Category Archives: Metabolomics

April 27, 2015

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Events:

Life Science Sunset Mixer and Protocols Hackathon – ZappyLab – Berkeley, CA – Thursday April 30 5:30 pm PDT

Microbiome webinar: can diet can modify GI bacteria? – May 6, 2015 at 1:00pm ET – American Society for Nutrition’s Nutritional Science Council

Microbiome of pregnancy and birth

The neonatal gut harbours distinct bifidobacterial strains – Eoin Barrett – Arch Dis Child Fetal Neonatal Ed

Doctoral thesis: Early Life Intestinal Microbiota in Health and in Atopic Eczema – Lotta Nylund – Turku, Finland

In mice: Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother – Joseph G Daft – Microbiome

Human gut microbiome

Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT – E Biagi – Bone Marrow Transplantation

Review: Characterization of the intestinal microbiota and its interaction with probiotics and health impacts – Carine Nunes de Almada – Applied Microbiology and Biotechnology

Commentary: The Gut Microbiome: A New Frontier for Alcohol Investigation – Gail A. Cresci – Alcoholism: Clinical and Experimental Research

Review: The Microbiome for Gastroenterologists – Amit Dutta – Gastroenterology & Endoscopy News

Animal microbiome

Dynamic Distribution of the Gut Microbiota and the Relationship with Apparent Crude Fiber Digestibility and Growth Stages in Pigs – Qing Niu – Scientific Reports

Rumen: A new family of hybrid virophages from an animal gut metagenome – Natalya Yutin – Biology Direct

Rumen: Exploring the sheep rumen microbiome for carbohydrate-active enzymes – Lucas Dantas Lopes – Antonie van Leeuwenhoek

Fish: Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota – Chris CR Smith – The ISME Journal

Insects: Characterization of the microbiota in the guts of Triatoma brasiliensis and Triatoma pseudomaculata infected by Trypanosoma cruzi in natural conditions using culture independent methods – Marcia Gumiel – Parasites and Vectors

Plant root and soil microbiome

Link to PDF on Fierer lab website (PNAS link still not working): Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition – Andrzej Tkacz – The ISME Journal

Forest harvesting reduces the soil metagenomic potential for biomass decomposition – Erick Cardenas – The ISME Journal

Peatland vascular plant functional types affect methane dynamics by altering microbial community structure – Bjorn JM Robroek – Journal of Ecology

Structure and function of rhizosphere and non-rhizosphere soil microbial community respond differently to elevated ozone in field-planted wheat – Zhan Chen – Journal of Environmental Sciences

Review: Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential – Shyamalina Haldar – The Open Microbiology Journal

Water microbiome

Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea – Paraskevi N. Polymenakou – Research in Microbiology

Characterization of the Relative Importance of Human- and Infrastructure-Associated Bacteria in Graywater: A Case Study – Scott P. Keely – Journal of Applied Microbiology

Extremophiles

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh – Verena Salman – The ISME Journal

Book: Microbial Evolution under Extreme Conditions – Corien Bakermans – Google Books/Nature

Microbiome of the built environment

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system – Li-Yang Hsu – Genome Biology

Food microbiology

Evolution of microbial counts and chemical and physico-chemical parameters in high-moisture Mozzarella cheese during refrigerated storage – Annamaria Ricciardi – LWT – Food Science and Technology

Phages, viruses, and CRISPRs

CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus – David Paez-Espino – mBio

Perspective: Can Plant Viruses Cross the Kingdom Border and Be Pathogenic to Humans?
Fanny Balique – Viruses

Diversity of putative archaeal RNA viruses in metagenomic datasets of a yellowstone acidic hot spring – Hongming Wang – Springer Plus

Metagenomics and Bioinformatics

He’s alive! Elviz – exploration of metagenome assemblies with an interactive visualization tool – Michael Cantor – BMC Bioinformatics

Genome assembly using Nanopore-guided long and error-free DNA reads – Mohammed-Amin Madoui – BMC Genomics

Protocol: Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing – Carolina Grob – Springer Protocols Handbooks 2015

PhD thesis: MetaPathways : a modular pipeline for the analysis of environmental sequence information – Niels William Hanson – University of British Columbia

Metabolomics

Identification of Metabolic Signatures Linked to Anti-Inflammatory Effects of Faecalibacterium prausnitzii – Sylvie Miquel – mBio

MetaboAnalyst 3.0—making metabolomics more meaningful – Jianguo Xia – Nucleic Acids Research

Microbes in the news

Crowd funding: Stayin’ alive: how do microbes help corals recover from bleaching? The roles of bacteria in corals – Laura Núñez-Pons – Experiment.com

Building a better microbiome – Richard A. Marini – Express News

The Truth About C-Sections, Probiotics, and the Bacteria in Your Gut: Dr. Neil Stollman on fecal microbiota transplants

Your make-up could be a breeding ground for bacteria – Kimberley Hibbert – Jamaica Observer

Learning from Earth’s Smallest Ecosystems (Kavli Hangout) – Alan Brown – Live Science

Spoiled rotten: how breweries are trying to spot bad beer through DNA – Josh Lowensohn -The Verge

The Fecal Bacterium You’ll Learn to Love – Jason Tetro – Huffington Post

Pet Talk: Research reveals canine skin microbiome – Your Houston News

Physician-scientist cautions against indiscriminate use of antibiotics – Bob Kustra – Idaho Statesman

Waterproof bacteria inspire special coatings – Tim Sandle – Digital Journal

Metanome changes name to Diversigen – News Medical

Solving Real-World Problems With Unconventional Solutions: Using Bacteria To Heal Wounds – Texas A&M Today

Strike a healthy bacteria balance in your gut – Scott Scanlon – Buffalo News

How Safe is Your Shrimp? – Consumer Reports study finds 60% of frozen shrimp contaminated with bacteria – Food Safety News

Science, publishing, and career

Trove of VA reports reveals research misconduct, medical malpractice – Brendan Borrell – Retraction Watch

Lab Bloopers: Reddit users share the worst mishaps they’ve witnessed while working in the lab – Jenny Rood – The Scientist

Peer review, explained (cartoon) – Academia Obscura

Bik’s Picks

Why pregnant women in Mississippi keep dying – Danielle Paquette – Washington Post

Oil May Have Killed Gulf Dolphins – David Biello – Scientific American

Photos: 7-Year-Old Boy Discovers T. Rex Cousin – Live Science
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April 23, 2015

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Earth Day initiative by Jonathan Eisen – I took the pledge! Become a Guardian of Microbial Diversity – Jonathan Eisen – Change.org

Due to the importance of microbes and microbial diversity to the planet, and due the risks that may come from a reduction in this diversity, we are calling here for people to take a pledge to become “A Guardian of Microbial Diversity” By taking this pledge you state that you will make efforts to consider the effects of your actions on microbes and their diversity. In addition, you pledge here to support efforts to limit and prevent unnecessary damage to the diversity of microbes on the planet.

