Category Archives: General Microbiome

Microbiome digest, October 24, 2014

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Microbiome of placentas, infant respiratory microbiome, metabolomics, mutipartite genomes, microbes in the news, and some weekend picks.
Human microbiome general

Microbiome/microbiota and allergies – Yuzaburo Inoue, Naoki Shimojo – Seminars in Immunopathology

“In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.”

Pregnancy and birth

Term and preterm labour are associated with distinct microbial community structures in placental membranes which are independent of mode of delivery – Ronan M. Doyle – Placenta

“In this study, 16S rDNA pyrosequencing was used to identify bacteria in placental membranes. Caesarean sections and vaginal deliveries at term were found to harbour common genera”

Early Respiratory Microbiota Composition Determines Bacterial Succession Patterns and Respiratory Health in Children – Giske Biesbroek – Am J Respir Crit Care Med.

“Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12 and 24 months were characterized by 16S-based pyrosequencing”

From the “old NEC” to the “new NECs” – Melania Puddu – Journal of Pediatric and Neonatal Individualized Medicine

“This review describes in detail the new NECs especially those which affect preterm infants: contagion or lymphocytosis associated, transfusion associated and cow’s milk allergy associated.”

Metagenomics

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

“We investigated the interacting effects of DNA input and library amplification by PCR on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis-associated microbial community.”

Metabolomics 

The nexus of syntrophy-associated microbiota in anaerobic digestion revealed by long-term enrichment and community survey – Takashi Narihiro – Environmental Microbiology

“16S pyrotag analysis revealed core populations of known syntrophs (six clades) and methanogens (nine clades) associated with acid degradation, and evidence for substrate- and/or inoculum-dependent specificity in syntrophic partnerships.”

In Vitro Fermentation of Lactulose by Human Gut Bacteria – Bingyong Mao – Journal of Agricultural and Food Chemistry

“This study aimed to identify lactulose-metabolizing bacteria in the human gut, using in-silico and traditional culture methods. “

Epigenomic regulation of host–microbiota interactions – Theresa Alenghat, David Artis – Trends in Immunology

“We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host–microbiota interactions.”

More microbiology

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction – George C. diCenzo – PLOS Genetics

“To gain insight into the role and evolutionary history of these replicons, we have ‘reversed evolution’ by constructing a S. meliloti strain consisting solely of the chromosome and lacking the pSymB chromid and pSymA megaplasmid.”

Microbes in the news

How An Antibiotic Gene Jumped All Over The Tree of Life – Ed Yong – National Geographic

“Metcalf showed that it has also jumped from bacteria into every other major branch of life. It’s in animals, plants, fungi, archaea, and even some viruses.”

Research investigates bacteria on banknotes – Harper Adams University

“This study investigates how easy it is for bacteria and pathogens to survive on currency and whether the material the notes are made of, has an effect on the transfer.”

How millennials will save us all – Jennifer Block – Quartz

“Millennials get a bad rap for loading up on debt, mooching off their parents, and hiding behind technology. But there’s one problem that they may be particularly suited to tackling: our shrinking microbiome.“

Bik’s Picks

World’s Most Asked Questions: How Much Water Should I Drink a Day? – SciShow – Youtube

“People ask Google everything under the sun. One of the most commonly searched questions in the world is “How much water should I drink a day?” SciShow has the answer!”

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article – Harriet Dashnow – PLOS Computational Biology

“This search left us wanting, until we discovered the PLOS Ten Simple Rules collection. We have found them to be a series of concise articles that capture the professional zeitgeist of being a scientist in an approachable manner.”

Satire: Ambitious New High-Speed Rail Plan Will Fly Americans To Japan To Use Their Trains – The Onion

“The transit system that the U.S. has needed for so long is now just a 7,000-mile plane journey to Tokyo’s Narita International Airport and a brief passage through Japanese customs away,” Obama continued.”

Microbiome Digest, October 20, 2014

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Oral core microbiome, symbionts in crabs, sponges, and Drosophila, metabolites in dolphin’s breath, and retraction of a paper favored by Dr. Oz.

Pregnancy and birth

NEC in Twin Pregnancies: Incidence and Outcomes – Sathyaprasad C Burjonrappa, Brian Shea, Diya Goorah – Journal of Neonatal Surgery

“There is a remarkable higher incidence of NEC amongst twins. Abnormal colonization of the gastrointestinal tract appears to be an immediate postpartum event.”

