Category Archives: Pregnancy and birth

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 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 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 7, 2015

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

Course: Frontiers in Host-Microbe Interactions – August 2015

Pregnancy and birth microbiome

The FASEB Journal Abstracts:

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

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

Human skin microbiome

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

Human oral microbiome

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

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

Human gut microbiome

The FASEB Journal Abstracts:

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

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

Animal models of microbiome research

The FASEB Journal Abstracts:

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

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

Animal microbiome

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

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

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

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

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

Soil microbiome

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

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

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

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

Water microbiome

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

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

Book: Microbiology of the Everglades Ecosystem – CRC Press

Extremophile microbiome

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

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

Food microbiome

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

Bioreactor and biofilter microbiome

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

Metagenomics, Metabolomics, and Transcriptomics

The FASEB Journal Abstracts:

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

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

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

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

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

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

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

Microbial Ecology

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

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

Techniques

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

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

Microbes in the news

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

May deadline: 2015 MO BIO Microbiome Awards – MoBIO

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

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

Video: Why Your Beard Is Disgusting – Discovery News

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

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

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

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

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

Science, publishing, and career

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

Bik’s Picks

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

The Brontosaurus Is Back, Baby – Rich Juzwiak – Gawker

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

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

Pregnancy and birth

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

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

Food microbiology

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

Metabolomics

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

Microbes in the news

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

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

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

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

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

Microbes scared to death by virus presence – ScienceDaily

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

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

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

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

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

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

Bik’s Picks

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

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

What Americans Think About Climate Change in Seven Maps – Eric Roston – Bloomberg
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April 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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April 1, 2015

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April 1st science

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

Zoology: Here be dragons – Andrew J Hamilton – Nature

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

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

Human oral microbiome

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

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

Pregnancy and birth microbiome

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

Animal microbiome

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

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

Plant microbiome

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

Soil and plant root microbiome

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

Extremophile microbiome

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

Built environment microbiome

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

Metagenomics

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

Metabolomics

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

Ecology

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

Techniques

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

Microbes in the news

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

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

Cool Jobs: The Cave Microbiologist – Scientiflix

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

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

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

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

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

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

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

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

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

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

Science, publishing, career

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

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

Bik’s Picks

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

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

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

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