Category Archives: Human oral

February 5, 2015

Posted on by

Microbiome of pregnancy and birth

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes – Aleksandar D. Kostic – Cell Host & Microbe

Meeting abstracts in the Journal of Allergy and Clinical Immunology:
Influence of Infant Gut Microbiome on Development of Infant Regulatory T Cells – Kevin Bobbitt
The Infant Gut Microbiome Mediates the Association Between Breastfeeding and Allergic-like Response to Pets in Children – Alexandra R. Sitarik
Association of the Infant Gastrointestinal Microbiome with Nocturnal Symptoms in Children with Asthma – Albert M. Levin
Decrease in Diversity of Nasal Microbiota during Wheezing Episodes in Preschool Children – Gorka Alkorta-Aranburu

Maternal influences on fetal microbial colonization and immune development – Joann Romano-Keeler & Jörn-Hendrik Weitkamp – Pediatric Research

Human oral microbiome

Evaluation of human and microbial DNA content in subgingival plaque samples collected by paper points or curette – P.J. Pérez-Chaparro – Journal of Microbiological Methods

Human vaginal microbiome

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR – Takashi Kurakawa – Journal of Microbiological Methods

Human gut microbiome

Weight Gain After Fecal Microbiota Transplantation – Neha Alang and Colleen R. Kelly – Open Forum Infectious Diseases

The Gut Microbiota, Intestinal Permeability, Bacterial Translocation, and Nonalcoholic Fatty Liver Disease: What Comes First? – Erin Spengler, Rohit loomba – CMGH Cellular and Molecular Gastroenterology and Hepatology

$70 to read this one: Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy – Xiaobo Feng – The American Surgeon

Review: Gut Microbiota: Association with NAFLD and Metabolic Disturbances – E. Lau – BioMed Research International

Review: Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry – Eva M Selhub – Journal of Physiological Anthropology

Animal models of microbiome research

Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec – R. Khiaosa-ard – Journal of Dairy Science

Effect of feeding Jerusalem artichoke (Helianthus tuberosus) root as prebiotic on nutrient utilization, fecal characteristics and serum metabolite profile of captive Indian leopard (Panthera pardus fusca) fed a meat-on-bone diet – S.K. Pradhan – Zoo Biology

Comparative Analysis of Gastrointestinal Microbiota Between Normal and Caudal-Related Homeobox 2 (Cdx2) Transgenic Mice – Hirotsugu Sakamoto – Intestinal Research

Plant microbiome

Impact of mycorrhizal inoculation on the development of Intsia bijuga grown on soil under exotic species Casuarina equisetifolia plantation – Dina Ratahiriarisoa – Journal of Plant Sciences

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient – Susan G. Jarvis – New Phytologist

Bacterial diversity associated with the coccolithophorid algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii – David H. Green – BioMed Research International

Review: The importance of the microbiome of the plant holobiont – Philippe Vandenkoornhuyse – New Phytologist

Soil microbiome

Soil microbial response to waste potassium silicate drilling fluid – Linjun Yao – Journal of Environmental Sciences

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218O – Elizabeth A. Rettedal and Volker S. Brözel – MicrobiologyOpen

Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils – Shamsa Akbar – Journal of Basic Microbiology

Microbiome of the built environment
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics – Ebrahim Afshinnekoo – Cell Systems

Food microbiology

Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos – Junichiro Marui – Bioscience of Microbiota, Food and Health

Review: Zooming into food-associated microbial consortia: A “cultural” evolution – Luca Cocolin, Danilo Ercolini – Current Opinion in Food Science

Bioinformatics

Programming: Pick up Python – A powerful programming language with huge community support – Jeffrey M. Perkel – Nature

Microbes in the news

Podcast: What lived in ancient human intestines? Interview with Jessica Metcalf – The Naked Scientists

Woman becomes obese after fecal transplant from overweight donor – Brooks Hays – UPI

Microbiome linked to type 1 diabetes: Shift in microbiome species diversity prior to disease onset – Science Daily

Gut microbes are good for mood – Xanthe Hunt – LongevityLive

Satire: Five Dead As Pro- and Anti-Microbiome Demonstrators Clash – The Allium

Video: The role of gut bacteria in brain disease – Robert Friedland – YouTube

Book: I, Superorganism – Jon Turney – IconBooks

Big Data and Bacteria: Mapping the New York Subway’s DNA – Robert Lee Hotz – Wall Street Journal

Drug-resistant bacteria lurk in subway stations, high school students discover – Science Daily

Among New York Subway’s Millions of Riders, a Study Finds Many Mystery Microbes – Elizabeth A. Harris – New York Times

Environmental factors may affect how infants’ gut bacteria mature – News Medical

Could Genetically Engineered Bacteria in Your Colon Replace Vitamins? – Sarah Zhang – GizModo

Why Measles Is the Most Contagious Virus – Mandy Oaklander – Time

Busting the 5-second rule: Robot, Petri dishes of bacteria part of science fair – Leigh Guidry – The Town Talk

Not about microbiology, but a very good read: High throughput sequencing for neuroscience – Sean Eddy – Cryptogenomicon

No Bik’s Picks today, sorry guys.

