B Streptococcus.

Bacteria colonies removed from Savannah River Site using special vacuum – Meg Mirshak – The Augusta Chronicle

“Scientists studied samples and determined the white, stringy “cobwebs” were made up of a broad variety of bacteria and a few types of microbes.”

ASU experts follow gut reaction in autism treatment study – Arizona State University

“A new study approved by the U.S. Food and Drug Administration and led by Arizona State University will examine a novel treatment – called fecal microbiota transplant (FMT) – for GI problems in children with autism.”

Science and career

Ailing academia needs culture change – Viviane Callier, Nathan L. Vanderford – Science

“The research enterprise has become unsustainable in its current form. Research funding levels/mechanisms, the peer-review process, and the methods of training Ph.D.’s are flawed, and these issues are crippling the pipeline of future, successful academic researchers”

Science Media Beset with Gender Gaps – By Curtis Brainard – Scientific American

“One antidote, summit participants suggested, would be having more reporters abide by the seven-part Finkbeiner Test”

Bik’s Picks

* Why does asparagus make our urine smell? – Claudia Hammond – BBC Future

“After eating asparagus, some people can detect a strange smell, while others claim not to notice a thing. What’s going on?”

Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery – Danielle L. Dixson – Science

“We show that juveniles of both corals and fishes are repelled by chemical cues from fished, seaweed-dominated reefs but attracted to cues from coral-dominated areas where fishing is prohibited. “

Scientists discover how lizards regrow tails – John von Radowitz – The Independent

“Researchers have identified a genetic programme that triggers new tissue growth after a lizard sacrifices its tail to escape a predator.”

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Microbiome digest, August 18, 2014

Mushroom microbiome, mice fed T7 phages, and uBiome got some money.

Plant microbiome

Comparative analysis of bacterial diversity and communities inhabiting the fairy ring of Tricholoma matsutake by barcoded pyrosequencing – M. Kim – Journal of Applied Microbiology

“The bacterial communities in soil samples collected from inside, beneath and outside the T. matsutake fairy ring were investigated using barcoded pyrosequencing. “

Rhizospheric fungal community structure of a Bt brinjal and a near isogenic variety – A.K. Singh – Journal of Applied Microbiology

“..this study concludes that genetic modification of brinjal crop has minor effect on the fungal community.”

Phages and viruses

Observation of inflammatory responses in mice orally fed with bacteriophage T7 – K. Park – Journal of Applied Microbiology

“A histopathological analysis of tissue samples from the stomach, small intestine and colon revealed no significant pathological change.”

Microbes in the news

GW High students to name bacterium – Maria Hernandez – Pacific Sunday News

“Students from George Washington High School got the opportunity to name a bacterium that was discovered during a historic underwater expedition to the Mariana Trench, which was led by filmmaker James Cameron in 2012.”

uBiome Raises $4.5M From Angel Investors, Andreessen Horowitz To Crowdsource Microbiome Research – Julian Chokkattu – Techcrunch

“uBiome also has the largest private dataset of human microbiome samples in the world, giving participants a quick way to compare what’s in their microbiome to a large group.”

Bik’s Picks

All Things Considered podcast (3 min): Often On The Move, Restless Elephants Are Tough To Count — And Keep Safe – Gregory Warner – NPR

The reason elephants are so hard to protect is the same that makes them so hard to count: They roam — exceptionally far.”

Mapping Cell Fate Conversion via CellNet, a Network Biology Tool – Kevin Mayer – GenEngNews

“The differentiation of engineered stem cells may be imagined as a subway journey, where the genetic equivalents of missing a transfer or getting off at the wrong stop can take your stem cells far off course.”

Camouflage sheet inspired by octopus – Jonathan Webb – BBC Science

“Based on the camouflage abilities of octopuses and cuttlefish, engineers in the US have built a flexible material that changes colour to match its surroundings.”

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Microbiome digest, August 17, 2014

Childhood undernutrition and the gut microbiome, hibernating ground squirrels, Sphagnum, nematodes, and forensic discrimination of soils.

