Author Archives: eliesbik

Microbiome digest, October 10, 2014

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A quiet day in microbiome literature. Some general microbiome reviews, a phage commonly found in insect symbionts, and an unusual fecal transplant.

General microbiome

Viruses and the Microbiota – Christopher M. Robinson and Julie K. Pfeiffer – Annual Review of Virology

“This review examines the known effects and mechanisms by which microbiota influence mammalian virus infections.”

Review: The Microbiota, Chemical Symbiosis, and Human Disease – Matthew R. Redinbo – Journal of Molecular Biology

“Here, the recent literature linking the microbiota to diseases of three of the key mammalian mucosal epithelial compartments – nasal, lung and gastrointestinal (GI) tract – is reviewed with a focus on new knowledge about the taxa, species, proteins and chemistry that promote health and impact progression toward disease.”

Human gut microbiome

Alien Invasions and Gut “Island Biogeography” – Edward F. DeLong – Cell

“Now, Seedorf et al. show that microbiota from a variety of disparate habitats can successfully colonize and compete in the mammalian gut environment.”

Review: The small intestine microbiota, nutritional modulation and relevance for health – Sahar El Aidy – Current Opinion in Biotechnology (April 2015 issue!)

“This review highlights the recent advances made in the study of the human small intestine microbiota”

The Opposing Forces of the Intestinal Microbiome and the Emerging Pathobiome – Jennifer Defazio – Surgical Clinics of North America

Insect microbiome

Arsenophonus insect symbionts are commonly infected with APSE, a bacteriophage involved in protective symbiosis – Olivier Duron – FEMS Microbiology Ecology

“APSE was found in association with two-thirds of the Arsenophonus strains examined and from a variety of insect groups such as aphids, white flies, parasitoid wasps, triatomine bugs, louse flies, and bat flies.”

Microbes in the news

Beyond the call: Scientist self-administers fecal transplant in search for healthy microbiome – Helen Clark – GizMag

“Jeff Leach’s first-person narrative bookends a fascinating discussion on the changing nature of gut bacteria in many Western societies”

Dr. Raphael Kellman’s Microbiome Diet – Faith Middleton, Lori Mack, Jonathan McNicol – WNPR News

“Repair and boost the bacteria in the gut with the right food, prebiotics and probiotics, and you’ll feel better and lose weight. That’s the theory of Dr. Raphael Kellman of New York, author of The Microbiome Diet.”

The Mad Science Behind OMSI’s Greatest Exhibits – Nathan Tucker

“During my visit, the primary focus is on the shop’s next big traveling exhibition, an NSF-funded exploration of the human microbiome called The Zoo in You. “

Study Shows Rebiotix Microbiota-based Drug Candidate Targeted at Recurrent C. difficile Infection is Highly Effective – PR Newswire – SysCon

“Results for groundbreaking multi-center study of lead drug candidate RBX2660 (microbiota suspension) presented at IDWeek 2014”

Bik’s Picks

Gross! Or is it? University pushes peeing in the shower to save water – Megan Holohan – Today

“The campaign, aptly titled “Go with the Flow,” claims that if every student peed in the shower once daily, the university would save about $230,000 a year on water.”

‘Giant leap’ to type 1 diabetes cure – James Gallagher – BBC News Healthy

“A team at Harvard University used stem cells to produce hundreds of millions of the cells in the laboratory.”

Want to stay thin? Strap ice packs around body – Kounteya Sinha – Times of India

“Exposure to cold temperatures can convert white fat tissue from the thighs and belly to beige fat that burns calories for heat.“

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Microbiome Digest, October 9, 2014

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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 8, 2014

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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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General microbiology and science digest, October 7, 2014

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Transmission of Staph aureus in the hospital, a new assembler tool, metabolomics of the human gut microbiome, and a polio virus spill in Belgium.