Human oral microbiome

Intraindividual variation in core microbiota in peri-implantitis and periodontitis – Noriko Maruyama – Scientific Reports

“To improve our knowledge of the different communities of complex oral microbiota, we compared the microbial features between peri-implantitis and periodontitis in 20 patients with both diseases. “

Antimicrobial Effect of Lemongrass Oil against Oral Malodor Microorganisms and the Pilot Study of Safety and Efficacy of Lemongrass Mouthrinse on Oral Malodor – Panitta Satthanakul – Journal of Applied Microbiology

“Antimicrobial activity of LG mouthrinse was examined against common odorigenic microorganisms using broth microdilution assay and the disc diffusion method. A randomized double-blind clinical study was performed in 20 healthy volunteers.”

Animal microbiome

Molecular evidence of digestion and absorption of epibiotic bacterial community by deep-sea crab Shinkaia crosnieri – Tomo-o Watsuji – ISME Journal

“A phylogenetic analysis showed that many of the bacterial 16S ribosomal RNA gene sequences obtained from the intestine were closely related to the sequences of the epibionts, thus they were probably derived from the epibionts.”

* In vivo function and comparative genomic analyses of the Drosophila gut microbiota identify candidate symbiosis factors – Peter D. Newell – Frontiers in Microbiology

“We compared microbiota isolates with con-specific or closely related bacterial species isolated from non-fly environments. “

* Two distinct microbial communities revealed in the sponge Cinachyrella – Marie L. Cuvelier – Frontiers in Microbiology

“Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing.”

* Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality – Fan Zhang – FEMS Microbiology Ecology

“PCR cloning and sequencing of archaeal 16S rRNA and amoA genes showed that the archaeal community composition and structure were different from that in seawater and varied among sponge species. “

Plant microbiome

Reduced dependence of rhizosphere microbiome on plant-derived carbon in 32-year long-term inorganic and organic fertilized soils – Chao Ai – Soil Biology and Biochemistry

“Wheat rhizosphere microbiome was studied by stable isotope probing and pyrosequencing.”

Environmental microbiome

Characterization of bacterial communities associated with seasonal water masses from Tongyoung in South Sea of Korea – Sung-Suk Suh – Ocean Science Journal

“In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with two different water masses from Tongyoung in the South Sea of Korea. “

Bacterial community structure of a lab-scale anammox membrane bioreactor – Alejandro Gonzalez-Martinez – Biotechnology Progress

“In this study, next-generation sequencing techniques have been used for the investigation of the bacterial communities of this MBR Anammox for the first time ever. “

Metagenomics & Bioinformatics

GenomePeek: What exactly is that sequencing data? – Katelyn McNair – MicroBEnet

“I wrote the initial version of GenomePeek, and tested it with various data sets using this student’s data. I quickly found that some genes work better than others, and so currently the four genes analyzed are: 16S, recA, rpoB, and groEL.”

Metabolomics

Metabolite Content Profiling of Bottlenose Dolphin Exhaled Breath – Alexander A. Aksenov – Analytical Chemistry

“We have developed a method to reproducibly sample breath from small cetaceans, specifically Atlantic bottlenose dolphins (Tursiops truncatus). “

Proteomics

Symbiosis, Dysbiosis and Rebiosis – the value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

“After a brief review of the history and state-of-the-art of metaproteomics in the field of environmental health research, focus of this perspective article will be put on the role of cross-species joint efforts in symbiosis, dysbiosis and rebiosis of the human gut during human development, pathogenesis and aging.”

More microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

“This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.”

* Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite
Zhang Wang, Martin Wu – PLOS ONE

“Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria.”

Real-time video imaging as a new and rapid tool for antibiotic susceptibility testing by the disk diffusion method: a paradigm for evaluating resistance to imipenem and identifying extended-spectrum β-lactamases – Stéphanie Le Page – International Journal of Antimicrobial Agents

“..we present here for the first time video movies of the appearance of the diameter of inhibition by the disk diffusion in real-time. “

Microbes in the news

Can Microbes Help Feed the World? – Amy Mayer – BioScience

“To help meet the challenge for food, scientists are using new technologies to better understand the role that soil microbes might play in bolstering agricultural production. “

Dentists Want To See Studies On Pot-Cavity Link – CBS Local

“Patients are experiencing tooth decay, expensive dentist bills and the pain of dealing with it all. The biggest side effect is dry mouth.”

Bik’s Picks

Brain surgery, by robot, through the cheek – Science Daily

“Engineers have developed a surgical robot designed to perform brain surgery by entering through the cheek instead of the skull that can operate on a patient in an MRI scanner. Additionally, the engineers have designed the system so that much of it can be made using 3-D printing in order to keep the price low.”

* Hilarious cartoons on Imgur: Real Scientists vs. Movie Scientists 

* Authors retract green coffee bean diet paper touted by Dr. Oz – Ivan Oransky – Retraction Watch

“Two authors of a 2012 paper sponsored by a company that made grand claims about green coffee bean extract’s abilities to help people lose weight have retracted it. The study was cited by The Dr. Oz Show, and last month it cost the company a $3.5 million settlement with the Feds.”