Call for Grant Applications (deadline April 30): Gut Microbiome Grant Program – DNA Genotek

Animal models of microbiome research

Dysbiotic gut microbiota causes transmissible Crohn’s disease-like ileitis independent of failure in antimicrobial defence – Monika Schaubeck – Gut

Oral ampicillin inhibits liver regeneration by breaking hepatic innate immune tolerance normally maintained by gut commensal bacteria – Xunyao Wu – Hepatology

Animal microbiome

Alligator: The Good, the Bad, and the Unknown: Microbial Symbioses of the American Alligator – Sarah W. Keenan and Ruth M. Elsey – Integrative & Comparative Biology

Ticks: Concordance of bacterial communities of two tick species and blood of their shared rodent host – Evelyn C. Rynkiewicz – Molecular Ecology

Plant and soil microbiome

A new look at plant viruses and their potential beneficial roles in crops – Marilyn J. Roossinck – Molecular Plant Pathology

Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses – Kevin Garcia – New Phytologist

Fungus: Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome – C. Alisha Quandt – Environmental Microbiology

Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils – Adélia Varela – Environmental Microbiology

Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site – Ali Akbari – Environmental Microbiology

Impacts of Dimethyl Phthalate on the Bacterial Community and Functions in Black Soils – Zhigang Wang – Frontiers in Microbiology

Enzymatic and biological assessment of sulfonylurea herbicide impact on soil bacterial communities – Marioara Nicoleta Filimon – African Journal of Agricultural Research

Water microbiome

Water column methanotrophy controlled by a rapid oceanographic switch – Lea Steinle – Nature Geoscience

Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system – Edo Bar-Zeev – Frontiers in Microbiology

Extremophiles

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses – Anders Prieme – Frontiers in Microbiology

Bioreactor microbiome

The Impact of Injections of Different Nutrients on the Bacterial Community and Its Dechlorination Activity in Chloroethene-Contaminated Groundwater  – Takamasa Miura – Microbes and Environments

Metagenomics and bioinformatics

PDF, in press: Detecting bacterial genomes in a metagenomic sample using NGS reads – Camilo Valdes – Statistics and Its Interface

Metabolomics

Editorial about colibactin paper: Natural products: Hunting microbial metabolites – Eric W. Schmidt – Nature Chemistry

Microbial Ecology

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology – Ben Stenuit – Current Opinion in Biotechnology

Microbes in the news

What about Earth’s Microbiome? – Raina Maier – Scientific American

Effectiveness of methane-consuming bacteria in the ocean moderated by ocean currents – Anthony Watts – Watts Up With That

Researchers discover new method to detect most common bacteria contaminating oysters – Phys.org

DNA of bacteria crucial to the ecosystem defies explanation – Robert Perkins – University of Southern California

Bacteria Can Aid Aphids Against Predation and Parasitism – Meredith Swett Walker – Entomology Today

Editorial: Bacterial bonanza far from the West – Nature

Researchers develop computer model of bacterial colony interactions – Christopher Packham – Phys.org

DuPont buying microbiome firm, seeks edge in emerging crop products – Carey Gillam – Reuters

Science and Art

Artists Make Human Cheese From Toe, Armpit, And Belly Button Bacteria: Collaborative art project called Selfmade by Christina Agapakis and Sissel Tolaas – James Mailer -Smash.com
and
Scientists create cheese from human toe bacteria – IndiaToday

Science, publishing and career

Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm – Tracey L. Weissgerber – PLOS Biology

Bik’s Picks

Colour As a Signal for Entraining the Mammalian Circadian Clock – Lauren Walmsley – PLOS Biology

Peering Inside Yellowstone’s Supervolcano – Larry O’Hanlon – Discovery

World Happiness Report 2015 ranks happiest countries – Science Daily

Kermit the Frog Reacts to His Newly Discovered Lookalike: “Shorten your name if you want to make it in show business.” – Kermit – Disney Channel

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April 14, 2015

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Human oral microbiome

Bacteriophage and their potential roles in the human oral cavity – Anna Edlund – Journal of Oral Microbiology

A Potential Biofilm Metabolite Signature for Caries Activity – A Pilot Clinical Study
Zandona F – Metabolomics

Human gut microbiome

Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption – Emiley A. Eloe-Fadrosh – mBio

Siblings of patients with Crohn’s disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities – Charlotte Hedin – Gut

Effect of iron supplementation with or without vitamin E (VE) on gut microbiome (MB) in iron deficient (ID) infants and toddlers – Minghua Tang – The FASEB Journal

Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome – Evangelos Giamarellos-Bourboulis – Scandinavian Journal of Gastroenterology

Review: Viruses, Other Pathogenic Microorganisms and Esophageal Cancer – Xu W. – Gastrointestinal Tumors

Human genital tract microbiome

True love: Complementary seminovaginal microbiome in couples – Reet Mändar – Research in Microbiology

Metabolic Signatures of Bacterial Vaginosis – Sujatha Srinivasan – mBio

Pregnancy and birth microbiome

Low birthweight, gestational age, need for surgical intervention and gram-negative bacteraemia predict intestinal failure following necrotising enterocolitis – Anders Elfvin – Acta Paediatrica

Animal models of microbiome research

Gut microbiota depletion from early adolescence in mice: Implications for brain and behaviour – Lieve Desbonnet – Brain, Behavior, and Immunity