Human gut microbiome

An evolving perspective about the origins of childhood undernutrition and nutritional interventions that includes the gut microbiome – Tahmeed Ahmed – Annals of the New York Academy of Sciences

“This paper summarizes work on mechanisms underlying the varied manifestations of childhood undernutrition and discusses current gaps in knowledge and challenges to our understanding of undernutrition and infection/immunity throughout the human life cycle, focusing on early childhood growth. ”

Animal microbiome

Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defense in the gut of 13-lined ground squirrels – Kimberly A. Dill-McFarland – Molecular Ecology

“We used 16S rRNA pyrosequencing and cecal tissue protein analysis to investigate the effects of hibernation on the mucosa-associated bacterial microbiota and host responses in 13-lined ground squirrels.”

Diversity of Bacteria Carried by Pinewood Nematode in USA and Phylogenetic Comparison with Isolates from Other Countries – Diogo Neves Proença – PLOS ONE

“The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. “

Plant microbiome

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions – Anastasia Bragina – Molecular Ecology

“We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation.”

Soil microbiome

Random Whole Metagenomic Sequencing for Forensic Discrimination of Soils – Anastasia S. Khodakova – PLOS ONE

“Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles”

Microbial Community Structure of Relict Niter-Beds Previously Used for Saltpeter Production – Takashi Narihiro – PLOS ONE

“In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). “

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda? – Peter O Alele – PLOS ONE

“Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. “

Soil-Borne Microbial Functional Structure across Different Land Uses – Eiko E. Kuramae – The Scientific World Journal

“In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio.”

Water microbiome

Temperature response of denitrification and anammox rates and microbial community structure in Arctic fjord sediments – Andy Canion – Environmental Microbiology

“Community structure in intact sediments and slurry incubations was determined using Illumina MiSeq SSU rRNA gene sequencing.”

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems – Marianne Simon – Environmental Microbiology

“We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm-size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France.”

Metagenomics

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” – Brian P. Hedlund- Extremophiles

“Unraveling the mysteries of these candidate phyla is a grand challenge in microbiology and is especially important in habitats where they are abundant, including some extreme environments and low-energy ecosystems.”

Metabolomics

Metabolic Modelling of Spatial Heterogeneity of Biofilms in Microbial Fuel Cells Reveals Substrate Limitations in Electrical Current Generation – Nadeera Jayasinghe – Biotechnology Journal

“The goal of this work is to develop a model that integrates genome-scale metabolic models with the model of biofilm environment. “

Bioinformatics

Rarefaction and extrapolation of phylogenetic diversity – Anne Chao – Methods in Ecology and Evolution

“We develop in this paper the “PD accumulation curve” (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness.”

Microbes in the news

Can’t Stick to That Diet? Blame Your Gut Bacteria – Nolan Feeney – Time

“The gut microbiome, the collection of all the microbes in our digestive tracts, may influence our food choices and behavior, suggests a new study that recently appeared in the journal BioEssays.”

How Clean Is Your Produce? Testing Fruit For Bacteria – WFMyNews2.com

“Ellis took samples of the fruits one by one and placed the samples on a petri dish. She then washed some of the lettuce and repeated the testing procedure on both the head of lettuce and the pre-washed bag of lettuce, in 72-hours the results were in.”

Bik’s Picks

9/11 dust cloud may have caused widespread pregnancy issues – ScienceDaily

“Pregnant women living near the World Trade Center during the 9/11 attacks experienced negative birth outcomes, according to a new paper.”

Volunteers on the scent of science with whale carcass – Peter Fimrite – SF Gate

“If there’s anything as enjoyable to Dan Sudran as sawing through the stinking blubber of a whale carcass and extracting bones from the gooey tissues, it would be showing the results to children.”

Alaska’s Shrinking Glaciers Seen from Space – Kelly Dickerson – LiveScience

“Compared with a vintage satellite photo of the region, an image taken from space last year reveals just how much the glaciers have shrunk over the past 26 years.”

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Non-human microbiome, August 14, 2014

Microbial diversity in lichen, rhizosphere microbiome, and a trip to the bottom of the “seaquence”.

Plant microbiome

Algal and Fungal Diversity in Antarctic Lichens – Chae Haeng Park – Journal of Eukaryotic Microbiology

“In the current study, we analyzed algal and lichen-associated fungal community structure in lichen species from King George Island, Antarctica by pyrosequencing of eukaryotic LSU and algal ITS domains of the nuclear rRNA gene.”

