Category Archives: Extremophiles

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 20, 2015

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Happy 4/20! Here is a paper from last June that deserves renewed attention today: 

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome – Max E. Winston – PLOS ONE

Human oral microbiome

Review: Ecological Approaches to Oral Biofilms: Control without Killing – Marsh P.D. – Caries Research

Human vaginal microbiome

A multi-platform metabolomics approach identifies novel biomarkers associated with bacterial diversity in the human vagina – Amy McMillan – ArXiv

Comparison of detection methods for vaginal lactobacilli – I. Smidt – Beneficial Microbes

Human gut microbiome

Differences in Gut Microbiota Between Atopic and Healthy Children – Tiina Drell – Current Microbiology

DGGE: Is there interaction between gut microbial profile and cardiovascular risk in chronic kidney disease patients? – Amanda F Barros – Future Medicine

Thesis: Characterization and Investigation of Fungi Inhabiting the Gastrointestinal Tract of Healthy and Diseased Humans – Mallory J Suhr – University of Nebraska-Lincoln

Poster: The MS Microbiome Consortium (MSMC): an academic multi-disciplinary collaborative effort to elucidate the role of the gut microbiota in MS (P2.205)
Ilana Katz Sand – Neurology

Review: Gut microbiota and Ma-Pi 2 macrobiotic diet in the treatment of type 2 diabetes – Francesco Fallucca – World Journal of Diabetes

Animal microbiome

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts
Tracy D Ainsworth – The ISME Journal

Plant root and soil microbiome

Tree: Genetic Diversity and Functional Traits of Pterocarpus officinalis Jacq. Associated with Symbiotic Microbial Communities in Caribbean Swamp Forests in Relation to Insular Distribution, Salinity and Flooding – Amadou M. Bâ, Elsie Rivera-Ocasio – Wetlands

Plant: Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation – Ran Sun – Journal of Environmental Sciences

Effect of conventional and organic orchard floor management practices on enzyme activities and microbial counts in a ‘Cripp’s Pink’/M7 apple orchard – André H Meyer – South African Journal of Plant and Soil

Successional and seasonal variations in soil and litter microbial community structure and function during tropical post-agricultural forest regeneration: A multi-year study
A. Peyton Smith – Global Change Biology

Editorial: Increasing diversity – Andrea Du Toit – Nature Reviews Microbiology

Soils naturally suppressive to banana Fusarium wilt disease harbor unique bacterial communities – Zongzhuan Shen – Plant and Soil

Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil – Xiao H. Wu – Frontiers in Microbiology

Cave microbiome
Nutrient input influences fungal community composition and size and can stimulate Mn(II) oxidation in caves – SK Carmichael – Environmental Microbiology Reports

Water microbiome

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater – Dimitri Kalenitchenko – The ISME Journal

Extremophiles

In situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice – Christiane Uhlig – The ISME Journal

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula – Gareth A Pearson – The ISME Journal

Venn Diagrams galore: Multi-scale variability analysis reveals the importance of spatial distance in shaping Arctic soil microbial functional communities – Yu Shi – Soil Biology and Biochemistry

Microbes of the built environment

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

Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF – Anne Mette Madsen – Environmental Research

Molecular characterization of microbial communities and quantification of Mycobacterium immunogenum in metal removal fluids and their associated biofilms
Jianfeng Wu – Environmental Science and Pollution Research

Bioreactor and wastewater microbiology

Microbial Mats as a Biological Treatment Approach for Saline Wastewaters: The Case of Produced Water from Hydraulic Fracturing – Benay Akyon – Environmental Science & Technology

Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms – Gbemisola O. Sanni – Environmental Science and Pollution Research

Techniques

Flow cytometry as an auxiliary tool for the selection of probiotic bacteria – D. Mudroňová – Beneficial Microbes

Other microbiology papers

Shattering old beliefs: Gram’s stain does not cross the bacterial cytoplasmic membrane – Michael J. Wilhelm – ACS Chemical Biology

Dynamic Clustering in Suspension of Motile Bacteria – Xiao Chen – ArXiv

Microbes in the news

Jessica Richman, CEO of uBiome joins for short Toolmaker Talk about microbiome – Quantified Self Radio

Top 100 Most Influential People, with Martin Blaser – Almudena Bernabea – Time

Video: David Sela, PhD: Probiotics, nutrition & the microbiome – UMass Amherst – YouTube