Animal microbiome

Dog: Draft Genome Sequences of 26 Porphyromonas Strains Isolated from the Canine Oral Microbiome – David A. Coil – Genome Announcements

Ragworm: Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments – Joe D Taylor and Michael Cunliffe – Environmental Microbiology Reports

Just dropping by (Aphids): Do Bacterial Symbionts Govern Aphid’s Dropping Behavior? – Omer Lavy – Environmental Entomology

Review (corals): Nitrogen cycling in corals: the key to understanding holobiont functioning? – Nils Rädecker – Trends in Microbiology

Plant and soil microbiome

Below-ground abiotic and biotic heterogeneity shapes above-ground infection outcomes and spatial divergence in a host–parasite interaction – Ayco J. M. Tack – New Phytologist

A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies – Björn Hoppe – Scientific Reports

Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems – Caroline H. Orr – Journal of Applied Microbiology

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics – Carmelo Andújar – Molecular Ecology

Soil treatment-induced differential gene expression in tomato: Relationships between defense gene expression and soil microbial community composition – Shawn T. Lucas – Applied Soil Ecology

Diversity and characterization of Cd-tolerant dark septate endophytes (DSEs) associated with the roots of Nepal alder (Alnus nepalensis) in a metal mine tailing of southwest China – Runbing Xu – Applied Soil Ecology

Plant traits related to nitrogen uptake influence plant-microbe competition – Delphine Moreau – Ecology

Soil microbial functionality in response to dairy sewage sludge and mineral fertilisers application under winter rape – K. Oszust – International Journal of Environmental Science and Technology

Water microbiome

Dynamic succession of groundwater functional microbial communities in response to emulsified vegetable oil amendment during sustained in situ U(VI) reduction – Ping Zhang – Applied and Environmental Microbiology

Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean – C. Dong – Biogeosciences

Sulfate-reducing bacterial communities in the water column of the Gdansk Deep (Baltic Sea) – V. A. Korneeva – Microbiology

Bioreactor microbiology

Rare taxa have potential to make metabolic contributions in enhanced biological phosphorus removal ecosystems – Christopher E. Lawson – Environmental Microbiology

Extremophile microbiome

Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern – Nina S. Atanasova – Viruses

Review: 40 Years of archaeal virology: Expanding viral diversity – Jamie C. Snyder – Virology

Methane Yield Database: Online Infrastructure and Bioresource for Methane Yield Data and Related Metadata – Boštjan Murovec – Bioresource Technology

Call for papers: BIODESERT: Exploring and Exploiting the Microbial Resource of Hot and Cold Deserts – Hindawi BioMed Research International

Metagenomics and metabolomics

Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics – Tom O. Delmont – Frontiers in Microbiology

Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria – Ana Martínez-del Campo – mBio

Metabolic Signatures of Bacterial Vaginosis – Sujatha Srinivasan – mBio

Review: Prokaryotic functional gene diversity in the sunlit ocean: Stumbling in the dark
Isabel Ferrera – Current Opinion in Microbiology

Techniques

Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA – Samart Dorn-In – Journal of Microbiological Methods

More microbiology papers

Bacterial Raincoats: Interfacial self-assembly of a bacterial hydrophobin – Keith M. Bromley – PNAS USA

A New Synthesis for Dual Use Research of Concern – Michael J. Imperiale, Arturo Casadevall – PLOS Biology

Microbes in the news

Here’s Your New Science-Backed Reason to Eat More Cheese Your good bacteria love stinky fromage as much as you do – Mandy Oaklander – Time

Making a microbe subway map – Bethany Brookshire – Student Science

Video: Can gut bacteria help us live longer? – Simin Nikbin Meydani – Tufts University

Bacterial raincoat discovery paves way to better crop protection – Phys.org

CRISPR Shows How A Bacterial Cell Can Recognize Its Own DNA – Science 2.0

Spotlight on the Banfield lab: Longer DNA fragments reveal rare species diversity  – TANN – Archaeology News Network

Submission for the ASM Global Video Challenge 2015: Bacterial Friends Within You – YouTube

Spread of bacteria an issue in doctors’ white coat debate – Murray Feingold – Standard Speaker

Science, publishing, and career

How should journalists cover quacks like Dr. Oz or the Food Babe? – Julia Belluz – Vox

Great news: National hiring experiments reveal 2:1 faculty preference for women on STEM tenure track – Wendy M. Williams and Stephen J. Ceci – PNAS USA

Bik’s Picks

Four Corners Methane ‘Hot Spot’: NASA Joins Team Of Scientists Attempting To Pinpoint Source Of Gas – Avaneesh Pandey – International Business Times

Natural Selection May Help Account for Dutch Height Advantage – Carl Zimmer – New York Times

This Doughnut In Space Went Where No Breakfast Pastry Has Been Before – Cameron Keady – Huffington Post
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April 9, 2015

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Events and conferences

3rd Microbiome R&D and Business Collaboration Forum: USA – 10-11 September 2015, San Diego

Symposium ‘Women & Their Microbes’, Amsterdam, The Netherlands, May 8, 2015 in Micropia

Human gut microbiome

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease – Xochitl C Morgan – Genome Biology

Animal models of microbiome research

High-grain feeding causes strong shifts in ruminal epithelial bacterial community and expression of Toll-like receptor genes in goats – Jun-hua Liu – Frontiers in Microbiology

Site-specific programming of the host epithelial transcriptome by the gut microbiota – Felix Sommer – Genome Biology

Animal microbiome

Bats: Bacteria Isolated from Bats Inhibit the Growth of Pseudogymnoascus destructans, the Causative Agent of White-Nose Syndrome – Joseph R. Hoyt – PLOS ONE

Plant microbiome

Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria – Hiroyuki Iguchi – Microorganisms

Soil and sediment microbiome

Effects of 100 years wastewater irrigation on resistance genes, class 1 integrons and IncP-1 plasmids in Mexican soil – Sven Jechalke – Frontiers in Microbiology

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany – Friederike Gründger – Frontiers in Microbiology

Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture – Stephen A. Wood – Frontiers in Microbiology

