Category Archives: Human respiratory

April 30, 2015

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General human microbiome

Microbiome Analysis: Trends in Cancer Epidemiology, Challenges and Opportunities – Elizabeth F. Hebert – International Journal of Cancer Research and Molecular Mechanisms

Human respiratory microbiome

Still under embargo/technical difficulties: Swine Farming Is a Risk Factor for Infection With and High Prevalence of Carriage of Multidrug-Resistant Staphylococcus aureus – Shylo E. Wardyn – Clinical Infectious Diseases

The Culturome of the Human Nose Habitats Reveals Individual Bacterial Fingerprint Patterns – Ursula Kaspar – Environmental Microbiome

Human gut microbiome

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods – Mamun-Ur Rashid – Clinical Infectious Diseases

Animal models of microbiome research

Modulation of growth performances, survival, digestive enzyme activities and intestinal microbiota in common carp (Cyprinus carpio) larvae using short chain fructooligosaccharide – Seyed Hossein Hoseinifar – Aquaculture Research

Plant microbiome

Simulation of the evolution of the legume-rhizobia symbiosis under the conditions of ecological instability – N. I. Vorobyov – Russian Journal of Genetics: Applied Research

Review: Plant-associated fungal communities in the light of meta’omics – Derek Peršoh – Fungal Diversity

Water microbiome

Editorial : Roles and mechanisms of parasitism in aquatic microbial communities – Télesphore Sime-Ngando – Frontiers in Microbiology

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Relationships between Microbial Compositions and Hydrochemical Factors in Nitrate Contaminated Groundwater of Hun River Alluvial Proluvial Fan, China – A.X. Zhou – Journal of Agricultural Science and Technology

Extremophile microbiome

Picoplankton and nanoplankton variability in an Antarctic shallow coastal zone (Admiralty Bay) during the austral summer of 2010/2011 – Mariana Vanzan – Polar Biology

Microbiome of the built environment

Screening of bacteria and concrete compatible protection materials – Yusuf Çağatay Erşan – Construction and Building Materials

Bioreactor microbiology

Metal Oxide Nanoparticles Induce Minimal Phenotypic Changes in a Model Colon Gut Microbiota – Alicia A Taylor – Environmental Engineering Science

Metagenomics

Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes – Gajender Aleti – Computational and Structural Biotechnology Journal

Book: VIRONOMICS: The Study of Viral Genomics in Human Cancer and Disease – Dirk P. Dittmer – Next Generation Sequencing in Cancer Research, Volume 2

Microbes in the news

An Atlas of the Bacteria and Fungi We Breathe Every Day – Neel V. Patel – Wired

Deadly Gut Bacteria Infections Peak in Spring – Rachael Rettner – Live Science

Study finds swine farming is a risk factor for drug-resistant staph infections – University of Iowa

Turning to Bacteria to Fight the Effects of Climate Change – Esther Ngumbi – Scientific American

Are We Less “Gutsy” Than we Used to Be? New Clues about the Evolution of the Human Microbiome from Research in Apes – Sharon Greenblum – Food Insight

How Fluid Flow Affects Bacteria – Science 2.0

Four Exceptional Contributions to the Advancement of Clinical Microbiology and Infectious Diseases Recognised at ECCMID – Select Science

Microbiome Hypome (articles that overstate microbiome importance)

The Cure for Brain Diseases Is in Your Gut – David Perlmutter – The Daily Beast

Microbes and money

Irish Microbiome Research Institute Partners With San-Francisco Based Second Genome On Bowel Disease Research – IBD News Today

Bik’s Picks

Low Sunlight Increases Pancreatic Cancer Risk; Why It’s Important To Get Enough Vitamin D – Justin Caba – Medical Daily

Bat Wings Harbor Special Sensory Cells – Stephanie Pappas – Live Science

Sea Lion Pup Waddling Around San Francisco’s Marina District Safely Captured – KPIX / KCBS

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April 29, 2015

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Events

Friday May 1: Del Mar College, Corpus Christi, TX Hosts a Day of Science with “How to Train Your Superorganism: Via the Microbiome” – Record Star

Pregnancy and birth microbiome

Colostrum of Healthy Slovenian Mothers: Microbiota Composition and Bacteriocin Gene Prevalence – Tanja Obermajer – PLOS ONE

Human respiratory microbiome

The Importance of Bacterial and Viral Infections Associated with Adult Asthma Exacerbations in Clinical Practice – Motoyasu Iikura – PLOS ONE

Human gut microbiome

Fat, fibre and cancer risk in African Americans and rural Africans – Stephen J. D. O’Keefe – Nature Communications

Characterization of Bacterial and Fungal Microbiome in Children with Hirschsprung Disease with and without a History of Enterocolitis: A Multicenter Study – Philip K. Frykman – PLOS ONE

Animal models of microbiome research

Editorial: Host–microbe interactions and the enteric nervous system: a new connection? – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal gut microbiome

Integrated Community Profiling Indicates Long-Term Temporal Stability of the Predominant Faecal Microbiota in Captive Cheetahs – Anne A. M. J. Becker – PLOS ONE

Plant microbiome

The Intracellular Scots Pine Shoot Symbiont Methylobacterium extorquens DSM13060 Aggregates around the Host Nucleus and Encodes Eukaryote-Like Proteins – Janne J. Koskimäki – mBio