More Microbes

Absence of Patient-to-Patient Intrahospital Transmission of Staphylococcus aureus as Determined by Whole-Genome Sequencing – S. Wesley Long – mBio

“To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. “

Bioinformatics

Improved Assemblies Using a Source-Agnostic Pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of Contigs – Matthew Scholz, Chien-Chi Lo & Patrick S. G. Chain – Nature Scientific Reports

“MeGAMerge consistently outperforms individual assembly methods, producing larger contigs with an increased number of predicted genes, without replication of data. “

Inferring phylogenies of evolving sequences without multiple sequence alignment – Cheong Xin Chan – Nature Scientific Reports

“Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. “

Gut Check: Exploring Your Microbiome – Coursera / University of Colorado Boulder

“Join us on a guided tour of the human gut and its microscopic inhabitants.”

Metabolomics

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Microbes in the news

* Petri Dish: The third branch of life – David Woodland – Summit Daily

“In addition to being an interesting branch on the tree of life, archaebacteria have turned out to be an incredibly valuable source of new products for science and industry. “

Pharmaceutical Giant GlaxoSmithKline “Accidentally” Released 45 Liters of Concentrated Live Polio Virus in the Environment – Global Research

“As reported to ECDC by Belgian authorities, on 2 September 2014, following a human error, 45 litres of concentrated live polio virus solution were released into the environment by the pharmaceutical company, GlaxoSmithKline (GSK), in Rixensart city, Belgium.”

Science, publishing and career

* Science is innate! (behind a paywall, even at Stanford) – Jack A Gilbert – Genome Biology

“….when I am asked, as I often am, about how my research findings have influenced my day-to-day activities, I like to take a step back and think about what it means to be a scientist.”

Why I have taken a leave of absence from Science: to protest the abrupt firing of 4 colleagues – Michael Balter – Letter to Science

“Thus it is particularly painful and sad for me to tell you that I will be taking a three-month leave of absence in protest of recent events at Science and within its publishing organization, the American Association for the Advancement of Science (AAAS).
“

Bik’s Picks

Killer whales learn to communicate like dolphins – Science Daily

“…killer whales can engage in cross-species vocal learning: when socialized with bottlenose dolphins, they shifted the sounds they made to more closely match their social partners.”

NASA selects astrobiologists to study life origins and extraterrestrial possibilities – Jim Algar – Tech Times

“NASA announced 5-year grants adding up to nearly $50 million for seven research groups across the U .S. to study life in the universe and its origins, distribution, evolution and future.”

The most passive aggressive acknowledgement ever – BioDataGanache – SciEasterEggs

“The authors in this paper put some serious time in on this sucker, and they wanted to make a statement about it.”

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Non-human microbiome digest, October 7, 2014

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Weaning piglets, fungus-farming termites, mosquito larval stages, antibiotic resistant bacteria in soil after fertilization, and biogeography of marine microbiomes.

Mammal microbiome

Assessment of fecal bacterial diversity among healthy piglets during the weaning transition – Edward Alain B. Pajarillo – Journal of General and Applied Microbiology

“This study describes the fecal microbial shifts of healthy piglets during the weaning transition using barcoded pyrosequencing of the prokaryotic 16S rRNA gene.”

Insect microbiome

Complementary symbiont contributions to plant decomposition in a fungus-farming termite – Michael Poulsen – PNAS USA

“We analyzed the genomic potential for biomass decomposition in a farming termite, its fungal symbiont, and its bacterial gut communities. “

Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages – Geoffrey Gimonneau – Infection, Genetics and Evolution

“We characterized bacterial communities from aquatic habitats, at surface microlayer and subsurface water levels, to freshly emerge adult mosquitoes using multiplexed 16S rRNA gene pyrosequencing”

Soil microbiome

From the Handelsman lab: Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization – Nikolina Udikovic-Kolic – PNAS USA

“In this study, we found that dairy cow manure amendment enhanced the proliferation of resident antibiotic-resistant bacteria and genes encoding β-lactamases in soil even though the cows from which the manure was derived had not been treated with antibiotics. “

* Niche-Partitioning of Edaphic Microbial Communities in the Namib Desert Gravel Plain Fairy Circles – Jean-Baptiste Ramond – PLOS ONE