Water microbiome

Viruses and bacteria in floodplain lakes along a major Amazon tributary respond to distance to the Amazon River – Rafael M. Almeida – Frontiers in Microbiology

Extremophile microbiome

Permafrost thawing in organic Arctic soils accelerated by ground heat production – Jørgen Hollesen – Nature Climate Change
See also:
Bacteria warm up permafrost – Nature

Alternative lifestyle: The processes that allow life to thrive in deep-sea vents are happening all around us – Nick Higgs – New Scientist

Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems – Sophie Crevecoeur – Frontiers in Microbiology

Influence of Martian regolith analogs on the activity and growth of methanogenic archaea, with special regard to long-term desiccation – Janosch Schirmack – Frontiers in Microbiology

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals – Lukasz Dziewit – Frontiers in Microbiology

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland – Malin Bomberg – BioMed Research International

Food microbiology

Review: Recent trends in non-invasive in situ techniques to monitor bacterial colonies in solid (model) food – María M. Lobete – Frontiers in Microbiology

Bioreactor and wastewater microbiome

Bacteriophages as indicators of human and animal faecal contamination in raw and treated wastewaters from Tunisia – M. Yahya – Journal of Applied Microbiology

Microbial Ecology

Taking advantage of quorum sensing – Cláudio Nunes-Alves – Nature Reviews Microbiology

Metagenomics and bioinformatics

Phylogenomics and systematics in Pseudomonas – Margarita Gomila – Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments – Derrick E Wood and Steven L Salzberg (HT: Tomer Altman)

Metabolomics

Exometabolomics and MSI: deconstructing how cells interact to transform their small molecule environment – Leslie P Silva – Current Opinion in Biotechnology

 

Microbes in the news

Life below Antarctic ice survives on ancient forests – Catherine Brahic – New Scientist

Eden Project’s ‘Human Biome’ is a gross, musical microbe showcase – Katie Collins – Wired

Company provides easy access to microbiome data – Mark Niu – CCTV America

 

Gates Foundation Issues Call for Application for Round 15 of Grand Challenges Initiative  – Philanthropy News Digest

Changes in Lung Microbiota May Help Predict Cystic Fibrosis Pulmonary Exacerbations – Patricia Silva – Cystic Fibrosis News today

Body maps reveal the bacteria and chemicals lurking on skin – Meera Senthilingam – CNN

 

Gut Bacteria May Be Associated with Parkinson’s Phenotype – Neurology Advisor

Microbes Engineered to Prevent Obesity – Katherine Bourzac – Technology Review
Cornell Researchers Identify Gut Microbes that May Help Some People Remain Thin; Findings Could Result in Clinical Laboratory Tests to Analyze the Microbiomes of Individuals – Dark Daily

Silver linings: a personal memoir about Hurricane Katrina and fungal volatiles
Joan W. Bennett – Frontiers in Microbiology

 

Sequencing the intestinal microbiome to target therapies: Vanni Bucci looking for probiotic cocktails – Bryan Goodchild and Ellie Castano – University of Massachusetts Medical School Communications

Bacteria inhibit bat-killing fungus, could combat white-nose syndrome – Tim Stephens – University of California Santa Cruz

Turtle phage therapy might help develop alternative to antibiotic treatments for humans, Queensland researchers say – Nance Haxton – ABC Australia

9 Types Of Bacteria You Didn’t Know You’re Sharing Your House With – Esther Inglis-Arkell

 

Science, publishing, and career

Chris Butler: Wants to snuggle up to bacteria – BMJ Observations

‘Plagiarism, fraud, and predatory publishing’ are polluting science, says bioethicist Arthur Caplan – Susan Perry – MinnPost

Bik’s Picks

Hair Regrowth Discovery Suggests Skin Cells Communicate Like Bacteria – Dina Fine Maron – Scientific American

Genome sequencing mountain gorillas reveals the genetic impact of inbreeding – Aylwyn Scally – The Conversation

Gem lover donates $13M for Smithsonian’s science education – Brett Zongker  – Washington Post

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April 8, 2015

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Events

#UMassMedChat on the microbiome is Thursday at 11:30 a.m.- UMass Center for Microbiome Research to answer questions on gut health

Microbes in the City: Mapping the Urban Genome, Friday, June 19, 2015 – The New York Academy of Sciences

Human respiratory microbiome

Analysis of microbiota in stable patients with chronic obstructive pulmonary disease – Estefania Aguirre – APMIS

Human gut microbiome

Site-specific programming of the host epithelial transcriptome by the gut microbiota – Felix Sommer – Genome Biology

Animal microbiome

Horses and pigs: Lactobacillus ruminis strains cluster according to their mammalian gut source – Michelle M O’ Donnell1 – BMC Microbiology

Turkeys: Rye Affects Bacterial Translocation, Intestinal Viscosity, Microbiota Composition and Bone Mineralization in Turkey Poults – Guillermo Tellez – PLOS ONE

Amphibians: Larval exposure to polychlorinated biphenyl 126 (PCB-126) causes persistent alteration of the amphibian gut microbiota – Kevin D. Kohl – Environmental Toxicology and Chemistry

Tsetse fly: Paternal transmission of a secondary symbiont during mating in the viviparous tsetse fly – Linda De Vooght – Molecular Biology and Evolution

Squid and Vibrio fisheri: Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology
Sponges: Phylogenetic diversity of sulphate-reducing Desulfovibrio associated with three South China Sea sponges – D. Zhang – Letters in Applied Microbiology

Plant root and soil microbiome

Plant diversity increases soil microbial activity and soil carbon storage – Markus Lange – Nature Communications

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA
genes in actinobacteria – Marketa Sagova-Mareckova – BMC Microbiology

Water microbiome

Functional Gene Composition, Diversity and Redundancy in Microbial Stream Biofilm Communities – Andrew Dopheide – PLOS ONE

Metabolomics

Distributing a metabolic pathway among a microbial consortium enhances production of natural products – Kang Zhou – Nature Biotechnology

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Molecular Signatures of Nicotinoid-Pathogen Synergy in the Termite Gut – Ruchira Sen – PLOS ONE