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Non-human microbiome digest, October 14, 2014

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Diatoms in aquatic animals, bacteria in agaves and soybeans, and bacteria in artificial soil.

Animal microbiome

Diatoms in cytologic specimens of aquatic animals – Part I, fecal samples – Nicole StacyDiatoms in cytologic specimens of aquatic animals – Part II, dermal, respiratory, and gastric samples – Nicole Stacy – Veterinary Clinical Pathology

“Diatoms are a common finding in cytologic samples of aquatic animals…and it is necessary to differentiate these microbiota from parasite ova or protozoa.”

Impacts of large-bodied crustaceans on the microbial loop – Krystyna Kalinowska – Hydrobiologia

“Three alien crustacean species (Daphnia pulex, Simocephalus vetulus and Macrocyclops albidus) were collected from the regional species pool and added to mesocosms that were filled with water from a eutrophic lake “

Bacterial Community Composition of Three Candidate Insect Vectors of Palm Phytoplasma (Texas Phoenix Palm Decline and Lethal Yellowing) –  Christopher M. Powell – Current Microbiology

“Individuals from each species were subjected to 16S bacterial community sequencing using the Roche 454 platform, providing new information regarding the previously unexplored bacterial communities present in putative vectors.”

Plant microbiome

Diazotrophic potential among bacterial communities associated with wild and cultivated agaves – Damaris Desgarennes – FEMS Microbiology Ecology

“Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA-DGGE fingerprinting and sequencing.”

Spatio temporal influence of isoflavonoids on bacterial diversity in the soybean rhizosphere – Laura J White – Molecular Plant-Microbe Interactions

“We silenced the biosynthesis of isoflavonoids, a major component of soybean rhizodeposits, using RNA interference in hairy root composite plants, and examined changes in rhizosphere bacteriome diversity.”

Soil microbiome

Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particles size fractions – Michael Hemkemeyer – FEMS Microbiology Ecology

“this study demonstrates that the mineral composition and the particle size fractions have specific and different selective effects on the three domains”

Improving soil bacterial taxa–area relationships assessment using DNA meta-barcoding – S Terrat – Heredity

“Our objectives in this study were to compare DNA fingerprinting and meta-barcoding approaches for evaluating soil bacterial TAR and the determinism of soil bacterial community assembly on a broad scale. “

The role of stochasticity differs in the assembly of soil- and root-associated fungal communities – Sarah Beck – Soil Biology and Biochemistry

“The importance of spatial and environmental factors in shaping fungal beta diversity was determined over a 500 km transect.”

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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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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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Human microbiome digest, October 2, 2014

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Catching up after some long days of paper writing. Lots of microbiome papers in the Journal of Clinical Investigation, microbiome and Lupus, and biography of skin microbiome.

General (human) microbiome

The Journal of Clinical Investigation has a microbiome issue this month (all behind a subscription wall). Titles include:

The microbiome revolution – Martin J. Blaser
Bacteroides fragilis subverts mucosal biology: from symbiont to colon carcinogenesis – Cynthia L. Sears, Abby L. Geis, Franck Housseau
Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics – Rachel N. Carmody, Peter J. Turnbaugh
Clostridium difficile and the microbiota – Anna M. Seekatz, Vincent B. Young
The microbial basis of inflammatory bowel diseases – Sushila R. Dalal, Eugene B. Chang
Deciphering the tête-à-tête between the microbiota and the immune system – Neeraj K. Surana, Dennis L. Kasper
The contributory role of gut microbiota in cardiovascular disease – W.H. Wilson Tang, Stanley L. Hazen
Antibiotics and the gut microbiota – Sheetal R. Modi, James J. Collins, David A. Relman

When, where and how does microbial community composition matter? – Diana R. Nemergut*, Ashley Shade and Cyrille Violle – Frontiers in Microbiology

“Several papers in this special issue, “The Causes and Consequences of Microbial Community Structure,” use empirical or modeling approaches as well as literature reviews to enrich our mechanistic understanding of the controls over the relationship between community structure and ecosystem processes. “

The bacteriome-mycobiome interaction and antifungal host defense – Jaap ten Oever and Mihai G. Netea – European Journal of Immunology

“In this review, we describe the role of the bacterial microbiome in antifungal host defense.”

Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers and pathogens based on the interaction of these fungi with the human immune system.”

Pregnancy and Birth

Second trimester amniotic fluid cytokine concentrations, Ureaplasma sp. colonisation status and sexual activity as predictors of preterm birth in Chinese and Australian women
Matthew S Payne – BMC Pregnancy and Childbirth

“Second trimester amniocentesis for measurement of inflammatory markers and Ureaplasma sp. DNA was not indicative of risk of preterm birth, at least in these populations.”