Extremophile microbiome

Deep groundwater and potential subsurface habitats beneath an Antarctic dry valley –
J. A. Mikucki – Nature Communications

Microbial Diversity in a Permanently Cold and Alkaline Environment in Greenland – Mikkel A. Glaring – PLOS ONE

Bioinformatics

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

Maximum likelihood tree estimation using codon substitution models with multiple partitions – Stefan Zoller – Molecular Biology and Evolution

Techniques

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions – Julia Birtel – PLOS ONE

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows – Dáithí C. Murray – PLOS ONE

Microbes in the news

Diet swap has dramatic effects on colon cancer risk for Americans and Africans – Science Daily

Mapping Genomes of Pine Bacteria Yields Unexpected Results – UC Merced

Salty aquifer, previously unknown microbial habitat discovered under Antarctica – Science Daily

Chemistry of seabed’s hot vents could explain emergence of life – Eureka Alert
and
Hydrothermal Vents Able to Create Simple Organic Molecules, Study Says – Sci-News

Understanding genetic diversity of bacteriophages – Phys.org

Deadly Gut Bacteria Peak in Spring (about C. difficile) – Rachael Rettner – LiveScience

30 min podcast about Antonie van Leeuwenhoek: The ‘first’ microbiologist and climate modelling – SocGenMicro – SoundCloud

Drug resistant bacteria common for nursing home residents with dementia – Science Daily

Rubella Has Been Eliminated From the Americas, Health Officials Say – Donald G. McNeil Jr. – New York Times

Science, publishing, and career

Symposium overview: Raising standards – International Symposium on Research Assessment and Evaluation in Shanghai, China – Michelle Grayson – Nature

Collateral damage: How one misconduct case brought a biology institute to its knees – The fall out from the STAP case is still being felt across Japan – David Cyranoski – Nature

Bik’s Picks

‘Obesity Signature’ Written in Pee – Rachael Rettner – LiveScience

Childhood bullying: Worse long-term mental health than maltreatment by adult – Science Daily

FDA Approves Double-Chin Eliminator Injection, Kybella – Sydney Lupkin – ABC News

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April 22, 2015

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Happy Earth Day! Today, I screened 371 papers for you from ISME Journal, Nature, Applied and Environmental Microbiology, PLOS ONE, and others. Here is what I found:

Human oral microbiome

Quorum-Sensing Dysbiotic Shifts in the HIV-Infected Oral Metabiome – Robert E. Brown – PLOS ONE

Full mouth periodontal debridement with or without adjunctive metronidazole gel in smoking patients with chronic periodontitis: A pilot study – C. C. Bergamaschi – Journal of Periodontal Research

Human respiratory microbiome

Changes in Cystic Fibrosis Airway Microbial Community Associated with a Severe Decline in Lung Function – Patrizia Paganin – PLOS ONE

Bacteriological Assessment of Healthcare-Associated Pneumonia Using a Clone Library Analysis – Shingo Noguchi – PLOS ONE

Human gut microbiome

Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome – Christine Dominianni – PLOS ONE

Editorial: Gut Bacteria Combined With Poor Diet May Promote Childhood Malnutrition – M. J. Friedrich – JAMA

Animal models of microbiome research

Effects of dietary supplementation of selenium-enriched probiotics on production performance and intestinal microbiota of weanling piglets raised under high ambient temperature – C. H. Lv – Journal of Animal Physiology and Animal Nutrition

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation – A. Corrigan – Applied and Environmental Microbiology

Animal microbiome

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats – Jinzhen Jiao – Applied and Environmental Microbiology

Shifts in Bacterial Communities of Eggshells and Antimicrobial Activities in Eggs during Incubation in a Ground-Nesting Passerine – Stéphanie Grizard – PLOS ONE

Plant microbiome

Fungi on leaves: Host genotype is an important determinant of the cereal phyllosphere mycobiome – Rumakanta Sapkota – New Phytologist

Soil and plant soil microbiome

Continental-scale distributions of dust-associated bacteria and fungi – Albert Barberán – PNAS USA

Missing forests: Soil microbiome responses to the short-term effects of Amazonian deforestation – Acacio A. Navarrete – Molecular Ecology

Distinct soil microbial diversity under long-term organic and conventional farming – Martin Hartmann – The ISME Journal

Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms – Maxime Bonhomme – Molecular Biology and Evolution

Differential Assemblage of Functional Units in Paddy Soil Microbiomes – Yongkyu Kim – PLOS ONE

The Effect of Biochar and Its Interaction with the Earthworm Pontoscolex corethrurus on Soil Microbial Community Structure in Tropical Soils – Jorge Paz-Ferreiro – PLOS ONE

Water microbiome

Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments – Vanessa Rédou – Applied and Environmental Microbiology

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems – Delphine Lallias – The ISME Journal

Food microbiology

Spoiler alert: Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage – Stéphane Chaillou – ISME Journal

Proteomics

“You produce while I clean up,” a strategy revealed by exoproteomics during Synechococcus–Roseobacter interactions – Joseph A. Christie-Oleza – Proteomics

Microbes in the news

How Modern Life Depletes Our Gut Microbes – Michaeleen Doucleff – NPR Goats and Soda

Great longread: Forensic science: The soil sleuth – Forensic geologist Lorna Dawson helps convict criminals using the dirt from their shoes – Chelsea Wald – Nature

A Microbiome Three-Conference Summary – Kristina Campbell – The Intestinal Gardener