Unique Honey Bee (Apis mellifera) Hive Component-Based Communities as Detected by a Hybrid of Phospholipid Fatty-Acid and Fatty-Acid Methyl Ester Analyses – Kirk J. Grubbs – PLOS ONE

Bioinformatics

A Robust ANOVA Approach to Estimating A Phylogeny from Multiple Genes – Ximing Xu – Molecular Biology and Evolution

More microbiology papers

Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe – Gemma L. Kay – Nature Communications

Microbes in the news

Beneficial bacteria – Ella Nonni – The Cornell Daily Sun

Mapping All The Chemicals And Tiny Bacteria Living On Our Skin – Adele Peters – FastCoExist

uBiome and HelloFlo are teaming up to explore how the vaginal microbiome changes during pregnancy and postpartum

Video: Gut Microbiome and Its Role in Allergy and Asthma – Christine Cole Johnson – JSPRQ.com

Colorado startup’s microbiome-modulating drug could improve metformin tolerability – Meghana Keshavan – MedCityNews

Race to stamp out animal plague begins – Ewen Callaway – Nature

Science, publishing, and career

The future of the postdoc: There is a growing number of postdocs and few places in academia for them to go. But change could be on the way – Kendall Powell – Nature

Opinion: Addressing systemic problems in the biomedical research enterprise – Bruce Alberts – PNAS USA

History: Women at the edge of science – Jennifer Rampling – Nature

Bik’s Picks

Efficacy of Commercial Weight-Loss Programs: An Updated Systematic Review
Kimberly A. Gudzune – Annals of Internal Medicine

Ecology: Recovering the potential of coral reefs – Nicholas K. Dulvy & Holly K. Kindsvater – Nature
Complex organic molecules discovered in infant star system: Hints that building blocks of chemistry of life are universal – Science Daily

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April 7, 2015

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Lots of abstracts today that were published in the FASEB Journal. Although not clearly marked, these appear to be abstracts from an ASBMB meeting held in March 2015 in Boston, called “The Human Microbiome“. None of these have a link to a PDF.

Course: Frontiers in Host-Microbe Interactions – August 2015

Pregnancy and birth microbiome

The FASEB Journal Abstracts:

Review: Normal flora and bacterial vaginosis in pregnancy: an overview – Mathys Jacobus Redelinghuys – Critical Reviews in Microbiology

Review: The Infant Gut Microbiome: Evidence for Obesity Risk and Dietary Intervention – Petya T. Koleva – Nutrients

Human skin microbiome

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin – Jared Liu – The ISME Journal

Human oral microbiome

The Repertoire of Archaea Cultivated from Severe Periodontitis – Hong T. T. Huynh – PLOS ONE

Review: Filifactor alocis – a new emerging periodontal pathogen – A. Wilson Aruni – Microbes and Infection

Human gut microbiome

The FASEB Journal Abstracts:

Autism spectrum disorders and intestinal microbiota – Maria De Angelis – Gut Microbes

Review: Impacts of Gut Bacteria on Human Health and Diseases – Yu-Jie Zhang – International Journal of Molecular Sciences

Animal models of microbiome research

The FASEB Journal Abstracts:

Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model – Shaoping Wu – Physiological Reports

Metabolomic Modeling To Monitor Host Responsiveness to Gut Microbiota Manipulation in the BTBRT+tf/j Mouse – Matthias S. Klein – Journal of Proteome Research

Animal microbiome

The FASEB Journal Abstract: The Extraordinary Evolution of the Great Ape Microbiome
Howard Ochman

Pigs: How host gender affects the bacterial community in pig feces and its correlation to skatole production – Zhenjin Zhou – Annals of Microbiology

Pigs: Analysis of swine fecal microbiota at various growth stages – Jungman Kim – Archives of Microbiology

Fish / Review: Disinfection of teleost eggs: a review – Evelien De Swaef – Reviews in Aquaculture

Ticks: Concordance of bacterial communities of two tick species and blood of their shared rodent host – Evelyn C. Rynkiewicz – Molecular Ecology

Soil microbiome

Over 150 Years of Long-Term Fertilization Alters Spatial Scaling of Microbial Biodiversity – Yuting Liang – mBio

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field – Cai-Yun Li – International Journal of Molecular Sciences

Effects of Functionalized and Raw Multi-Walled Carbon Nanotubes on Soil Bacterial Community Composition – Dorsaf Kerfahi – PLOS ONE

Review: Effective role of indigenous microorganisms for sustainable environment – Baduru Lakshman Kumar and D. V. R. Sai Gopal – 3 Biotech

Water microbiome

Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone – M.T. Duret – FEMS Microbial Ecology

Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols – Camilla Fahlgren – Environmental Microbiology Reports

Book: Microbiology of the Everglades Ecosystem – CRC Press

Extremophile microbiome

Physiochemical control of bacterial and protist community composition and diversity in Antarctic sea ice – Anders Torstensson – Environmental Microbiology

Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment – Jamile Queiroz Pereira – Genome Announcements

Food microbiome

Microbial Ecology of Watery Kimchi – Kyu Hang Kyung – Journal of Food Science

Bioreactor and biofilter microbiome

Characterization of the microbial community structure and nitrosamine-reducing isolates in drinking water biofilters – Wanfeng Wang – Science of the Total Environment

Metagenomics, Metabolomics, and Transcriptomics

The FASEB Journal Abstracts:

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities – Jacob Moran-Gilad – BMC Infectious Diseases

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis – Yuzhen Ye, Haixu Tang – ArXiv

Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton – Jessica M Labonté – The ISME Journal

Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample – Koen Illeghems – Food Microbiology

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone – Sangita Ganesh – The ISME Journal

Transcriptomic evidence for microbial sulfur cycling in the eastern tropical North Pacific oxygen minimum zone – Molly Carolan and J Michael Beman – Frontiers in Microbiology

Review: Progress and Challenges in Developing Metabolic Footprints from Diet in Human Gut Microbial Cometabolism – Linda C Duffy – Journal of Nutrition

Microbial Ecology

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities – Ville-Petri Friman – Proceedings B

Local–global overlap in diversity informs mechanisms of bacterial biogeography – Joshua A Livermore – The ISME Journal