Human oral microbiome

Tongue images and tongue coating microbiome in patients with Colorectal Cancer -Shuwen Han – Microbial Pathogenesis

“To evaluate the differences of tongue images and tongue coating microbiome between patients with colorectal cancer and healthy people.”

Hydrogen Sulfide Production from subgingival plaque samples – A. Basic, G. Dahlén – Anaerobe

“The Karen population studied in Northern Thailand showed poor oral hygiene, general gingivitis and moderate periodontal destruction and little tooth loss.”

Italian-style gluten-free diet changes the salivary microbiota and metabolome of African (Saharawi) celiac children – Ruggiero Francavilla – Digestive and Liver Disease

Human skin microbiome

* Microbiology: An integrated view of the skin microbiome – Patrick D. Schloss – Nature

Biogeography and individuality shape function in the human skin metagenome – Julia Oh – Nature

“Here metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. “

Human respiratory microbiome

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

“Ethmoid samples from 54 CRS patients collected during endoscopic sinus surgery were analyzed by both clinical culture and 16S ribosomal RNA (rRNA) gene sequencing. The association between 16S relative abundance and detection by culture was determined using logistic regression.”

Methicillin-Sensitive and Methicillin-Resistant Staphylococcus aureus Nasal Carriage in a Random Sample of Non-Hospitalized Adult Population in Northern Germany – Jaishri Mehraj – PLOS ONE

“A total of 2026 potential participants were randomly selected through the resident’s registration office and invited by mail. They were requested to collect a nasal swab at home and return it by mail. S. aureus was identified by culture and PCR. “

Severity-related changes of bronchial microbiome in COPD – Marian Garcia-Nunez – Journal of Clinical Microbiology

“Bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stability. “

Human gut microbiome

* Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus – Arancha Hevia – mBio

“A group of 20 SLE patients in remission, for which there was strict inclusion and exclusion criteria, was recruited, and we used an optimized Ion Torrent 16S rRNA gene-based analysis protocol to decipher the fecal microbial profiles of these patients and compare them with those of 20 age- and sex-matched healthy control subjects.”

Systems Biology Analysis of Omeprazole Therapy in Cirrhosis Demonstrates Significant Shifts in Gut Microbiota Composition and Function – Jasmohan Singh Bajaj- American Journal of Physiology – Gastrointestinal and Liver Physiology

“15 compensated cirrhotics and 15 age-matched controls underwent serum gastrin measurement, stool microbiota profiling with multi-tagged pyrosequencing and urinary metabolic profiling with NMR spectroscopy to assess microbial co-metabolites before/after a 14-day course of 40mg/day omeprazole under constant diet conditions’

The Impact of Proton Pump Inhibitors on the Human Gastrointestinal Microbiome
Daniel E. Freedberg – Clinics in Laboratory Medicine

The intestinal microbiota and allergic asthma – Marie-Claire Arrietaa, Brett Finlay- Journal of Infection

“By describing some of the most relevant human and animal studies in this field, we explore the concept that significant perturbations of the intestinal and perhaps the lung microbiota are a cause of allergic asthma.”

Minireview: Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome’s potential to cause inflammation – Cynthia A. Leifer – Immunology Letters

“Loss of TLR5 has profound effects on the microbiota that include greater temporal instability of major lineages and upregulation of flagellar motility genes that may be linked to the reduced levels of anti-flagellin antibodies in the TLR5-/- host.”

A Little O2 May Go a Long Way in Structuring the GI Microbiome – Thomas M. Schmidt, John Y. Kao – Gastroenterology

Microbiome, Innate Immunity, and Esophageal Adenocarcinoma – Jonathan Baghdadi – Clinics in Laboratory Medicine

Animal models of microbiome research

Immunology: Starve a fever, feed the microbiota – Seth Rakoff-Nahoum & Laurie E. Comstock – Nature – belongs to:

Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness – Joseph M. Pickard – Nature

“We hypothesized that the host might utilize internal resources to support the gut microbiota during the acute phase of the disease.”

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut – Henning Seedorf – Cell

“Microbiota from diverse habitats colonize and compete in the guts of gnotobiotic mice”

Dynamics of gut microbiota in autoimmune lupus – Husen Zhang – Applied and Environmental Microbiology

“We investigated the effects of host genetics, sex, age, and dietary intervention on the gut microbiome in a murine lupus model.”

Clostridium ramosum Promotes High-Fat Diet-Induced Obesity in Gnotobiotic Mouse Models – Anni Woting – mBio

“To clarify the possible obesogenic potential of this bacterial species and to unravel the underlying mechanism, we investigated the role of C. ramosum in obesity development in gnotobiotic mice.”

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