University brews up artificial kopi luwak coffee with even more flavor using civet microbiome – Katherine Wei – China Post

Science, publishing, and career

The postdoc series: What comes next? A postdoc sets you up for a variety of careers, including academia, editing, working in industry, core laboratories and more – Julie Gould – Nature Jobs

Is it fair to evaluate Ph.D. students based on their personalities? Fallout from a gutless adviser – Alice Huang – Science

Minority Ph.D. students: Where do they go? – Beryl Lieff Benderly – Science

Bibliometrics: The Leiden Manifesto for research metrics – Diana Hicks – Nature

Rita Colwell: Women in science still battle bias – Mike McInally – Mid-Valley Health

Bik’s Picks

The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop – Tina Kyndt – PNAS

How exactly do mosquitoes track us down – and what makes humans their meal of choice? – Biodetectives

Construction workers in China accidentally unearth dinosaur eggs – Sean O’Kane – The Verge
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April 21, 2015

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I don’t always eat steak, but when I do, I will put some garlic on it.

Conferences

WAO Symposium on Food Allergy and the Microbiome – December 2015 – Miami, FL, USA

Call for papers: Interactions of the Human Microbiome and Immune System in Health Resilience and Disease Pathogenesis – Journal of Immunology Research

Microbiome of pregnancy and birth

Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health – Ted Jost – Nutrition Reviews

Human oral microbiome

Editorial on “The oral microbiome in an ecological perspective: More than just a sum of microbes” – Egija Zaura and Alex Mira – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Rapid detection of emerging pathogens and the loss of microbial diversity associated with severe lung disease in cystic fibrosis – William G. Flight – Journal of Clinical Microbiology

Review behind a thick paywall: The pediatric microbiome and the lung – Michael Tracy – Current Opinion in Pediatrics

Review: Lung Microbiomes: New Frontiers? – Kathryn DeRiemer – American Journal of Respiratory and Critical Care Medicine

Review: A systematic review and meta-analysis of probiotics for the treatment of allergic rhinitis – Alexander E. Zajac – International Forum of Allergy & Rhinology

Human gut microbiome

Ménage-à-trois of bariatric surgery, bile acids and the gut microbiome – Rajendra Raghow – World Journal of Diabetes

Gut Microbiome Compositional and Functional Differences between Tumor and Non-tumor Adjacent Tissues from Cohorts from the US and Spain – Gut Microbes

Review: No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens – Martina Sassone-Corsi and Manuela Raffatellu – The Journal of Immunology

Review on chronic kidney disease: Altered intestinal microbial flora and impaired epithelial barrier structure and function in CKD: the nature, mechanisms, consequences and potential treatment – Nosratola D. Vaziri – Nephrology Dialysis Transplantation

Review: The Role of Microbial Amino Acid Metabolism in Host Metabolism – Evelien P. J. G. Neis – Nutrients

Review: Linking Smoking, Coffee, Urate, and Parkinson’s Disease – A Role for Gut Microbiota? – Filip Scheperjans – Journal of Parkinson’s Disease

Animal and other models of microbiome research

Have some garlic with your steak: Dietary allicin reduces transformation of L-carnitine to TMAO through impact on gut microbiota – Wei-Kai Wu – Journal of Functional Foods

Innate Lymphoid Cells Control Early Colonization Resistance against Intestinal Pathogens through ID2-Dependent Regulation of the Microbiota – Xiaohuan Guo – Immunity

Effect of donor animal species and their feeding on the composition of the microbial community establishing in a rumen simulation – M. Witzig – Journal of Applied Microbiology

Impact of a novel protein meal on the gastrointestinal microbiota and host transcriptome of larval zebrafish Danio rerio – Eugene Rurangwa – Frontiers in Physiology

Animal microbiome

Shit happens: Shifts in the gut microbiome observed in wildlife (Giraffa camelopardalis, Antidorcas marsupialis) fecal samples exposed to natural weather conditions: lessons from time series analyses using next generation sequencing for application in field studies – Sebastian Menke – Methods in Ecology and Evolution

Caste-Specific Differences in Hindgut Microbial Communities of Honey Bees (Apis mellifera) – Karen M. Kapheim – PLOS ONE

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Tieshan Jiang – PLOS ONE

Plant root and soil microbiome

Bacterial diversity amplifies nutrient-based plant–soil feedbacks – Simone Weidner – Functional Ecology

Non-random species loss in bacterial communities reduces antifungal volatile production –
W. H. Gera Hol – Ecology

Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis – N. Kh. Sergaliev – Eurasian Soil Science

Physiological profiles of microbial communities in mine soils afforested with different tree species – Marcin Chodak – Ecological Engineering

Microbial lipid and amino sugar responses to long-term simulated global environmental changes in a California annual grassland – Chao Liang – Frontiers in Microbiology

Water microbiome

Seasonal diversity and dynamics of haptophytes in the Skagerrak, Norway, explored by high-throughput sequencing – Elianne Sirnæs Egge – Molecular Ecology

Extremophiles

Relationship between phylogenetic and nutritional diversity in Arctic (Kandalaksha Bay) seawater planktonic bacteria – Chiara Pesciaroli – Annals of Microbiology

Geochemical Characteristics and Microbial Community Composition in Toxic Metal-Rich Sediments Contaminated with Au-Ag Mine Tailings – Man Jae Kwon – Journal of Hazardous Materials