[hr]

February 3, 2015

Posted on by

Pregnancy and birth

Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio

Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE

Human oral microbiome

Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports

Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology

Human respiratory microbiome

Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE

Human gut microbiome

The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Animal microbiome

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE

Plant microbiome

Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils

Soil microbiome

Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology

Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry

Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments

Water microbiome

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography

Microbiome of the built environment

Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment

Bioreactor microbiome

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports

Food microbiology

Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology

Techniques

PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE

Bioinformatics, metagenomics

Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE

In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research

SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics

A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology

Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics

Book: Biocode: The New Age of Genomics

Phages and viruses

Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE

Microbes in the news

The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio

The Human Microbiome and Media Confusion – Science in the News – Harvard

Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos

Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome

Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live

Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain

How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio

Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients

Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes

Science, publishing, and career

From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog

Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI

A Future Segregated by Science? – Charles M. Blow – New York Times

Bik’s Picks

Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily

Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs

Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press

[hr]

February 2, 2015

Posted on by

The etiology of dental caries, viruses as commensals, genitalia-associated microbes in insects, and pizza metabolomics.

Human oral microbiome

Solving the etiology of dental caries – Aurea Simón-Soro, Alex Mira – Trends in Microbiology

Human gut microbiome

Expanding the Role of the Virome: Commensalism in the Gut – Ken Cadwell – Journal of Virology

Animal microbiome

Review: Genitalia-associated microbes in insects – Oliver Otti – Insect Science

Plant microbiome

Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale – Maarten van Geel – Molecular Ecology

Water microbiome

Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir – Peike Gao – Microbiology Open

Microbiome of the built environment

Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood – Joanne B Emerson – Environmental Science & Technology

Techniques

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLife

Microbial Ecology

Mycorrhizal ecology and evolution: the past, the present, and the future – Marcel G. A. van der Heijden – New Phytologist

Biotic interactions boost spatial models of species richness – Heidi K. Mod – Ecography

Metabolomics

Metabolomic applications in nutritional research: a perspective – Aoife O’Gorman and Lorraine Brennan – Journal of the Science of Food and Agriculture

Microbes in the news

Viral Virtuosos: New understanding of noncoding RNAs may solve a long-standing puzzle about how viruses orchestrate lifelong infections – Christopher S. Sullivan – The Scientist

The answer to fewer viruses in human DNA? We stopped biting each other – SBS

Bacteria used to yield pure water and produce hydrogen, the fuel of the future – Jayalakshmi K – IBTimes

Intestinal microbiome research – Rob Levey – New Hampshire Union Leader

The Energy of Life: Extremophiles should not be viewed through an anthropocentric lens – Jeffrey Marlow and Jan Amend – The Scientist

Bacteria May Help Battle Cancer, Study Suggests – Philly.com

Science and art

Gorgeous Photos Made From the Bacteria on Toilet Seats and iPhones – Liz Stinson – Wired.com

Lab Agar Drawings: Chromobacterium violaceum shaped into Biohazard Symbol – MicrobeWorld

Science, publishing, and career

Trust me, I’m a medical researcher – Jennifer Couzin-Frankel – Science

Balancing Privacy versus accuracy in research protocols – Science

Ten Simple Rules for Organizing an Unconference – Aidan Budd – PLOS Computational Biology

Bik’s Picks

‘DivSeek’ aims to mine the genetic treasure in seed bank vaults – Virginia Gewin – Science Magazine

Baby’s genes, not mom’s, may trigger some preterm births – ScienceDaily

Energy and Nutrient Intake From Pizza in the United States – Lisa M. Powell – Pediatrics

[hr]

February 1, 2015

Posted on by

Ah, the revenge of being away from work: my in-box was bursting out of the seams with new papers. Today I am quickly catching up after being offline for just 3 days, and I will skip most formatting to save some time (e.g. I will only do the bare essentials, and won’t add the hyperlinks). Enjoy.

General microbiome

Review? Discovering Emergent Behavior of Host-Microbiome Interactions with Biomimetic Robotics – Keith C. Heyde, Warren C. Ruder – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514046268

Book: Microbiome Community Ecology – Muhammad Saleem – Springer Briefs in Ecology
http://link.springer.com/book/10.1007/978-3-319-11665-5

Human oral microbiome

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis – Nursen Topcuoglu, Guven Kulekci – Anaerobe
http://www.sciencedirect.com/science/article/pii/S1075996415000128

Human respiratory microbiome

Dynamics of the nasal microbiota in infancy: A prospective cohort study – Moana Mika – Journal of Allergy and Clinical Immunology
http://www.sciencedirect.com/science/article/pii/S0091674914037099

Review: The microbiome of the upper airways: focus on chronic rhinosinusitis – Thanit Chalermwatanachai – World Allergy Organization Journal
http://link.springer.com/article/10.1186/s40413-014-0048-6/fulltext.html

