Microbiome Digest, November 4, 2014

Tomorrow, Wednesday November 5, at 1:00pm USA-EST : Upcoming AMA (Ask Me Anything) in reddit/r/science: “Microbiota of the human gut” with my co-worker Les Dethlefsen. Ask him anything! You can submit questions, vote for the best questions, and the top questions will be answered by Les.

Human gut microbiome

* Rapid changes in the gut microbiome during human evolution – Andrew H. Moeller – PNAS USA

“To establish how the gut microbiome has changed since the diversification of human and ape species, we characterized the microbial assemblages residing within hundreds of wild chimpanzees, bonobos, and gorillas.”

and: Human Gut Bacteria Much Different Than Apes – Science 2.0

* Blastocystis Is Associated with Decrease of Fecal Microbiota Protective Bacteria: Comparative Analysis between Patients with Irritable Bowel Syndrome and Control Subjects – Céline Nourrisson – PLOS ONE

“Here, we first compared the prevalence of Blastocystis among 56 IBS patients (40 IBS with constipation (IBS-C), 9 IBS with diarrhea (IBS-D), 4 mixed IBS (IBS-M) and 3 unsubtyped IBS (IBS-U) according to the Rome III criteria) and 56 control (i.e. without any diagnosed chronic or acute gastrointestinal disorder) subjects. “

Animal models of microbiome research

* Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis – Stacey L. Burgess – mBio

“In studies utilizing a murine model, we demonstrated that colonization of the gut with the commensal Clostridia-related bacteria known as segmented filamentous bacteria (SFB) is protective during E. histolytica infection.”

Animal microbiome

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis – Ren-Mao Tian – mBio

“16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. “

Bioinformatics tools

Massive fungal biodiversity data re-annotation with multi-level clustering – Duong Vu – Scientific Reports

“An implementation of the algorithm allowed clustering of all 344,239 ITS (Internal Transcribed Spacer) fungal sequences from GenBank”

Viruses and phages

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification – Adriana Calderaro – Scientific Reports

“The results revealed MALDI-TOF MS to be an effective and inexpensive tool for the identification of the three poliovirus serotypes. “

More microbiology

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbial Ecology

“About 25% of the bacterial isolates contained virulence gene homologues representing toxin (hblA, cytK2), adhesin (fimH), regulator (phoQ) and resistance (yfbI) determinants in pathogenic bacteria.”

Science, publishing, and career

* Don’t Worry Your Pretty Little Heads – Rebecca Schuman – Slate

“I don’t understand how they wrote the paper or the op-ed they did while looking at the same results I see in their paper. … Where I come from,” she concludes, “we call that institutional bias.”

Bik’s Picks

Birds found using human musical scales for the first time – Virginia Morell – Science Blog

“The flutelike songs of the male hermit thrush (Catharus guttatus) are some of the most beautiful in the animal kingdom.”

Vaccine-resistant polio strain discovered – Science Daily

“The DNA sequence shows two mutations, unknown until now, of the proteins that form the “shell” (capsid) of the virus.”

The appliance of science: home experiments with your kids – Louise Holden – Irish Times

“Next week is Science Week, and one of the messages that McCarthy is hoping to put out there is that science is for everybody, not just those hoping to work in the sector. Helping your child to become science-literate is a great gift.”

The top 20 catchiest songs of all time, according to science – Michelle Starr – CNET

“A year-long survey by the Museum of Science and Industry in Manchester has revealed the top 10 most persistent earworms — with the Spice Girls topping the list.”

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Microbiome digest, November 3, 2014

Human oral and vaginal microbiomes, rumen microbiome of impalas, sample handling and sponges, and two remarkable pieces in the New York Times.

Human oral microbiome

The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China – Guoqin Yu – BMC Public Health

“Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. “

Pregnancy and birth microbiome

Poster: Comparison of the Vaginal Microbiomes of Pregnant Women of Four Ethnicities
and Identification of Taxa Associated with Urogenital Disease – Mendz GL – ECCMID Poster

“Principal component analysis suggested differences in the bacterial populations of healthy women and those with genital infections, with clustering of the latter along the Protobacteria axis “

Animal microbiome

Examination of the Rumen Bacteria and Methanogenic Archaea of Wild Impalas (Aepyceros melampus melampus) from Pongola, South Africa – Laura M. Cersosimo – Microbial Ecology

“In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas”

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges – Cristiane C. Hardoim – Frontiers in Microbiology

Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. “

Plant microbiome

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

“16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. “

Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis? – David M Wilkinson – Mycology: An International Journal on Fungal Biology

“In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis.”