Can Specks of Dust Help Solve Crimes? – Mandy Oaklander – Time

Bacterial flora of remote tribespeople carries antibiotic resistance genes – Science Daily

In fight against Crohn’s, professor battles bacteria – Scott Goss – USA Today

Are gut bacteria manipulating your mood? – Viviane Richter – Cosmos Magazine

To fight nasty digestive bugs, U-M scientists set out to build a better gut – using stem cells – HealthCanal

Mouth bacteria can tell the status of liver disease – Zee News

How the gut garden affects fat-burning – Sylvia Harral, Michele Stewart – Recorder Online

Maple Syrup Extract May Fight Infection-Causing Bacteria: Study – Joanna Adams – Huffington Post

How Things Work: Phages occupy bacteria to cure infection – Sharon Wu – The Tartan

The Bacteria Will See You Now: How Little Bugs Create Big Problems in Hospitals – Brian Krans – HealthLine

Cytokinins Cannot Be Associated with Plants Only: Being Present in Bacteria, They Also Affect Resistance to TB – Martina Šaradínová

Microbes and art

Video: Anna Dumitriu – “Don’t try this at home” – creating microbial artwork from faecal transplants – YouTube

Now with a Colon and Rectum – but Super Stomach and Tremendous Testicle are cute too. Bladder is on sale! I Heart Guts Plush Organs

Science, publishing, and career

University of Victoria student diving for his master’s – Jeff Bell – Times Colonist (HT: Ed Yong)

Bik’s Picks

Roundup and Risk Assessment – Michael Specter – New Yorker

Vampire Squid Outlast Their Shallower Peers – SindyaN. Bhanoo – New York Times

New species of frog found in Costa Rica looks just like Kermit – Andrea Romano – Mashable

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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 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 11, 2015

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Another new paper on gorilla gut microbiome, reviews on role of microbes in obesity, and finding the microbial equivalent of cockroaches.

Pregnancy and birth microbiome

Pathogenesis of neonatal necrotizing enterocolitis – Joanna C. Lim – Pediatric Surgery International

Human oral microbiome

Differentiation of salivary bacterial profiles of subjects with periodontitis and dental caries – Daniel Belstrøm – Journal of Oral Microbiology

Secretome of gingival epithelium in response to subgingival biofilms – N. Bostanci – Molecular Oral Microbiology

Human gut microbiome

Perspective: Integrating host gene expression and the microbiome to explore disease pathogenesis – Allyson L Byrd and Julia A Segre – Genome Biology

Review: Recent Advances in Characterizing the Gastrointestinal Microbiome in Crohn’s Disease: A Systematic Review – Emily K Wright – Inflammatory Bowel Diseases

Review: Dietary effects on human gut microbiome diversity – Zhenjiang Xu and Rob Knight – British Journal of Nutrition

Review: Obesity and the gastrointestinal microbiota: a review of associations and mechanisms – Catherine Graham – Nutrition Reviews

Review: Gut Microbiome and Obesity: A Plausible Explanation for Obesity – Claudia Sanmiguel – Current Obesity Reports

Animal model microbiome

Distinct Commensals Induce Interleukin-1β via NLRP3 Inflammasome in Inflammatory Monocytes to Promote Intestinal Inflammation in Response to Injury – Sang-Uk Seo – Immunity
Animal microbiome

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology – Andres Gomez – Molecular Ecology

Soil and plant root microbiome

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests – Cedar N. Hesse – Frontiers in Microbiology

Parent materials have stronger effects than land use types on microbial biomass, activity and diversity in red soil in subtropical China – Huan Deng – Pedobiologia

Changes in soil microbial functional diversity and biochemical characteristics of tree peony with amendment of sewage sludge compost – Xiangdong Huang – Environmental Science and Pollution Research

16S rRNA study, not metagenomics: Cataloguing the bacterial diversity of the Sundarbans mangrove, India in the light of metagenomics – Pijush Basak – Genomics Data

Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system – Ana R. Lopes – Environmental Science and Pollution Research

Soil microbial responses over 2 years following biochar addition to a north temperate forest – Genevieve L. Noyce – Biology and Fertility of Soils

Water microbiome

Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea – Mylène Hugoni – Microbial Ecology

Extremophile microbiome

Finding the microbial equivalent of cockroaches: The impact of gamma radiation on sediment microbial processes – Ashley R. Brown – Applied and Environmental Microbiology