“T-RFLP fingerprinting of the bacterial (16S rRNA gene) and fungal (ITS region) communities, in parallel with two-way crossed ANOSIM, showed that FC communities were significantly different to those of external control vegetated soil”

Temporal Changes in Soil Bacterial Diversity and Humic Substances Degradation in Subarctic Tundra Soil – Ha Ju Park – Microbial Ecology

“Culture-independent microbial community analysis showed that during the microcosm experiments, the relative abundance of phyla Proteobacteria (bacteria) and Euryarchaeota (archaea) largely increased, indicating their involvement in HS degradation. “

Water microbiome

Distinct patterns of marine bacterial communities in the South and North Pacific Oceans – Sung-Suk Suh – Journal of Microbiology

“In this study, 16S rRNA gene tag pyrosequencing was used to investigate change in bacterial community structure between summer and winter water masses from Gosung Bay in the South Sea of Korea and Chuuk in Micronesia, located in the North and South Pacific Oceans, respectively.”

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Human microbiome digest, October 7, 2014

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Treating toxic arsenic levels with yoghurt, colonization patterns in low birthweight infants, evil alliances in breastmilk, and smoking and oral microbiome.

Human microbiome general

Opinion: Conservation and stewardship of the human microbiome – Kieran C. O’Doherty – PNAS USA

“Just as humans have impacted many large animal species in the environment, drastic changes in human lifestyle over the past century may have altered the global pool of human-associated microbes; if so, these shifts may pose substantial threats to individual and public health.”

Friends with Social Benefits: Host-Microbe Interactions as a Driver of Brain Evolution and Development? – Roman M. Stilling – Frontiers in Cellular and Infection Microbiology

“Here in this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. “

Pregnancy and birth

Intestinal Colonization Among Very Low Birth Weight Infants in First Week of Life (PDF) – Sourabh Dutta – Indian Pediatrics

“Very low birth weight infants admitted in neonatal intensive care units have abnormal intestinal colonization patterns”

Is a fetus developing in a sterile environment? – Trudy M. Wassenaar and Pinaki Panigrahi – Letters in Applied Microbiology

Probiotics and Necrotizing Enterocolitis – Josef Neu – Clinics in Perinatology (paywalled even at Stanford)

Potential involvement of Campylobacter curvus and Haemophilus parainfluenzae in preterm birth – George Louis Mendz – BMJ Case Reports

“A woman presented with prelabour premature preterm rupture of membranes and delivered extremely preterm at 26 weeks by caesarean section.”

Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities – Zhanshan Ma – arXiv

“..we reconstructed a milk bacterial community network with the data from Hunt et al (2011), which is the largest 16S-rRNA sequence data set of human milk microbiome available to date.”

Randomized Open-Label Pilot Study of the Influence of Probiotics and the Gut Microbiome on Toxic Metal Levels in Tanzanian Pregnant Women and School Children – Jordan E. Bisanz – mBio

“Consumption of probiotic yogurt had a protective effect against further increases in mercury (3.2 nmol/liter; P = 0.035) and arsenic (2.3 nmol/liter; P = 0.011) blood levels in the pregnant women, but this trend was not statistically significant in the children.”

Human oral microbiome

* Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms – Andrew Maltez Thomas – BMC Microbiology

“DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. “

* Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients – Ji-Hoi Moon – Molecular Oral Microbiology

“Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples each group, in Korean moderate chronic periodontitis patients using 16S rRNA gene-based pyrosequencing.”

Human respiratory microbiome

Sinus culture poorly predicts resident microbiota – Leah J. Hauser – International Forum of Allergy & Rhinology

“The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus – Ute Schwab – Infection and Immunity

“We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. “

Human gut microbiome

* Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity – Sophie Leclercq – PNAS USA

“In this study, we showed that alcohol-dependent subjects with altered intestinal permeability had also altered gut-microbiota composition and activity and remained with high scores of depression, anxiety, and alcohol craving after a short-term detoxification program.”