Soil microbiome

Selection on soil microbiomes reveals reproducible impacts on plant function – Kevin Panke-Buisse – ISME Journal

“Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment.”

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA – Magdalena R. Osburn – Frontiers in Microbiology

“Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment.”

Bioinformatic tools

* Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities – Noah Fierer – Frontiers in Microbiology

“Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated.”

Metabolomics

Fructan supplementation of senior cats affects stool metabolite concentrations and fecal microbiota concentrations, but not nitrogen partitioning in excreta – K.A. Barry – Journal of Animal Science

“Fructan supplementation may benefit senior cats as it modulates stool odor-forming compounds and decreases some protein catabolites and pathogenic gut microbiota concentrations without affecting N retention.”

Proteomics

From the Banfield lab: Development of an enhanced metaproteomic approach for deepening the microbiome characterization in the human infant gut – Weili Xiong – Journal of Proteome Research

“….we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. “

More microbiology

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases – A.-S. Morel – European Journal of Clinical Microbiology & Infectious Diseases

“Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.”

Microbes in the news

There Is No ‘Healthy’ Microbiome – Ed Yong – New York Times

“The microbiome is complex, varied, ever changing and context-dependent — qualities that are the enemies of easy categorization.”

Study: Ice Man has traces of bacteria that undermined his health – BetaWired

“…they found evidence of the presence of Treponema denticola, an opportunistic pathogen implicated in the development of periodontal diseases. “

Science, publishing, and career

How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions – Chandana Jasti – The American Biology Teacher

“In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models.”

2014 Life Sciences Salary Survey – Jyoti Madhusoodanan – The Scientist

“This year’s data reveal notable variation in compensation for life scientists working in different fields, sectors, and regions of the world.”

Academic Science Isn’t Sexist – Wendy M. Williams and Stephen J. Ceci – New York Times

Our analyses show that women can and do prosper in math-based fields of science, if they choose to enter these fields in the first place.”

and two rebuttals:
Academic science is sexist: We do have a problem here – Emily Willingham
The flawed and offensive logic of “Academic Science Isn’t Sexist” in the @nytimes – Jonathan Eisen – The Tree of Life

Bik’s Picks

Standing time and all-cause mortality in a large cohort of Australian adults – Hidde P. van der Ploeg – Preventive Medicine

“Increasing standing may hold promise for alleviating the health risks of prolonged sitting.”

A Face to Remember – Kerry Grens – The Scientist

“Once dominated by correlational studies, face-perception research is moving into the realm of experimentation—and gaining tremendous insight.”

* With a very cute picture: Rovers Disguised as Baby Penguins Can Quietly Infiltrate Penguin Colonies – Rachel Nuwer – Smithsonian

“Pursuing this hunch, they outfitted the rover with a big ball of fluff and a little penguin head and arms. ”

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General microbiology and science digest, October 28, 2014

Viruses in humans and caribous, metabolomics of losing weight, and microbes on rough surfaces.
Metabolomics

Impact of a 6-week very low-calorie diet and weight reduction on the serum and fecal metabolome of overweight subjects – Mette S. Schmedes – European Food Research and Technology

“NMR-based metabolomics was carried out on serum and fecal samples obtained from healthy female subjects pre- and post-weight reduction. “

Book with lots of plagiarized text (in at least 3 chapters), so not worth the $25 for the physical book, or even the free download:
Metabonomics and Gut Microbiota in Nutrition and Disease – Springer Link

Metagenomics

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – PeerJ Preprints

“Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. “

Viruses and phages

Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources – Michael J. Strong, Zhen Lin, Erik K. Flemington – mBio

“We thank Ladner and colleagues for their conversation about standardizing viral genome sequences derived from high-throughput (HT) sequencing technology.”

Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice – Robert H. Yolken – PNAS USA

“Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. “

* Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch – Terry Fei Fan Ng – PNAS USA

“Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. “

Microbial Ecology

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces – Gang Wang, Dani Or – Scientific Reports

“A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields.”