Uranium isotopes fingerprint biotic reduction – Malgorzata Stylo – PNAS

Bioreactor microbiome

Metaproteomics of complex microbial communities in biogas plants – Robert Heyer – Microbial Biotechnology

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane – Florence Braun – PLOS ONE

Reactor performance and methanogenic archaea species in thermophilic anaerobic co-digestion of waste activated sludge mixed with food wastewater – Hyun Min Jang – Chemical Engineering Journal

Functional food microbiology

A proposed framework for an appropriate evaluation scheme for microorganisms as novel foods with a health claim in Europe – Sylvie Miquel – Microbial Cell Factories

Metagenomics and bioinformatics

CoMeta: Classification of Metagenomes Using k-mers – Jolanta Kawulok, Sebastian Deorowicz – PLOS ONE

Large-scale contamination of microbial isolate genomes by Illumina PhiX control – Supratim Mukherjee – Standards in Genomic Sciences

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL – Ali May – Nucleic Acids Research

Mini review: The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life – Eugene V. Koonin – Journal of Molecular Evolution

Not really metagenomics but of interest: Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis – Guillaume Méric – Genome Biology and Evolution

Haven’t we microbiologists already been doing this for years?
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform – Shadi Shokralla – Scientific Reports

Techniques

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction – Conny Mathay – Biopreservation and Biobanking

Microbes in the news

Housing characteristics and microbial communities in homes of asthmatic children – Elisabeth Bik – MicroBEnet

OCHS science experiment finds space a hospitable place for bacteria – Cindy Nevitt – Press of Atlantic City

Uranium isotopes carry the fingerprint of ancient bacterial activity – Phys.org

Immune cells support good gut bacteria in fight against harmful bacteria – University of Chicago

Q&A: What Is Listeria? Bacteria Found in Blue Bell Ice Cream – Mary Clare Jalonick – ABC News

Grant will help University of Minnesota study antibiotic-resistant bacteria – Star Tribune

Science, publishing, and career

Mya Breitbart awarded the 2015 STEM Woman of the Year – University of South Florida

Bik’s Picks

Fast imaging of live organisms with sculpted light sheets – Aleksander K. Chmielewski – Scientific Reports

Cheesy, metallic, sweet: 170-year-old champagne is clue to winemaking’s past – Allie Wilkinson – Nature

New Evidence of Prehistoric Trade With Asia Found at Bering Land Bridge Site – Huffington Post
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April 17, 2015

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Two new papers on the microbiome of not-western populations, and the influence of the microbiome on the circadian rhythm (or is it the other way around?).

Events

Session on “The Microbiome” at the AHCJ (Association of Health Care Journalists) annual meeting, Santa Clara, CA – Friday April 24 – HT: Jonathan Eisen

Human oral microbiome

Review: Oral infections and cardiovascular disease – Karim El Kholy – Trends in Endocrinology & Metabolism

Human skin microbiome

Review: Rosacea : Part I. Introduction, categorization, histology, pathogenesis, and risk factors – Aimee M. Two – Journal of the American Academy of Dermatology

Human respiratory microbiome

Review: Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis – Michael D. Parkins – Journal of Cystic Fibrosis

Human gut microbiome

The microbiome of uncontacted Amerindians – Jose C. Clemente – Science Advances

The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes – Inés Martínez – Cell Reports

Altered fecal microbiota composition in patients with major depressive disorder – Haiyin Jiang – Brain, Behavior, and Immunity

Forum: Keeping gut lining at bay: impact of emulsifiers – Patrice D. Cani, Amandine Everard

Review: Possible role of the microbiome in the development of acute malnutrition and implications for food-based strategies to prevent and treat acute malnutrition – Ellen Murray, Mark Manary – Food and Nutrition Bulletin

Review: The gut microbiota and liver disease – Cristina Llorente – CMGH Cellular and Molecular Gastroenterology and Hepatology

Animal and other models

Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism – Vanessa Leone – Cell Host & Microbe

Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations – Özgün C O Umu – Microbiome Journal

In-vitro model for studying methanogens in human gut microbiota – William Tottey – Anaerobe

Relationship between the gut microbiota, lipopolysaccharide, inflammation, and metabolic osteoarthritis development: Studies in a rat model – K.H. Collins – Osteoarthritis and Cartilage

Effects of dietary supplementation with β-glucan and synbiotics on growth, haemolymph chemistry, and intestinal microbiota and morphology in the Pacific white shrimp – S. Boonanuntanasarn – Aquaculture Nutrition

Extremophiles / rock microbiome

On the rocks: Autoendoliths: a distinct type of rock-hosted microbial life – J. Marlow – Geobiology

Food microbiology

Evaluation of the Dynamics of Microbiological Quality in Lightly Pickled Napa Cabbages During Manufacture – Kazuya Masuda – Journal of Food Safety

Microbes in the news

Western lifestyle may limit the diversity of bacteria in the gut – Joseph Caputo – Cell Press
What Your Poop Says About Your Lifestyle – Agata Blaszczak-Boxe – Live Science
Is super-diverse Amazon microbiome something to strive for? – Penny Sarchet – New Scientist
Yanomami, An Amazon Tribe, Could Provide Answers To Antibiotic Resistance – Susan Scutti – Medical Daily
Study Reveals Microbiome Diversity, Antibiotic Resistance Genes in Isolated Amazon Tribe – Andrea Anderson – Genome Web
Bacteria bonanza found in remote Amazon village – Boer Deng – Nature