Techniques

Assessing the performance of the Oxford Nanopore Technologies MinION – T. Laver – Biomolecular Detection and Quantification

Next-generation sequencing data analysis on cloud computing – Taesoo Kwon – Genes & Genomics

Microbes in the news

It’s a microbe’s world…we’re just living and dying in it – Margaret Leigh Sinrod – SciTechNow

May deadline: 2015 MO BIO Microbiome Awards – MoBIO

After cancer diagnosis, MIT student 3-D prints tumor, has microbiome analyzed – Nidhi Subbaraman – BetaBoston

Most of the text appears stolen from an article by Lita Proctor:  Human Microbiome: Quiz – Target Health

Video: Why Your Beard Is Disgusting – Discovery News

Episode 4 of The Microbiome Podcast: What’s hot in the microbiome field with Kristina Campbell – American Microbiome Institute

Solving the complex problem of recurrent C. diff with a simple solution: 
Physician scientists are using fecal transplants to break the deadly cycle of a killer infection – Bryan Goodchild and Ellie Castano – University of Massachusetts Medical School

Gut Bacteria May Influence Parkinson’s Risk, Phenotype – Pauline Anderson – Medscape

Summing up: Bassis et al.’s take on the influence of the URT on other human-associated biogeographies – Fiona Whelan – Human Microbiome Journal Club:

Under the microscope, strong-swimming swamp bacteria spontaneously organize into crystals – Phys.org

Science, publishing, and career

Female peers in small work groups enhance women’s motivation, verbal participation, and career aspirations in engineering – Nilanjana Dasgupta – PNAS USA

Bik’s Picks

How California can survive the drought — State is not in complete control – Danielle Venton – Nature

The Brontosaurus Is Back, Baby – Rich Juzwiak – Gawker

Endangered Tortoises Feasting on Invasive Plants – Richard Farrell – Discovery
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April 6, 2015

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Not all human breast milk sold online is 100% human, microbiome of veggies, and a book by Rob Knight.

Pregnancy and birth

Cow’s Milk Contamination of Human Milk Purchased via the Internet – Sarah A. Keim – Pediatrics

Review: Milk Bioactives May Manipulate Microbes to Mediate Parent-Offspring Conflict – Cary R. Allen-Blevins – Evolution, Medicine, and Public Health

Food microbiology

Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables – Colin R. Jackson – Agriculture

Metabolomics

Link did not work as of now – might work later? The colibactin warhead crosslinks DNA – Crawford – Nature Chemistry

Microbes in the news

Beyond Probiotics: Can You ‘Hack’ Your Microbiome? – Beth Skwarecki – LifeHacker Australia

Glyphosate, Roundup, GMOs and the microbiome part 1: crowdsourcing literature – Jonathan Eisen – The Tree of Life

Book by Rob Knight – Follow Your Gut – The Enormous Impact of Tiny Microbes – TED books

Ice Worm Guts Tell a Story of Partnership – Manon Verchot – Glacier Hub

An Amazonian Tribe May Hold The Secret To Better Gut Health – Anna Almendrala – Huffington Post

Microbes scared to death by virus presence – ScienceDaily

Spotting a molecular warhead for disease in the human gut – Jim Shelton – Yale News

Microbes are partly to blame for Arctic’s melting permafrost – Mary Beth Griggs – Popular Science

That Vagina Yogurt Probably Wasn’t Really Vagina Yogurt, Says Expert – Ben Richmond – Motherboard

MRSA Bacteria Thrives In Cigarette Smoke Environment – Paola Celedonio – Diabetes Insider

Raising money to go the ASM conference: E. coli and Ebola already sold out: Microbiology students sell giant plush microbes – KCCI

Glowing GE bacteria produced from kits ‘illegally’ in New Zealand – Tom Hunt – The Dominion Post

Bik’s Picks

Breast Milk Sold Online May Not Be 100% Human Milk – Cari Nierenberg – LiveScience

Please learn the difference between tortoises and sea turtles, say Florida wildlife officials – Rowena Lindsay – CS Monitor

What Americans Think About Climate Change in Seven Maps – Eric Roston – Bloomberg
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April 4, 2015

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In this weekend edition, I found papers on iron supplements, phage and TM6 genomics, millipedes, ground squirrels, and coffee consumption. 

Human oral microbiome

Salivary Microbiota Reflects Changes in Gut Microbiota in Cirrhosis with Hepatic Encephalopathy – Jasmohan S Bajaj – Hepatology

The Peri-Implant and Periodontal Microbiota in Patients with and without Clinical Signs of Inflammation – Meike Luise Jakobi – Dental Journal

Almost completely plagiarized Review: Interspecies communication in oral biofilm: An ocean of information – Amit Parashar – Oral Science International

Human respiratory microbiome

Possible role of anaerobes in the pathogenesis of nontuberculous mycobacterial infection – Kei Yamasaki – Respirology

Human gut microbiome

Isn’t that Ironic: Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants – Tanja Jaeggi – Gut

Review: The gut microbiome in cardio-metabolic health – Tue H Hansen – Genome Medicine

Review: The role of the commensal microbiota in the regulation of tolerance to dietary allergens – Berni Canani – Current Opinion in Allergy and Clinical Immunology

Review: The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems – Marilia Carabotti – Annals of Gastroenterology

Human urine microbiome

Review: “Sterile Urine” and the Presence of Bacteria – Alan J. Wolfe and Linda Brubaker – European Urology

Animal and other models of microbiome research

Lacking vitamin D receptor leads to intestinal dysbiosis – Dapeng Jin – The FASEB Journal

Evidence for a link between Gut Microbiota and Hypertension in the Dahl rat model – Blair Mell – Physiological Genomics

In vitro colonic metabolism of coffee and chlorogenic acid results in selective changes in human faecal microbiota growth – Charlotte E. Mills – British Journal of Nutrition

Ingestion of coffee polyphenols increases postprandial release of the active glucagon-like peptide-1 (GLP-1(7–36)) amide in C57BL/6J mice – Yoshie Fujii – British Journal of Nutrition

 

Animal microbiome

Squirrels: Functional Analysis of Seasonally-Changing Gut Microbiotas in Hibernating Ground Squirrels – Hannah Carey – The FASEB Journal