Scaling laws governing stochastic growth and division of single bacterial cells – Srividya Iyer-Biswas – PNAS USA

“Now, by using a unique combination of measurement and analysis technologies, together with mathematical modeling, we discover quantitative features that are conserved across physiological conditions. “

Microbes in the news

Gut feelings – Microbiome and mental health – Fabio Piccini – Wall Street International

“Might people suffering from certain forms of mental health problems benefit from a fecal transplant from someone with more happy-go-lucky bacteria? “

Small Things Considered: Bacteria Allow Woodrats to Eat Poison – Anne A. Madden – ASM blog

“Despite such dire consequences, woodrats ingest enough of these plant toxins to kill a lab rat. Every day. But the desert is not littered with woodrat corpses, so clearly they are able to detoxify this poisonous salad somehow. “

Saving The Bees Using Microscopic Bugs – RedOrbit

“Phages are the most abundant life form on the planet and each phage has a unique bacteria that it will attack,” said Sandra Burnett, BYU professor of microbiology and molecular biology. “This makes phage an ideal treatment for bacterial disease because it can target specific bacteria while leaving all other cells alone.”

Science, publishing, and career

Reputation and impact in academic careers – Alexander Michael Petersen – PNAS USA

“Here, we develop a framework for quantifying the influence author reputation has on a publication’s future impact.”

NPRs All Things Considered (Podcast, 5 min): Is ‘Leaning In’ The Only Formula For Women’s Success In Science? – Kelly McEvers – NPR

“Don’t wait to be invited or encouraged to make a career in science, engineering or technology, Frances Arnold advises the young women she teaches at the California Institute of Technology. “

Bik’s Picks

Doctors Making Housecalls: Better, Cheaper Care at Home? – Jennifer Ferris – MedPageToday

“In a little over a decade the practice has exploded in popularity — with Taavoni and more than 40 other providers in North Carolina innovating new ways to bring healthcare home.”

Oil platforms off California are among the most productive marine fish habitats globally –
Jeremy T. Claisse – PNAS USA

“Here, we find that fish communities living on the complex hardscape habitat created throughout the water column by the structure of oil and gas platforms off California have the highest secondary production per unit area of seafloor of any marine ecosystem for which similar estimates exist.”

Can Science Perfect Food? – Daniela Galarza – Eater.com

“A research team in Japan is blowing past molecular gastronomy to discover new ways of perfecting already flawless dishes.”

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Microbiome Digest, October 9, 2014

Human microbiome general

Advancing the Microbiome Research Community – Curtis Huttenhower – Cell

“We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. “

Human oral microbiome

Bioinformatic investigation of the cost management strategies of five oral microbes – K.J. Cross – Molecular Oral Microbiology

“The aim of this study was to investigate if five oral bacterial species implement cost management strategies to reduce the energy burden of extracellular unrecyclable proteins.”

Human skin microbiome

Identification of molecular mechanisms used by Finegoldia magna to penetrate and colonize human skin – Elizabeth C. Murphy – Molecular Microbiology

“This study examines the molecular mechanisms F. magna uses when colonizing or establishing an infection in the skin. “

Human gut microbiome

Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders – N Tennoune – Translational Psychiatry

“Here, using proteomics, we identified ClpB heat-shock disaggregation chaperone protein of commensal gut bacteria Escherichia coli as a conformational antigen mimetic of α-MSH.”

Animal models of microbiome research

Effects of essential oil supplementation of a low-energy diet on performance, intestinal morphology and microflora, immune properties and antioxidant activities in weaned pigs – Zhikai Zeng – Animal Science Journal

Soil microbiome

Poster presentation: Starting study of microbial genetics diversity in soils of mangrove preserved in sergipe – Karla Cristina Santos Freire – BMC Proceedings

“This paper proposes the characterization and evaluation of structures and diversity of microbial communities in the soil of mangroves in three conservation areas located in Sergipe.“

Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession – Cheng Gao – New Phytologist

“We examined the communities of ectomycorrhizal (EM) fungi in young, intermediate and old forests in a Chinese subtropical ecosystem, using 454 pyrosequencing”

Metagenomics / Bioinformatics

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam – Juanjuan Chai – BMC Evolutionary Biology

“A total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accurate comparison. “

More Microbiology

Halting harmful helminths – Karl F. Hoffmann, Paul J. Brindley, Matthew Berriman – Science

“More than 300 million people are infected each year with parasitic flatworms such as hydatid tapeworms and blood fluke schistosomes. “

Chromosome position effects on gene expression in Escherichia coli K-12 – Jack A. Bryant – Nucleic Acids Research

“Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. “

Microbes in the news

‘Good Poop’ Diet Is the Next Big Thing – Daniela Drake – The Daily Beast

“Now a new book, The Skinny Gut Diet, by nutritionist Brenda Watson, tracks the progress of people who follow a diet specifically designed to alter the gut microbiome. “

Another probiotic advantage: Bacteria protects against heavy metal poisoning – Jim Algar – Tech Times

“Probiotic bacteria found in yogurt can protect people from the effects of exposure to heavy metals, particularly in pregnant women and children, a Canadian study suggests.”