Gut Microbes Influence Circadian Clock – Anna Azvolinsky – The Scientist

“Computers are the new microscopes, and data is the new blood draw,” UCSD hiring ‘big data’ stars – Gary Robbins – UT San Diego

Brushing teeth regularly can save you from future heart attacks – Business Standard

Escape by dilution: dissolved organic matter in the ocean is too dilute to be consumed – Jack J. Middelburg – Science

Microbiome Researcher Also Fan Of Guns And Roses – The Allium

Science, publishing, and career

A PI is forced to close his lab: The reality that dare not speak its name – Andrew D. Hollenbach
A harsh response:
On productivity and the “unfair” grant funding game – DrugMonkey

Survey: Help solve the mystery of the disappearing Ph.D.s – Beryl Lieff Benderly – Science

Ten Simple Rules for Effective Online Outreach – Holly M. Bik – PLOS Computational Biology

The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences – Melanie I. Stefan – PLOS Computational Biology

On the ‘benefits’ of Postdocs – Michelle Collins – The Spectroscope

Claiming sexism in science is over is just wishful thinking – Lisa Grossman – New Scientist

Bik’s Picks

Through This Chemical Loop, Dogs Win Our Hearts – Ed Yong – National Geographic

Octopuses Have Moves, But No Rhythm – Laura Geggel – Live Science

The Roomba for Lawns Is Really Pissing Off Astronomers – Davey Alba – Wired

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April 15, 2015

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Microbiome of pregnancy and birth

The Gut Microbiota Composition in Dichorionic Triplet Sets Suggests a Role for Host Genetic Factors – Kiera Murphy – PLOS ONE

Human oral microbiome

Periodontitis and Porphyromonas gingivalis in Preclinical Stage of Arthritis Patients – Motomu Hashimoto – PLOS ONE

Investigation of Salivary Function and Oral Microbiota of Radiation Caries-Free People with Nasopharyngeal Carcinoma – Jingyang Zhang – PLOS ONE

Human respiratory microbiome

Impact of the CFTR-Potentiator Ivacaftor on Airway Microbiota in Cystic Fibrosis Patients Carrying A G551D Mutation – Cédric Bernarde – PLOS ONE

An Observational Study Examining the Relationship between Respiratory Symptoms, Airway Inflammation and Bacteriology in Children with Severe Neurodisability – Ruth E. Trinick – PLOS ONE

Sinonasal Microbiome Sampling: A Comparison of Techniques – Ahmed Bassiouni – PLOS ONE

Animal models of microbiome research

Robust Vaginal Colonization of Macaques with a Novel Vaginally Disintegrating Tablet Containing a Live Biotherapeutic Product to Prevent HIV Infection in Women– Laurel A. Lagenaur – PLOS ONE

Animal microbiome

Not exactly microbiome but nice: Detection of Mitochondrial COII DNA Sequences in Ant Guts as a Method for Assessing Termite Predation by Ants – Tom M. Fayle – PLOS ONE

Soil microbiome

Forensic Biology: Fungi Identify the Geographic Origin of Dust Samples – PLOS ONE

The Impact of Resource Availability on Bacterial Resistance to Phages in Soil – Pedro Gómez – PLOS ONE

Water microbiome

Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary – Peeter Laas – PLOS ONE

Food microbiology

Cheese’omics: Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses – Eric Dugat-Bony – PLOS ONE

More microbiology

Sackler Colloquium: Reproduction, symbiosis, and the eukaryotic cell – Peter Godfrey-Smith – PNAS USA

Alternating Antibiotics Render Resistant Bacteria Beatable – Lauren Richardson – PLOS Biology

Microbes in the news

University doctoral candidate Joanna Adadevoh researches bacterial microbe groundwater purification – Anna Pollard – Cavalier Daily

13 min video: Connecting the Microbiome and Antibiotics to Obesity – Eric Topol talks to Martin Blaser

Probiotics might be like a DJ in a club: In the gut, one key probiotic helps by orchestrating others – Melissa Healy – Los Angeles Times

Microbiology and art

Extremophiles on Display: A new American Museum of Natural History exhibit highlights the incredible range of conditions under which life on Earth survives – Ashley P. Taylor – The Scientist

Science, publishing, and career

AMA: Peer review process and retractions in scientific publishing – Ivan Oransky and Charon Pierson – Reddit/science

Opinion: Senior Scientists Should Be Writing – Three reasons why authorship matters, even—perhaps especially—to established scholars – Jens P. Goetze and Jens F. Rehfeld – The Scientist

Bik’s Picks

Scientists unveil sex-linked control of genes – Stanford Medicine

Distinct metabolomic signatures are associated with longevity in humans – Susan Cheng – Nature Communications

Female Chimps – The Possible Inventors Of Spears – Kurt Cottrell – MidDay Daily

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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 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 3, 2015

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Check out today’s #PLOSBuzzFeed on Twitter for some Friday fun.