Built environment microbiome

Methods to Assess Human Occupancy and Occupant Activity in Hospital Patient Rooms – Sandra Dedesko – Building and Environment

Bioreactor microbiology

Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing – Jiemin Zhou – Journal of Hazardous Materials

Microbial Ecology

Antimicrobial Resistance: The Major Contribution of Poor Governance and Corruption to This Growing Problem – Peter Collignon – PLOS ONE

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

Metagenomics and bioinformatics

Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics – Jie Ren – ArXiv

Techniques

Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members – J.-B. Ramond – Letters in Applied Microbiology

Estimating Protistan Diversity using High-throughput Sequencing – Sarah K. Hu – Journal of Eukaryotic Microbiology

Microbes in the news

Connecting Indoor Microbiome Studies with Indoor Chemistry – Jonathan Eisen – MicroBE.net

Smart Sewers Will Reveal What’s in Cambridge Citizens’ Guts – Elie Dolgin – IEEE Spectrum

Microbes disprove long-held assumption that all organisms share a common vocabulary – Science Daily

Scientists study mystery of Lake Erie toxic bacteria – Detroit Free Press

Jessica Cofield puts degrees in microbiology to good use – Crystal Garrett – Sun Journal

MRSA Bacteria From Borrowed Makeup Brush Paralyzes 27-Year-Old Woman – Lecia Bushak – Medical Daily

Science, publishing, and career

Virginia student earns admission to all eight Ivy League schools, and others – T. Rees Shapiro – Washington Post

China’s medical research integrity questioned – The Lancet

The seven sins of peer review – Technologist

Bik’s Picks

Review: Innovations in Health Value and Functional Food Development of Quinoa (Chenopodium quinoa Willd.) – Brittany L. Graf – Comprehensive Reviews in Food Science and Food Safety

In Hawaii, Chickens Gone Wild – Kenneth Chang – New York Times

Komodo dragon named Smaug gets a leg up from a new prosthetic – Rachel Feltman – Washington Post

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April 10, 2015

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Pregnancy and birth microbiome

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants – Zachery T Lewis – Microbiome

The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development – Shu Mei Teo – Cell Host & Microbe

Mid-trimester amniotic fluid pro-inflammatory biomarkers predict the risk of spontaneous preterm delivery in twins: a retrospective cohort study – S M Lee – Journal of Perinatology

Risk for Preterm and Very Preterm Delivery in Women Who Were Born Preterm – Boivin, Ariane – Obstetrics & Gynecology

Human oral microbiome

Clinical and microbiological effects of probiotic lozenges in the treatment of chronic periodontitis: a 1-year follow-up study – Merve Tekce – Journal of Clinical Periodontology

Review: Beyond microbial community composition: Functional activities of the oral microbiome in health and disease – Ana E. Duran-Pinedo, Jorge Frias-Lopez – Microbes and Infection

Human gut microbiome

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood – Laura Steenbergen – Brain, Behavior, and Immunity

Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community – Heather E. Hallen-Adams – Fungal Ecology

Changes in human gut microbiota influenced by probiotic fermented milk ingestion – Tatsuya Unno – Journal of Dairy Science

Fecal Microbiota Transplantation Induces Remission in Patients with Active Ulcerative Colitis in a Randomized, Controlled Trial – Paul Moayyedi – Gastroenterology

Review: The Microbiota and Microbiome in Aging: Potential Implications in Health and Age-Related Diseases – Heidi J. Zapata – Journal of the American Geriatrics Society

Review: Gastric cancer and the microbiome – Nivedita Arora – Asian Pacific Journal of Tropical Disease

Review: The Role of Microbiota on the Gut Immunology – Yang Won Min – Clinical Therapeutics

Animal models of microbiome research

Editorial: Gut Microbiota: The Link to Your Second Brain – Vanessa Ridaura – Cell
Belongs to: Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis – Jessica M. Yano – Cell

Inoculation of tannin-degrading bacteria into novel hosts increases performance on tannin-rich diets – Kevin D. Kohl – Environmental Microbiology

Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function – Caleb J. Kelly – Cell Host & Microbe

Effect of a new recombinant Aeromonas hydrophila vaccine on the grass carp intestinal microbiota and correlations with immunological responses – Lei Liu – Fish & Shellfish Immunology

Colonization and induction of Th17 cells by segmented filamentous bacteria in the murine intestine – Adam M. Farkas – Journal of Immunological Methods