Science, publishing, career

The scientists who get credit for peer review – Richard Van Noorden – Nature

“Publons rewards researchers for putting their peer-review activity online. Nature spoke to the startup’s co-founder and two super-users.”

Meet the New Underclass: People With Ph.D.s in Science – Mark Strauss – iO9

“Once upon a time, newly-minted science Ph.D.s would get research jobs at a senior scientist’s laboratory, to train and hone the ideas they would explore at their own labs. But now the supply of post-doctoral students is outpacing demand, creating a new, hyper-educated underclass.”

Glut of postdoc researchers stirs quiet crisis in science –  Carolyn Y. Johnson – Boston Globe

Japan’s Missing Female Scientists – Jack Grove – Times Higher Education

“Too many female scientists are leaving Japan because they do not feel they can get ahead in its “male-dominated” society, a senior university leader has said.”

Bik’s Picks

Cave paintings change ideas about the origin of art – Pallab Ghosh – BBC

“Researchers tell the journal Nature that the Indonesian discovery transforms ideas about how humans first developed the ability to produce art.”

A timeline of a baby’s first hour – Laura Sanders – Science News

Fired science teacher did not have state license – 9 News

“The teacher fired after his science experiment injured four students, one seriously, did not have a valid Colorado teacher’s license.”

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Microbiome Digest, October 3, 2014

Antibiotics in the first 24 months of life associated with obesity, Giant Pandas are no cul-de-sac, and microbiome and inflammatory disease. And lots of weekend reads!

Pregnancy and birth

Association of Antibiotics in Infancy With Early Childhood Obesity – L. Charles Bailey – JAMA Pediatrics

“Cumulative exposure to antibiotics was associated with later obesity …; this effect was stronger for broad-spectrum antibiotics”

Human gut microbiome

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome – Jonna Jalanka-Tuovinen – Gut

“Using a phylogenetic microarray and selected qPCR assays, we analysed differences in the faecal microbiota of 57 subjects from five study groups”

Animal models of microbiome research

Dietary modulation of the microbiome affects autoinflammatory disease – John R. Lukens – Nature

“Here we show that the intestinal microbiota of diseased Pstpip2cmo mice was characterized by an outgrowth of Prevotella. “

Mammal microbiome

Giant pandas are not an evolutionary cul-de-sac: Evidence from multidisciplinary research
Fuwen Wei – Molecular Biology and Evolution

“The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological and genetic adaptations and co-adaptation of gut microbiota.”

Plant microbiome

Multi-symbiotic systems: functional implications of the coexistence of grass–endophyte and legume–rhizobia symbioses – Pablo A. García Parisi – Oikos

“After five months, we quantified the number of nodules in Trifolium roots, shoot biomass of both plant species, and the contribution of atmospheric nitrogen fixation vs. soil nitrogen uptake to above ground nitrogen in each plant species. “

Microbes in the news

Young companies, big ideas – The 2014 edition of the CNN 10: Startups – CNN

“Her doubts were assuaged when supporters donated $350,000 to help launch her startup, uBiome. Now, two years later, uBiome is exploring an emerging field of human biology while giving users a glimpse into how their bodies work.”

No women, unfortunately! And they did not accept my application to be a judge either. MO BIO Laboratories, Inc. announces Microbiome Awards winners – PR NewsWire

“MO BIO Laboratories, Inc. is proud to announce the winners of the MO BIO Microbiome Awards, which provide young, extraordinary scientists with funding and recognition to carry out scientific work in the field of microbiome research.”

Super-bacteria are growing in space … and we’re the ones breeding them – Meera Senthilingam – CNN

“You might think of space as a germ-free environment, but microbes can be carried to space inside human gut flora as well as in food and water and once up there, can be expelled by humans in their breath.”

There’s a simple way to stop the spread of antibiotic-resistant bacteria – Melinda Mary Pettigrew – Washington Post

“The issue boils down to this: we use too many antibiotics. Studies show that up to half of all antibiotics are prescribed unnecessarily.”