Human general microbiome

Only 10 microbes are designated by the International Agency for Cancer Research (IACR) as carcinogenic to humans (Review): Cancer and the microbiota – Wendy S. Garrett – Science

Microbiome of pregnancy and birth

Administration of a multistrain probiotic product (VSL#3) to women in the perinatal period differentially affects breast milk beneficial microbiota in relation to mode of delivery – Paola Mastromarino – Pharmacological Research

Conference abstract: Preterm Infant Gut Microbiome and Weight at 36 Weeks Corrected Gestational Age – Diana Taft – The FASEB Journal

Still in press: Should Infants Cry Over Spilled Milk? Fecal Glycomics as an Indicator of a Healthy Infant Gut Microbiome – Steven A Frese – Journal of Pediatric Gastroenterology & Nutrition

Human respiratory microbiome

Conference abstract: Correlative Changes in Macrophage Polarization and Pulmonary Microbiota in Lung Transplant Recipients – E. Bernasconi – The Journal of Heart and Lung Transplantation

Harder to breathe (Review): The changing face of asthma and its relation with microbes – Chris S. Earl – Trends in Microbiology

Human gut microbiome / functional foods

Metabolic and physiologic effects from consuming a hunter-gatherer (Paleolithic)-type diet in type 2 diabetes – U Masharani – European Journal of Clinical Nutrition

Findings from a Randomized Controlled Trial of Fecal Transplantation for Patients with Ulcerative Colitis – Noortje G. Rossen – Gastroenterology

Correlation between gut microbiota composition and parasitic infection of pre-adolescence in Malaysia – Chun-Wie Chong – Journal of Microbiology, Immunology and Infection

Fit to the bone (review): The intestinal microbiome and skeletal fitness: connecting bugs and bones – Julia F. Charles – Clinical Immunology

Poster abstract: Effect of Prebiotic Fiber Intake on Adiposity and Inflammation in Overweight and Obese Children: Assessing the Role of the Gut Microbiota – Alissa C. Nicolucci – Canadian Journal of Diabetes

Animal models of microbiome

Poster abstract: Parallel Improvement in Body Weight, Glycemia, and Intestinal Permeability but not Body Fat with Prebiotic- and Antibiotic-Induced Gut Microbiota Modification – Marc Bomhof – Canadian Journal of Diabetes

Animal microbiome

Drosophila: The Impact of Host Diet on Wolbachia Titer in Drosophila – Laura R. Serbus – PLOS Pathogens

Soil and compost microbiome

Soil plots in Burgundy (but no vineyards!): Mapping and determinism of soil microbial community distribution across an agricultural landscape – Florentin Constancias – MicrobiologyOpen

Molecular profile of microbiota of Finnish commercial compost suppressive against Pythium disease on cucumber plants – D. Yu – Applied Soil Ecology

Wildfire effects on the properties and microbial community structure of organic horizon soils in the New Jersey Pinelands – Robyn A. Mikita-Barbato – Soil Biology and Biochemistry

Extremophile microbiome (see also “Microbes in the news” below)

Microbial dwarves in the mines: Use of Phosphate Solubilizing Bacteria to Leach Rare Earth Elements from Monazite-Bearing Ore – Doyun Shin – Minerals

Food microbiology

This study smells: Microbiological spoilage and volatiles production of gutted European sea bass stored under air and commercial modified atmosphere package at 2oC – Foteini F. Parlapani – Food Microbiology

Viable cells differentiation improves microbial dynamics study of fermented milks – Davide Porcellato – International Dairy Journal

Wine electrophoresis? Inactivation of wine associated microbiota by continuous pulsed electric field treatments – Lucía González-Arenzana – Innovative Food Science & Emerging Technologies

Bioreactor microbiome

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

Bioinformatics

PhyloRelief: Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting – Davide Albanese – PLOS Computational Biology

One of the figures has the Giant Microbes in it! Personalized microbial network inference via co-regularized spectral clustering – Sultan Imangaliyev – Methods

Microbes in the news

“Life at the Limits” shows extremophiles aren’t just bacteria – AMNH exhibit includes live axolotls, nautiluses, and mantis shrimp – John Timmer – Ars Technica

uBiome’s Dental Campaign to Give Portion of Proceeds to Charitable Dental Organization
Partnering with Oral Health America’s Smiles Across America – PR Web

No Bonferroni correction but: Is The Microbiome Correlated with Income? The Answer Will Surprise You – Alexandra Carmichael – uBiome

Cross-posting this week’s contribution for MicroBE.net: Gently down the stream: the microbiome along a river’s course – Elisabeth Bik – MicroBE.net

Cleaning with Bleach May Lead to Childhood Infections – Laura Geggel – Live Science

How the guts of poultry affect performance – Jake Davies – FWI

Cigarette Smoke Makes Superbugs More Aggressive – Heather Buschman – UC San Diego

The Plague Bacteria Found in Flea Samples Near Flagstaff – NAZ Today

Travelers Bringing Drug-Resistant Bacteria to U.S.: Strain of Shigella is easily transmitted and causes tough-to-treat diarrhea, CDC says – WebMD

France bans imports of Puglia vegetables as olive bacteria starts mini trade war – Nicole Winfield – US News

Science, publishing, and career

Hoax-detecting software spots fake papers – John Bohannon – Science

A career is like a love affair – Madeleine Jacobs – Science

Ten Simple Rules to Win a Nobel Prize – Richard J. Roberts – PLOS Computational Biology

Science and art

This is gorgeous: A Sprawling New Cut Paper Bacterium by Rogan Brownby – Christopher Jobson – Colossal

Bik’s Picks

All animal phyla in 35 photos – Melissa Hogenboom – BBC

Shelled Out: 5 Egg-Citing Facts – Laura Geggel – Live Science

My Real-Time Response To Learning What The Rock Eats Every Day – Mallory Ortberg

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March 31, 2015

Posted on by

For today’s digest, I screened over 500 papers, and thousands of Tweets for you. Here is my selection:

Pregnancy and birth microbiome

PhD thesis [PDF]: Dynamics of co-existing Escherichia coli lineages in situ of the infant gut – Heidi Kira Gumpert – Technical University of Denmark

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis – Anne G Hoen – The Journal of Pediatrics

Review: Probiotics for Preterm Infants: A Premature or Overdue Necrotizing Enterocolitis Prevention Strategy? – Sharon Anderson – Neonatal Network

Review: Preterm infant nutrition, gut bacteria, and necrotizing enterocolitis – Josef Neu –  Current Opinion in Clinical Nutrition & Metabolic Care

Human oral microbiome

Periodontal Therapy Effects on Nitrite Related to Oral Bacteria: A 6-Month Randomized Clinical Trial – Sheila C Cortelli – Journal of Periodontology

Perspective: Mouthguards: Does the indigenous microbiome play a role in maintaining oral health? – Purnima S. Kumar and Matthew R. Mason – Frontiers in Cellular and Infection Microbiology

Human respiratory microbiome

Nasal Inoculation of the Commensal Neisseria lactamica Inhibits Carriage of Neisseria meningitidis by Young Adults: A Controlled Human Infection Study – Alice M. Deasy – Clinical Infectious Diseases

Human skin microbiome

Molecular cartography of the human skin surface in 3D – Amina Bouslimani – PNAS USA

Human gut microbiome

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection – Alexa Weingarden – Microbiome Journal

Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization – Zhang Lihua – Anaerobe

Review: The microbiota in inflammatory bowel disease – Donal Sheehan – Journal of Gastroenterology

Review: Promoting Health and Longevity through Diet: From Model Organisms to Humans – Luigi Fontana, Linda Partridge – Cell

Review: TLR4 at the crossroads of nutrients, gut microbiota and metabolic inflammation
Licio A. Velloso – Endocrine Reviews

Review: Cultivating Healthy Growth and Nutrition through the Gut Microbiota – Sathish Subramanian – Cell

Review: The human gut microbiome, a taxonomic conundrum – Senthil Alias Sankar – Systematic and Applied Microbiology

Review: The Role of Infectious Mediators and Gut Microbiome in the Pathogenesis of Celiac Disease – Mohammad Rostami-Nejad – Archives of Iranian Medicine

Review: Exercise and the microbiota – Orla O’Sullivan – Gut Microbes

Animal models of microbiome research

Abnormal Pregnancy Outcomes in Mice Using an Induced Periodontitis Model and the Haematogenous Migration of Fusobacterium nucleatum Sub-Species to the Murine Placenta – Sara Stockham – PLOS ONE

Lactobacillus rhamnosus lowers zebrafish lipid content by changing gut microbiota and host transcription of genes involved in lipid metabolism – Silvia Falcinelli – Scientific Reports

Interactive effects of oligofructose and obesity predisposition on gut hormones and microbiota in diet-induced obese rats – Nina L. Cluny – Obesity

Animal microbiome

Editorial to Baboon microbiome paper: Metagenomics: Social behavior and the microbiome – Jack A Gilbert – eLIFE

More baboons: Development, diet, and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons – Tiantian Ren – Environmental Microbiology

Spider monkey: Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks – Vanessa L. Hale – Journal of Microbiological Methods

Cats: Molecular identification of black-pigmented bacteria from subgingival samples of cats suffering from periodontal disease – L. Pérez-Salcedo – Journal of Small Animal Practice

Desert wool rat: Validating the use of trap-collected feces for studying the gut microbiota of a small mammal (Neotoma lepida) – Journal of Mammalogy

Tortoise: Kinship, inbreeding, and fine-scale spatial structure influence gut microbiota in a hindgut-fermenting tortoise – Michael L. Yuan – Molecular Ecology

Trout: Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes
Miray Etyemez, José Luis Balcázar – Research in Veterinary Science

Fruit fly: Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis – Awawing A. Andongma – Scientific Reports

Aphids: Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA – Jean-Pierre Gauthier – PLOS ONE

Plant microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Soil and plant root microbiome

A novel pathway producing ​dimethylsulphide in bacteria is widespread in soil environments – O. Carrión – Nature Communications

Metabolic characteristics of microbial communities of Aeolian sandy soils induced by saline water drip irrigation in shelter forests – Z. Jin – European Journal of Soil Science

Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities – Yi-Qi Hao – Environmental Microbiology

Effects of monoculture and mixed culture of grass and legume forage species on soil microbial community structure under different levels of nitrogen fertilization – Jie Zhao – European Journal of Soil Biology

Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus – Jean H. Burns – AoB Plants

Long-term oil contamination causes similar changes in microbial communities of two distinct soils – Jingqiu Liao – Frontiers in Environmental Science

Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments – Sadikshya R. Dangi – Applied and Environmental Soil Science

Water microbiome

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification – C. Harwood Theisen – Geobiology

The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth – Stephen M. Techtmann – PLOS ONE

Planktonic eukaryote molecular diversity: discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina) – Enrique Lara – J. Plankton Research

Extremophile microbiome

Ice cover extent drives phytoplankton and bacterial community structure in a large north-temperate lake: implications for a warming climate – B. F. N. Beall – Environmental Microbiology

Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep – Stephanie D. Mendes – Journal of Geophysical Research: Oceans