Animal microbiome

Microbiota and probiotics in canine and feline welfare – Łukasz Grześkowiak – Anaerobe

Isolation and use of beneficial microbiota from the digestive tract of lions-paw scallop Nodipecten subnodosus and winged pearl oyster Pteria sterna in oyster aquaculture – Fernando Abasolo-Pacheco – Aquaculture Research

Perspective: Does the Arthropod Microbiota Impact the Establishment of Vector-Borne Diseases in Mammalian Hosts? – Constance A. M. Finney – PLOS Pathogens

Plant and plant root microbiome

Seagrass biofilm communities at a naturally CO2-rich vent – Christiane Hassenrück – Environmental Microbiology Reports

Preferential Association of Endophytic Bradyrhizobia with Different Rice Cultivars and Its Implications for Rice Endophyte Evolution – Pongdet Piromyou – Applied and Environmental Microbiology

Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats – Petr Kohout – Molecular Ecology

Soil microbiome

Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil – Carl-Eric Wegner andWerner Liesack – Environmental Microbiology

Depth-related responses of soil microbial communities to experimental warming in an alpine meadow on the Qinghai-Tibet Plateau – B. Zhang – European Journal of Soil Science

Red Soils Harbor Diverse Culturable Actinomycetes That Are Promising Sources of Novel Secondary Metabolites – Xiaoxuan Guo – Applied and Environmental Microbiology

Water microbiome

Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples – Violetta La Cono –

Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland – María Victoria Quiroga – Environmental Microbiology Reports

The hidden seasonality of the rare biosphere in coastal marine bacterioplankton – Laura Alonso-Sáez- Environmental Microbiology

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans – Matthias Wietz – Environmental Microbiology

Extremophile microbiome

Nature special: Permafrost: overview articles and primary research from Nature papers, including role of microbes in permafrost soils

Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Joanne B. Emerson – Environmental Microbiology

Food microbiology

Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar – Zong-Min Wang – Food Microbiology

Microbial diversity and stability during primary cultivation and subcultivation processes of Tibetan kefir – Wei Gao – International Journal of Food Science & Technology

There is a serious problem with Figure 1: Tetragenococcus koreensis is part of the microbiota in a traditional Italian raw fermented sausage – C. Amadoro – Food Microbiology

Other  papers of interest

Development and utility of the FDA ‘GutProbe’ DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics – J.N. Patro – Journal of Applied Microbiology

Increased Biodiversity in the Environment Improves the Humoral Response of Rats
Cinthia Pi – PLOS ONE

Microbes in the news

Bundle Of Joyful Microbes: Mom’s DNA Alters Baby’s Gut Bacteria – Michaeleen Doucleff – NPR Shots

Worms, germs lead to better immune function – Science Daily
http://www.sciencedaily.com/releases/2015/04/150408145242.htm
What does the term microbiome mean? And where did it come from? A bit of a surprise .. – Jonathan Eisen – MicroBEnet

Leading expert on microbiome Rob Knight wins a 2015 Vilcek Prize for Creative Promise in Biomedical Science – PR NewsWire

Congrats: You Are Officially a Superorganism – Max Lugavere – Huffington Post

Genetically-Engineered Bacteria Can Keep Mice From Getting Fat – Sarah Zhang – Gizmodo

Your microbiome may hold keys to cancer treatment – Alexandra Ossola – Popular Science

Cheese: The latest piece of the French paradox puzzle? – Niamh Michail – Food Navigator

#BacteriaHysteria #BacteriaArePlural: How much bacteria is in your kid’s lunchbox? You might be surprised (and grossed out) – Alex Perez – ABC 7online

Science, publishing, and career

Wanted: staff-scientist positions for postdocs – Kendall Powell – Nature

Book review: Speaking of science – Scientific Babel: How Science Was Done Before and After Global English – Lynn K. Nyhart – Science

Gender Disparity in Peer Review? – Andrew Harrison – Publons

Citations are not enough: Academic promotion panels must take into account a scholar’s presence in popular media – London School of Economics and Political Science

Bik’s Picks

Incredible imprinting – ‘are you my mummy?’ – Biodetectives

Sea Turtle Toddlers’ ‘Lost Years’ Spent Swimming, Not Drifting In Seaweed Matts – Rebekah Marcarelli – HNGN.com

New species of ‘terror bird’ discovered – Sid Perkins – Science

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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 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 3, 2015

Posted on by

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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