Nitrogen-transforming archaea and bacteria in tropical soils are affected under transgenic as compared to non-transgenic maize – Simone Raposo Cotta – Applied and Environmental Microbiology

“The data show that significant changes occurred in the abundances (revealed by qPCR) of ammonia-oxidizing bacterial and archaeal communities as a result of the maize host being genetically-modified.”

Soil microbiome

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site
Shinjini Mukherjee – ISME Journal

“Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. “

Water microbiome

Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria – Barbara Klippel – Extremophiles

“Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes.”

Voyage to the bottom of the ‘seaquence’ – Rachael Wash & Carmen Diaz Soria – Nature Reviews Microbiology

“This month’s Genome Watch highlights the use of deep sequencing metagenomics to identify bacteriophages that carry sulphur-oxidizing genes in deep-sea hydrothermal vent plumes.”

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Non-human microbiome, August 5, 2014

Microbiome papers on giraffes, sheeps, sponges and corals, soybean, soil, seawater, and fungi found in vacuum cleaner dust.

Mammal microbiome

The giraffe (Giraffa camelopardalis) rumen microbiome – Michael Roggenbuck, Cathrine Sauer, Morten Poulsen, Mads F. Bertelsen, Søren Johannes Sørensen – FEMS Microbiology Ecology

“Here we investigated the microbial community of 7 wild-caught giraffes (Giraffa camelopardalis), 3 of which were fed natural browse and 4 were fed Boskos pellets, leafy alfalfa hay and cut savanna browse, by characterizing the 16S rRNA gene diversity using 454 FLX high throughput sequencing. “

Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep – Sandra Kittelmann – PLOS ONE

“Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields”

Invertebrate microbiome

Host-specific microbial communities in three sympatric North Sea sponges – Mohd Azrul Naim, Jose A. Morillo, Søren J. Sørensen, Waleed Abu Al-Soud, Hauke Smidt and Detmer Sipkema – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments.”

Host-specific microbial communities in three sympatric North Sea sponges– Mohd Azrul Naim – FEMS Microbiology Ecology

“In this study we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. “

Disturbance to conserved bacterial communities in the cold water gorgonian coral Eunicella verrucosa – Emma Ransome – FEMS Microbial Ecology

“The bacterial communities associated with healthy and diseased colonies of the cold water gorgonian coral Eunicella verrucosa at three sites off the south-west coast of England were compared using denaturing gradient gel electrophoresis (DGGE) and clone libraries. “

Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia – Dawoon Jung – FEMS Microbial Ecology

“The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment. “

Plant microbiome

Comparison of the Rhizosphere Bacterial Communities of Zigongdongdou Soybean and a High-Methionine Transgenic Line of This Cultivar – Jingang Liang – PLOS ONE

“Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved.”

Soil microbiome

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance – Leise Riber, Pernille Hasse Busk Poulsen, Waleed Abu Al-Soud, Lea Benedicte Skov Hansen, Lasse Bergmark, Asker Brejnrod, Anders Norman, Lars Hestbjerg Hansen, Jakob Magid andSøren Johannes Sørensen – FEMS Microbiology Immunology

“Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil-bacterial community structure was investigated using 16S-rRNA amplicon pyrosequencing.”

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing – Yongcui Deng – PLOS ONE

“Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. “

Seawater microbiome

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes – Alyse K. Hawley, Heather M. Brewer, Angela D. Norbeck, Ljiljana Paša-Tolić, and Steven J. Hallam – PNAS USA

“Here we use metagenomic and metaproteomic methods to chart in situ metabolic networks linking key microbial players driving carbon and nutrient cycling in a seasonally stratified fjord, Saanich Inlet”

Sequencing on the Seven Seas – Rina Shaikh-Lesko – The Scientist

“Researchers have installed an advanced genomics lab facility aboard a boat to create a floating molecular testing facility for marine life sciences”

Microbiome of the Built Environment

Characterization of Fungal Communities in House Dust Samples Collected From Central Portugal—A Preliminary Survey – Ana C.A. Sousa – Journal of Toxicology and Environmental Health

“A total of 28 samples were obtained from vacuum cleaner deposits from households located in central Portugal. DNA was extracted from dust samples and fungal communities were analyzed using a culture-independent polymerase chain reaction (PCR)– denaturing gradient gel electrophoresis (DGGE) approach. “

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