Fish: Community assembly of a euryhaline fish microbiome during salinity acclimation –
Victor T. Schmidt – Molecular Ecology

Aphids: Shifts in Buchnera aphidicola density in soybean aphids (Aphis glycines) feeding on virus-infected soybean – Bryan J. Cassone – Insect Molecular Biology

Millipedes: Litter-type specific microbial responses to the transformation of leaf litter into millipede feces – François-Xavier Joly – Soil Biology and Biochemistry

Plant root and soil microbiome

Spatial soil heterogeneity has a greater effect on symbiotic arbuscular mycorrhizal fungal communities and plant growth than genetic modification with Bacillus thuringiensis toxin genes – Tanya E. Cheeke – Molecular Ecology

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination – Yi Liang – Applied Microbiology and Biotechnology

A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes– Carolina Senés-Guerrero and Arthur Schüßler – Fungal Diversity

Built environment microbiome

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children – Karen C. Dannemiller – Indoor Air

Bioreactor microbiome

Characterisation of the complex microbial community associated with the ASTER™ thiocyanate biodegradation system – Robert J. Huddy – Minerals Engineering

A comprehensive study on algal-bacterial communities shift during thiocyanate degradation in a microalga-mediated process – Byung-Gon Ryu – Bioresource Technology

Metagenomics, genomes

TM6: Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae – Isabelle Pagnier – Biology Direct

Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage – Tung Gia Phan – Virology

Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment – Jessica M. Labonté – Frontiers in Microbiology

Rapid Genome Assembly and Comparison Decode Intrastrain Variation in Human Alphaherpesviruses – Lance R. Parsons – mBio

Techniques

Effect of different heterotrophic plate count methods on the estimation of the composition of the culturable microbial community – Eva Theres Gensberger – PeerJ

Microbes in the news

World’s largest microbiome conference held in Luxembourg – University Du Luxembourg

Wash U. Study Finds Bacteria More Antibiotic Resistant – OzarksFirst

What did the bacteria say to the cigarette? “Don’t make me get aggressive” — study finds that smoke strengthens bad bugs – Dave Rice – SanDiegoReader

Urine Isn’t Free of Bacteria – HealthDay

Bad bacteria in your beer? Problem Solvers put taps to the test – Shellie Bailey-Shah – KATU.com

Is it time to bid farewell to your Beats? Your pricey designer headphones could be causing bacteria build-up, acne and even nasty skin infections – Erica Tempesta – Daily Mail UK

Science, publishing, and career

Gender pay inequality at UK Universities: It’s not just bad, it’s wrong – John Gill – Times Higher Education

Bik’s Picks

Yes, Mice Can Sing. And You Won’t Believe How Much They Sound Like Songbirds – Macrina Cooper-White – Huffington Post

Mars rover Curiosity spots strange, 2-tone veins on planet’s surface – Amina Khan – LA Times

Archaeologists uncover 330 year old “war camel” skeleton – David Demar – The American Register

April 2, 2015

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Animal models of microbiome research

Dietary fat intake and age influence gut microbiota and colonic inflammation in C57BL/6J mice – Su Jeong Kim – The FASEB Journal

Maternal obesity alters gut microbial ecology in offspring of NOD mice – Meijun Zhu – The FASEB Journal

Metabolite-sensing receptors ​GPR43 and ​GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome – Laurence Macia – Nature Communications

Animal microbiome

Cheetah (not microbiome but could not resist): Dietary Factors Associated with Faecal Consistency and Other Indicators of Gastrointestinal Health in the Captive Cheetah (Acinonyx jubatus) – Katherine M. Whitehouse-Tedd – PLOS ONE

Ants: Genome evolution in an ancient bacteria-ant symbiosis: parallel gene loss among Blochmannia spanning the origin of the ant tribe Camponotini – Laura E. Williams, Jennifer J. Wernegreen – PeerJ

Sponges: Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea – Valliappan Karuppiah – Applied Microbiology and Biotechnology

Editorial: Sponge symbionts and the marine P cycle – Albert S Colman – PNAS USA

Soil and plant root communities

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert – Klára Řeháková – Frontiers in Microbiology

Soil microbial functional diversity and biomass as affected by different thinning intensities in a Chinese fir plantation – Xin-Li Chen – Applied Soil Ecology

Impact of organic and conventional peach and apple production practices on soil microbial populations and plant nutrients – Ramesh R. Pokharel, Rick Zimmerman – Organic Agriculture

Impact of preferential methane flow through soil on microbial community composition
Julia Gebert, Mirjam Perner – European Journal of Soil Biology

Characterization of bacterial strains and their impact on plant growth promotion and yield of wheat and microbial populations of soil – Ashok Kumar – African Journal of Agricultural

Metabolomics

Gut Commensal Immunomodulatory Factors: Identification and Structure-Function Studies – Sungwhan Oh – The FASEB Journal

Review: Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems – Stephen A Jackson – Current Opinion in Biotechnology

Techniques

Modification of a commercial DNA extraction kit for safe and rapid recovery of DNA and RNA simultaneously from soil, without the use of harmful solvents – E. Tournier

Other articles of interest

Dengue: Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference – Sam H. Shen – PNAS USA

Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes – David Roy Smith and Patrick J. Keeling – PNAS USA

Bioinformatics

A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments – Nicholas A. Bokulich – PeerJ Preprint

Microbes in the news

I enjoyed reading this: Microbiome Blues in E – Michael Tanner – Clinical Correlations
“You haven’t been squeaky clean since you were bunking with a placenta. “

Drinking water microbiology — from measurement to management – David Coil – MicroBEnet

Movie Night at Bozeman Public Library, April 7th: Bugs with Benefits, an Intro to the Human Microbiome – Bozeman Daily

Do Antibiotics Raise Diabetes Risk via Gut Microbiota? – Liam Davenport – Medscape

About Genome Biology study: Longer DNA fragments reveal rare species diversity – Phys.org

Editorial about mBio study: Soil source for vine bacteria – Nature

Treating the Root Cause of IBS: Small Intestine Bacterial Overgrowth – Maura Henninger – Huffington Post