Built environment microbiome

Are microbial communities in green roof substrates comparable to those in post-industrial sites?—a preliminary study – Chloe J. Molineux – Urban Ecosystems

Food microbiology

Some journals just have great titles: Microbial community changes in Makgeolli during brewing – Changhoon Chai – Journal of the Institute of Brewing

Review: Fermented Foods as Experimentally Tractable Microbial Ecosystems – Benjamin E. Wolfe, Rachel J. Dutton – Cell

Metagenomics and bioinformatics

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains
Marie Trussart – Nucleic Acids Research

CRISPR Detection from Short Reads Using Partial Overlap Graphs – Ilan Ben-Bassat, Benny Chor – Research in Computational Molecular Biology

CLARK: fast and accurate classification of metagenomic and genomic sequences using
discriminative k-mers – Rachid Ounit – BMC Genomics

FlowClus: efficiently filtering and denoising pyrosequenced amplicons – John M Gaspar and W Kelley Thomas – BMC Bioinformatics

Review: 16S rRNA gene high-throughput sequencing data mining of microbial diversity and interactions – Feng Ju, Dr. Tong Zhang – Applied Microbiology and Biotechnology

Book Chapter: Single-Cell Sequencing of Microorganisms – Ying Chen – Single Cell Sequencing and Systems Immunology

Metabolomics

Review: Rumen Nutrition Symposium How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J. L. Firkins and Z. Yu – Journal of Animal Science

Microbes in the news

Modeling microbial metabolism on indoor surfaces – Jack Gilbert – MicroBEnet

Body Maps Expose the Chemical Residue That Coats Our Skin – Marcus Woo – Wired.com
Crazy maps reveal colonies of bacteria and chemicals all over the human body – Kevin Loria – Business Insider
3D Human Skin Maps Aid Study of Relationships Between Molecules, Microbes and Environment – Heather Buschman – UC San Diego

Advancing the understanding of the dental microbiome – Maria Perno Goldie – Dentistry IQ

Who Let the Microbes Out: A Paw Print of Doggy Skin Bacteria – Daniella Lowenberg – PLOS blogs

Antibiotic-resistant bacteria are not match for medieval potion – Alexandra Ossola – Popular Science

Antibiotic-Resistant Bacteria From Texan Cattle Yards Are Now Airborne, Study Finds
Kevin McSpadden – Time

Growing a Baby Microbiome – Kevin Bonham – Scientific American

Poop Transplants Can Treat Severe Infection In Patients – FPJ Bureau – The Free Press Journal

Poo transplants could save thousands – Geoff Egan – Range News
Healthy Microbiome Changes Last After Fecal Transplant in New Research – Elizabeth Gough-Gordon – MPR

With sample collection videos: GoViral – collecting nasal and saliva samples from sick people – Boston Children’s Hospital

Northwestern leads research on effects of long-term stay in space – Peter Kotecki – The Daily Northwestern
Conference paper: Research from the NASA Twins Study and Omics in Support of Mars Missions – NASA Technical Reports

Podcast (1min30): Donate Your Health Data To Medical Science – Cynthia Graber – Scientific American – American Gut, GoViral

You Act What You Eat: How Gut Microbes Modify Our Behavior – Monica Thunder – ResetMe

Meet The Bacteria That Make A Stink In Your Pits – Poncie Rutsch – NPR
Bacterial genetic pathway involved in body odor production discovered – Science Daily

Should Gut Bugs Influence the 2015 Dietary Guidelines? – Cameron Wells – US News

Glowing Tampons Help Detect Sewage Leaks – Gwen Pearson – Wired

Nearly half of hospital uniforms are washed in temperatures too cool to kill bacteria, says DMU research – De Montfort University
Egyptians Brewed Beer in Tel Aviv 5,000 Years Ago – Megan Gannon – Live Science

Conferences

#IHMC2015: 5th International Human Microbiome Congress, March 31-April 2, 2015, Luxembourg (6/23 plenary speakers are women)

The 2nd Microbiome R&D and Business Collaboration Forum Europe, May 07 – 08, 2015, London, UK (10/36 listed speakers are women)

1st Annual Translational Microbiome Conference, 13–14 May 2015, Boston, United States (5/11 speakers are women)

ASM General Meeting, May 30 – June 2, 2015, New Orleans, LA, USA

Symbiomes: Systems Biology of Host-Microbiome Interactions, 5-10 June 2015, Pultusk, Poland (5/17 speakers are women)

The Human Microbiome, 10-12 Jun 2015, EMBL Heidelberg, Germany (8/23 confirmed speakers are women)

Exploring Human Host-Microbiome Interactions in Health and Disease, June 29 – July 1, 2015 , Cambridge, UK (7/17 speakers are women)

Science, publishing, and career

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

Writing a Good Peer Review to Improve Scholarship: What Editors Value and Authors Find Helpful – H. McLaughlin – Social Work Education: The International Journal

Discussion: Mistake index as a surrogate of quality in scientific manuscripts – Antoni Margalida – PNAS USA

What if you could replace performance evaluations with four simple questions? – Jena McGregor – Washington Post

Bik’s Picks

What 60 Minutes Got Right And Wrong On Duke’s Polio Virus Trial Against Glioblastoma – David Kroll – Forbes.com

The Astonishing beauty of Ordinary Sand magnified 250X – Aetherforce

What Elephants and Whales Look Like From Space – Robinson Meyer – The Atlantic

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