Across Indian zoos, rat pee spreading bacteria, killing big cats: Scientists – Priyangi Agarwal – The Times of India

“The leptospirosis bacteria, found in rodent urine, makes its way into blood samples of zoo animals and causes higher morbidity and mortality, scientists at the Indian Veterinary Research Institute (IVRI) in Bareilly have found. “

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever. The hope is they will multiply, breed and become the majority of mosquitoes, thus reducing cases of the disease.“

Science, Publishing, and Career

Young, Brilliant and Underfunded – Andy Harris – New York Times

“The bulk of that money goes to researchers who are in many cases esteemed in their fields — but also, in many cases, beyond the age when most scientists make their most important contributions to their fields.”

Why women leave tech: It’s the culture, not because ‘math is hard’ – Kieran Snyder – Fortune

“Stories from 716 women who left tech show that the industry’s culture is the primary culprit, not any issues related to science education.”

Satire: Tips For Working With A Lab Partner – FakeScience

Bik’s Picks

Is this the end of autumn as we know it? – Stephanie Pappas – BBC Earth

“The study of the basic triggers of autumnal leaf changes, never mind the impact of climate change on these, is still in its infancy in part because scientists have traditionally focused their attentions on the seasonal changes in March and April than those later in the year.”

The Incredible Rubber Glove – Olga Khazan – The Atlantic

“Basic protective gear was revolutionary for 19th-century medicine, and health workers trying to stop Ebola are recognizing its importance all over again.”

This Is Why Your Voice Sounds So Frickin’ Weird To You – Macrina Cooper-White – The Huffington Post

“Have you ever listened to a recording of your own voice and thought, “Whoa. Do I really sound like that?” Well, it’s time to face the music. You really do.”

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General microbiology and science digest, October 2, 2014

Viruses and metagenomics, the soil of Central Park, and sweat eating bacteria.

Ecology

Loops and autonomy promote evolvability of ecosystem networks – Jianxi Luo – Scientific Reports

“To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. “

Erosion of functional independence early in the evolution of a microbial mutualism
Kristina L. Hillesland – PNAS USA

“We show that as the bacterium Desulfovibrio vulgaris evolved for 1,000 generations in conditions forcing cooperation with the archaeon Methanococcus maripaludis, it lost a key metabolic trait that would be required for it to grow alone in most environments.”

Tree diversity does not always improve resistance of forest ecosystems to drought – Charlotte Grossiord – PNAS USA

“Within our study network of 160 forest stands across Europe, we found that mixed species forests are less exposed to drought stress in some regions only. “

Phages, viruses, and metagenomics

Dynamics of CRISPR Loci in Microevolutionary Process of Yersinia pestis Strains – Maria Paloma S. Barros – PLOS ONE

“This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. “

Metagenomic approaches for direct and cell culture evaluation of the virological quality of wastewater – Tiong Gim Aw – Journal of Virological Methods

“In this study, NGS and bioinformatics have been employed for the direct detection and characterization of viruses in wastewater and of viruses isolated after cell culture. “

Metagenomics / Bioinformatics

Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage, Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages – Hui-Qi Zhou – PLOS ONE

“The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. “

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets
Seyhan Yazar – PLOS ONE

“We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets”

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation – Brejnev Muhizi Muhire – PLOS ONE

“Here we present Sequence Demarcation Tool (SDT), …that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences.”

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes – Naruekamol Pookhao – Bioinformatics

“We propose a two-stage statistical procedure for selecting informative features and identifying differentially abundant features between two or more groups of microbial communities.”

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus – Emmanuel Prestat – Nucleic Acids Research

“A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. “

Microbes in the News

Soil Microbiome of Central Park – Jef Akst – The Scientist

“The soil of New York City’s Central Park is bursting with biodiversity spanning all three domains of life, according to a study published today”

Supporting the “Good” Gut Microbes – Anna Azvolinksy – The Scientist

“During systemic infection, mice kick-start the production of a specific sugar to feed and protect the beneficial bacteria in their guts while fighting pathogenic strains.”

Sweat-Eating Bacteria: Acne Miracle Cure? – Discovery News

“A new, small study has shown that applying a topical creme containing the bacteria leads to healthier skin and could be used to treat acne and promote healing in wounds.”

Women in Science

* Sexism in Science – sbhatnagar3 – Phylogenomics Blogspot

“Please don’t treat these seminars as a fashion show. It distracts the people away from your work”.”