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula – Jia Xu – ISME Journal

“Pyrosequencing of the V3 regions of 16S rRNA genes revealed a dose-dependent deviation of gut microbiota in response to GQD treatment.”

Modelling the emergent dynamics and major metabolites of the human colonic microbiota – Helen Kettle – Environmental Microbiology

“To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. “

Animal models of microbiome research

Transcriptome analysis of Escherichia coli O157:H7 grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes – Guillaume Le Bihan – Microbes and Infection

“A transcriptomic analysis was performed on the EHEC strain EDL933 incubated in vitro in the sterile-filtrated cecal content of human microbiota-associated rats (HMC) compared with EDL933 incubated in the sterile-filtrated cecal content of germ-free rat (GFC).”

Early Innate Immunity to Bacterial Infection in the Lung Is Regulated Systemically by the Commensal Microbiota via Nod-Like Receptor Ligands – Thomas B. Clarke – Infection and Immunity

“Microbiota depletion caused significant defects in the early innate response to lung infection by the major human pathogen Klebsiella pneumoniae.”

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General microbiology and science digest, October 6, 2014

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Phages to reduce biofilms or monitor virus outbreaks, binning metagenomic reads, lots of microbes in the news. In Bik’s Picks, we have the 2014 Nobel Prize for Medicine and a giant ant nest.

 

More Microbes

Combined Use of Bacteriophage K and a Novel Bacteriophage To Reduce Staphylococcus aureus Biofilm Formation – D. R. Alves – Applied and Environmental Microbiology

“DRA88 was mixed with phage K to produce a high-titer mixture that showed strong lytic activity against a wide range of S. aureus isolates, including representatives of the major international MRSA clones and coagulase-negative Staphylococcus. “

Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks – Maria Hellmér – Applied and Environmental Microbiology

“ In this study, the presence of eight pathogenic viruses (norovirus, astrovirus, rotavirus, adenovirus, Aichi virus, parechovirus, hepatitis A virus [HAV], and hepatitis E virus) was investigated in sewage to explore whether their identification could be used as an early warning of outbreaks. “

Bioinformatics

New software aims to improve sorting the microbiome – The Cherry Creek News

“MaxBin automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads,” says Singer, a chemist who also holds an appointment with Berkeley Lab’s Earth Sciences Division. “

Microbes in the news

* King’s launches British Gut – King’s College London

“British Gut – the UK’s largest open-source science project to understand the microbial diversity of the human gut – has been launched today by the Department of Twin Research at King’s College London, in collaboration with American Gut.”

Pay attention to your gut bacteria – Charles Wallace – Financial Times

“A number of organisations, such as Mr Leach’s own American Gut project and the commercial venture uBiome, offer an analysis of the bacteria in your gut for about $100. “

Home sweet microbiome – By Scott LaFee – UT San Diego

“The University of Chicago recently published findings from its Home Microbiome Project, which surveyed the domiciles of seven families: 18 people, three dogs and one cat.”

Medical superbugs: Antibiotic-resistant bacteria carried by more than a third of nursing home residents, study – ABC Australia

“Scientists from Monash University swabbed more than a 100 residents from four high-care facilities across the city.”

Special bacteria, 13000 cleaners to clean Dhaka – Rezaul Hoque – BDNews

“This special kind of microorganism will be sprayed on waste dumps. The spray has been developed in Thailand. We have introduced it here in Bangladesh with the aid of a Malaysian company.””

Yogurt bacteria could replace colonoscopies for cancer detection – Billy Steele – EnGadget

“MIT professor Sangeeta Bhatia is working on engineered bacteria that detects colorectal cancer. After the nanoparticles pass through the digestive system, a urine sample shows results on a reactive paper — similar to that of a pregnancy test.”