Origin Sciences Ltd: Newly-Published Data Shows the Effectiveness of OriCol™ for Sampling the Gut Microbiome – BusinessWire

Smart phone diagnosis? Biosensing platform quickly and accurately diagnoses disease and monitors treatment remotely – Science Daily

Science, publishing, and career

Peer review with Elizabeth Marincola (CEO of PLOS) – Royal Society

Fighting Plagiarism In Scientific Papers – Tommaso Dorigo – Science 2.0

Editor’s point of view: Science’s Big Scandal: Even legitimate publishers are faking peer review – Charles Seife – Slate

Stanford Graduate student charged with poisoning labmates’ drinks – Kylie Jue – Stanford Daily

Four simple tools to promote gender balance at conferences – Julie Pfeiffer – The Tree of Life

Bik’s Picks

The human sex ratio from conception to birth – Steven Hecht Orzack – PNAS USA

Failed synchronization of the womb’s clock with mother’s body clock critical in miscarriages – Science Daily

Watch the century’s fastest lunar eclipse Saturday – CBS News

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April 1, 2015

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April 1st science

Want to live chemical free? Try Doctor Bacfarc’s Dark Matter Diet™! – Galileo’s Pendulum

Zoology: Here be dragons – Andrew J Hamilton – Nature

CERN researchers confirm existence of the Force, with scientist Ben Kenobi – Cian O’Luanaigh – CERN

Against April Fools’ in Science Journalism – Lee Billings – Scientific American

Human oral microbiome

Comparison of Oral Microbial Profiles between Children with Severe Early Childhood Caries and Caries-Free Children Using the Human Oral Microbe Identification Microarray – Chen Ma – PLOS ONE

Like pulling teeth: Microbiota at teeth and implants in partially edentulous patients. A 10-year retrospective study – Sigrun Eick – Clinical Oral Implants Research

Human respiratory microbiome

The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation – Lisa A Carmody – Microbiome

Human gut microbiome

Fate, activity, and impact of ingested bacteria within the human gut microbiota – Muriel Derrien, Johan E.T. van Hylckama Vlieg – Trends in Microbiology

Gut Microbiota and Tacrolimus Dosing in Kidney Transplantation – John R. Lee – PLOS ONE

Gut microbiota: Optimal sampling of the intestinal microbiota for research – R. Balfour Sartor – Nature Reviews Gastroenterology & Hepatology

Review: Towards a more comprehensive concept for prebiotics – Laure B. Bindels – Nature Reviews Gastroenterology & Hepatology

Pregnancy and birth microbiome

Antibiotic Exposure in Infancy and Risk of Being Overweight in the First 24 Months of Life – Antti Saari – Pediatrics

Animal microbiome

Bats: External Microbiota of Western United States Bats: Does It Matter Where You Are From? – Ara Kooser – BioRxiv

Aphids: Infection Dynamic of Symbiotic Bacteria in the Pea Aphid Acyrthosiphon pisum Gut and Host Immune Response at the Early Steps in the Infection Process – François Renoz – PLOS ONE

Plant microbiome

Presentation: Mining the Agave Microbiome for Adaptations to Arid Environments – Devin Coleman-Derr – JGI

Soil and plant root microbiome

Baseline Survey of Root-Associated Microbes of Taxus chinensis (Pilger) Rehd – Qian Zhang – PLOS ONE

Extremophile microbiome

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics – Gabriel G. Perron – PLOS ONE

Built environment microbiome

Influence of a Non-Hospital Medical Care Facility on Antimicrobial Resistance in Wastewater – Mathias Bäumlisberger – PLOS ONE

Metagenomics

Staph in staff: Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission – Gavin K. Paterson

Metabolomics

Marine sequestration of carbon in bacterial metabolites – Oliver J. Lechtenfeld – Nature Communications

Ecology

Not microbial, but of interest: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity – Francesco Carrara – Methods in Ecology and Evolution

Techniques

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform – Melanie Schirmer – Nucleic Acids Research

Microbes in the news

Apparently, this is not a joke: #Kryptonia: Hiding in Plain Sight: Researchers using metagenomics and single-cell sequencing identify a potential new bacterial phylum – Kim Smuga-Otto – The Scientist

Can ‘ghosts’ cause bad air? Poor indoor air quality and ‘sightings’ – Science Daily

Cool Jobs: The Cave Microbiologist – Scientiflix

Bacteria are plural, Smithsonian. Found: The Bacteria That’s Making You Stink – Erin Blakemore – Smithsonian

Duke-UNC Collaboration Creating ‘Gut-on-a-Chip’ – Marla Vacek Broadfoot – Duke Translational Medicine Institute

Researchers Discover New Source Of Airborne Antibiotic-Resistant Bacteria – Erin Schumaker – Huffington Post

Research proves that intestinal bacteria can be used to classify the effects of different diseases – Medical Xpress

Vanillin: Are Microbes the Taste-Makers of the Future? – Jeffrey Marlow – Wired.com

Your Microbiome “Tree” – Spectrum MIT
Microbiome Research: A New Frontier in Medicine – Elizabeth Dougherty – Spectrum MIT

Manipulative Microbiomes – Gut bacteria control tumor growth via the mammalian immune system – Jenny Rood – The Scientist

This might be April 1st joke, but realistic results: Scientists reveal the thousands of bacteria colonies growing on dirty coins and notes – Sarah Griffiths – Daily Mail

New ‘Intraterrestrial’ Virus Found in Ocean Depths – Patrick J Kiger – Discovery

Best date ever: Date syrup shows promise for fighting bacterial infections – Science Daily

Science, publishing, career

How Articles Get Noticed and Advance the Scientific Conversation – Victoria Costello – PLOS Blogs

A Biotic Game Design Project for Integrated Life Science and Engineering Education –
Nate J. Cira – PLOS Biology

Bik’s Picks

Getting away with murder: Global analysis of fungal morphology exposes mechanisms of host cell escape – Teresa R. O’Meara – Nature Communications

Monarch Larva Monitoring Project Helps Citizen Scientists Build Connections to Nature – Eva Lewandowski – PLOS Blogs

Rats see the pain in other rats’ faces – Virginia Morell – Science Mag

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