Bik’s Picks

Behavior of bats at wind turbines – Paul. M. Cryan – PNAS USA

“Bats are dying in unprecedented numbers at wind turbines, but causes of their susceptibility are unknown. “

Flexible energetics of cheetah hunting strategies provide resistance against kleptoparasitism – David M. Scantlebury – Science

“We show that daily energy expenditure (DEE) of cheetahs was similar to size-based predictions and positively related to distance traveled.”

Previously unseen details of seafloor exposed in new map – Science Daily

“Twice as accurate as the previous version, the new map features a much more vivid picture of seafloor structures, including thousands of previously uncharted mountains.”

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Microbiome digest, September 25, 2014

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Asbestos and microbiome, human gut microbiome during a long stay in the hospital, gut microbiome of 15 mammals, Wolbachia in insects, microbiome of plant roots, and eukaryotes in Norwegian waters.

Human respiratory microbiome

Airways microbiota: Hidden Trojan horses in asbestos exposed individuals? – Dimitrios E. Magouliotis – Medical Hypotheses

“Here, we propose and discuss that certain proteins secreted by airways symbiotic microbiota create membrane pores to the airway epithelial cells, through which asbestos fibers can penetrate the lung parenchyma and reach the sub-pleural areas.”

Human gut microbiome

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness – Alexander Zaborin – mBio

“We analyzed the 16S rRNA amplicon composition in fecal samples of selected patients during their prolonged stay in an intensive care unit (ICU) and observed the emergence of ultra-low-diversity communities (1 to 4 bacterial taxa) in 30% of the patients.”

Mammal microbiome

Convergence of gut microbiomes in myrmecophagous mammals – Frederic Delsuc – Molecular Ecology

“Here, we expand upon previous mammalian gut microbiome studies … to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples.

Insect microbiome

Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains – Julien Martinez – PLOS Pathogens

“We have investigated antiviral protection in 19 Wolbachia strains originating from 16 Drosophila species after transfer into the same genotype of Drosophila simulans. “

Plant microbiome

Niche and host-associated functional signatures of the root surface microbiome – Maya Ofek-Lalzar – Nature Communications

“Metagenomic (genetic potential) analysis identifies a core set of functional genes associated with root colonization in both plant hosts, and metatranscriptomic (functional expression) analysis revealed that most genes enriched in the root zones are expressed. “

Water microbiome

Deep-branching Novel Lineages and High Diversity of Haptophytes in the Skagerrak (Norway) Uncovered by 454 Pyrosequencing – Elianne S. Egge – Journal of Eukaryotic Microbiology

“Nano- and picoplanktonic subsurface samples were collected monthly for 2 yr, and the haptophytes were targeted by amplification of RNA/cDNA with Haptophyta-specific 18S ribosomal DNA V4 primers. “

Microbes in the news

Intensive Loss of Gut Bacteria Diversity – Molly Sharlach – The Scientist

In a study published today (September 23) in mBio, researchers also fed ICU patients’ “ultra-low-diversity” gut microbes to C. elegans roundworms.

How Termites Evolved to Decompose Plant Matter: Gut Bacteria and Fungus – Catherine Griffin – Science World Report

“In order to better understand this interaction, the researchers analyzed plant decomposition genes in the first genome sequencing of a fungus-farming termite and its fungal crop, and bacterial gut communities.”

Science and Career

Scientists Are Not Trusted By Americans – Here’s Why – Science 2.0

“A paper in PNAS finds that Americans seem wary of researchers because they get grant funding and do not trust scientists pushing political and cultural agendas. “

Read The Nasty Comments Women In Science Deal With Daily – Macrina Cooper-White – Huffington Post

“Every day you’re faced with some comment, some snide remark, some inability to get a name on a research paper. “

Bik’s Picks

Water on Earth is older than the sun, scientists say – Deborah Netburn – Los Angeles Times

“Some of the water molecules in your drinking glass were created more than 4.5 billion years ago, according to new research.”

Science Graphic of the Week: Three Ways to Visualize Our Melting Northern Ice Cap – Nick Stockton – Wired.com

“These three visualizations, by NASA’s Scientific Visualization Studio, illustrate this steadily unfolding situation, which has nightmarish implications..“

Healthy food might be bad for patients – here’s why – Amanda Squire – The Conversation

“The truth is that healthy food as we think of it may not be what patients really need.”

Brazil releases ‘good’ mosquitoes to fight dengue fever – BBC News

“Brazilian researchers in Rio de Janeiro have released thousands of mosquitoes infected with bacteria that suppress dengue fever.”

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