Science and Publishing

Adjudicating “misbehavior”: how can scientists respond when they don’t get fair credit? –  Janet D. Stemwedel – Scientific American

“Denying someone of fair credit for the contribution they made to a piece of research is not a good thing. But who can you turn to if someone does it to you? “

Twitter’s science stars, the sequel – John Travis – Science

“We listed. You tweeted (often in outrage). We listened (mostly). And now we’re doubling down on our recent list of Twitter’s 50 most popular researchers with a revision that names 100 of the most followed scientists on the social media platform. “

Bik’s Picks

2014 Nobel Prize in Physiology or Medicine: Cells that constitute a positioning system in the brain – Science Daily

“The 2014 Nobel Prize in Physiology or Medicine has been awarded to John O´Keefe, May-Britt Moser and Edvard I. Moser for their discoveries of cells that constitute a positioning system in the brain.”

Concrete Cast of Ant Nest Reveals Huge Underground Metropolis – Lisa Winter – IFL Science

“Through a process that took a few months, researchers made a cast of an anthill by pumping it full of concrete, allowing it to cure and dry, then excavating it out to explore the intricacies of the ant civilization. “

Tall tale: scientists unravel the genetics of human height – Will Dunham – Daily Mail

“Researchers on Sunday unveiled what they called the biggest such study to date, analyzing genome data from more than a quarter million people to identify nearly 700 genetic variants and more than 400 genome regions relating to height.”

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Non-human microbiome digest, October 6, 2014

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

Mammal Microbiome

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

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

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

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

Avian microbiome

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

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

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

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

Insect Microbiome

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

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

Invertebrate microbiome

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

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

Plant microbiome

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

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

Soil microbiome

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

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

Water microbiome

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

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

Microbiome of the built environment

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

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

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Human microbiome digest, October 6, 2014

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Preterm birth, multiple sclerosis, aging, and Clostridium difficile infection in animal models.

Pregnancy and Birth

Necrotizing Enterocolitis: A Clinical Review on Diagnostic Biomarkers and the Role of the Intestinal Microbiota – Niemarkt, Hendrik J. – Inflammatory Bowel Diseases

“In this review, we discuss the pathogenesis, diagnosis, and treatment of NEC with a focus on the role of microbiota in the development of NEC.”

* Intestinal microbiota of preterm infants differ over time and between hospitals – Diana H Taft – Microbiome Journal

“DNA extracted from stool was used to sequence the 16S rRNA gene by Illumina MiSeq using universal primers. “

Babies’ Gut Bacteria Are Mostly Fixed By Time Spent In The Womb – Nicholas Ellaby – Science 2.0

“Now, a new study published in the journal Proceedings of the National Academy of Sciences has added a critical piece to the puzzle. “

Human Gut Microbiome

Gut microbiome and the risk factors in central nervous system autoimmunity – Javier Ochoa-Repárazemail, Lloyd H. Kasper – FEBS Letters

“Of interest to this review is the consistency between this range of MS risk factors and the gut microbiome. We postulate that the gut microbiome serves as the niche where different MS risk factors merge, thereby influencing the disease process.”

Compositional dynamics of the human intestinal microbiota with aging: Implications for health – B. Lakshminarayanan – The Journal of Nutrition, Health & Aging

“This review summarizes the age-related changes in the microbiota of the gastrointestinal tract (GIT) and the link between the gut microbiota in health and disease. “

Animal models of microbiome research

A Beneficial Effect of Oral Tigecycline Treatment on Clostridium difficile Infection in Gnotobiotic Piglets – Hyeun Bum Kim – Antimicrobial Agents and Chemotherapy

“The efficacy of oral tigecycline treatment (2mg/kg for 7 days) on Clostridium difficile infection (CDI) was evaluated in the gnotobiotic pig model, and its effect on human gut microflora transplanted into the gnotobiotic pig was determined. “

A novel multi-strain probiotic and synbiotic supplement for prevention of Clostridium difficile infection in a murine model – Kanthi Kiran Kondepudi – Microbiology and Immunology

“Feces and cecal contents were collected for microbial cell viability, quantitative PCR (qPCR), toxin analyses and histopathology.“

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Microbiome Digest, October 3, 2014

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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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