Human skin microbiome

Mapping axillary microbiota responsible for body odours using a culture-independent approach – Myriam Troccaz – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/3/abstract

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites – Ana M Misic – Microbiome Journal
http://www.microbiomejournal.com/content/3/1/2/abstract

Insights into bacterial colonization of intensive care patients’ skin: the effect of chlorhexidine daily bathing – N. Cassir – European Journal of Clinical Microbiology & Infectious Diseases
http://link.springer.com/article/10.1007/s10096-015-2316-y

Human gut microbiome

(see also Metagenomics) Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Gut microbiota composition correlates with changes in body fat content due to weight loss – M. Remely – Beneficial Microbes
http://wageningenacademic.metapress.com/content/ewq1620085607927/#.VM5HCVWJOuY

Genetic Modifier of the Gut Microbiome, GvHD and Bacterial Translocation Following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114008350

A Pilot Study of Donor Enteral Human Milk to Modulate the Gut Microbiome in Children Receiving Stem Cell Transplant – Stella M. Davies – Biology of Blood and Marrow Transplantation
http://www.sciencedirect.com/science/article/pii/S1083879114010441

This might be review (no access from my location): Microbiome, peptide autoantibodies, and eating disorders: a missing link between gut and brain – Akio Inui – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000386

Oral Supplementation with L-Glutamine Alters Gut Microbiota of Obese and Overweight Human Adults: A Pilot Study – Alessandra Zanin Zambom de Souza – Nutrition
http://www.sciencedirect.com/science/article/pii/S0899900715000350

Review: Growth Promotion and Gut Microbiota: Insights from Antibiotic Use – Harald Brüssow – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12786/abstract

Hypothesis: An Agent-Based Modeling Framework for Evaluating Hypotheses on Risks for Developing Autism: Effects of the Gut Microbial Environment – Bronson Weston – Medical Hypotheses
http://www.sciencedirect.com/science/article/pii/S0306987715000481

Hypothesis: Gut feelings: A role for the intestinal microbiota in anorexia nervosa? – Susan C. Kleiman – International Journal of Eating Disorders
http://onlinelibrary.wiley.com/doi/10.1002/eat.22394/abstract

Review??? Beyond Model Systems: Super-Resolving the Subcellular Dynamics of Starch Digestion in the Human Gut Microbiome – Krishanthi S. Karunatilaka – Biophysical Journal
http://www.sciencedirect.com/science/article/pii/S0006349514023030

Review: Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena? – Mirjana Rajilić-Stojanović – American Journal of Gastroenterology
http://www.nature.com/ajg/journal/vaop/ncurrent/full/ajg2014427a.html

Review: H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases
http://onlinelibrary.wiley.com/doi/10.1111/1751-2980.12233/abstract

Review: Implication of Gut Microbiota in Nonalcoholic Fatty Liver Disease
Jerome Boursier – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004559

Review: The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts – Michael C. Toh and Emma Allen-Vercoe – Microbial Ecology in Health and Disease
http://www.microbecolhealthdis.net/index.php/mehd/article/view/26309

Review: The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity – Ningwen Tai – Reviews in Endocrine and Metabolic Disorders
http://link.springer.com/article/10.1007/s11154-015-9309-0

Review: Diet, Gut Microbiome, and Bone Health – Connie M. Weaver – Current Osteoporosis Reports
http://link.springer.com/article/10.1007/s11914-015-0257-0

Review: Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota – I. A. Fedorova, V. N. Danilenko – Biology Bulletin Reviews
http://link.springer.com/article/10.1134/S2079086414060036

Animal models of microbiome

Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain – Fabiola Gutierrez-Orozco – Nutrients
http://www.mdpi.com/2072-6643/7/2/764/htm

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis
Lauren E. Ritchie – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/14/femsec.fiv008.abstract

Effects of chronic exposure to environmentally relevant concentrations of waterborne depleted uranium on the digestive tract of zebrafish, Danio rerio – Starrlight Augustine – Journal of Environmental Radioactivity
http://www.sciencedirect.com/science/article/pii/S0265931X15000041

Cross-Differentiation from the CD8 Lineage to CD4 T Cells in the Gut-Associated Microenvironment with a Nonessential Role of Microbiota – Jen Bon Lui – Cell Reports
http://www.sciencedirect.com/science/article/pii/S2211124714011061

Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota – P. Treven- Journal of Dairy Science
http://www.sciencedirect.com/science/article/pii/S0022030215000417

Animal microbiome

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing – Shuai Peng – Journal of Applied Genetics
http://link.springer.com/article/10.1007/s13353-014-0258-1/fulltext.html

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows – Fabio S. Lima – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1327.abstract

Relationship between honeybee nutrition and their microbial communities – Miriane Acosta Saraiva – Antonie van Leeuwenhoek
http://link.springer.com/article/10.1007/s10482-015-0384-8

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation – Gang Yang – Biochemical and Biophysical Research Communications
http://www.sciencedirect.com/science/article/pii/S0006291X15001047

Microbiome affects egg carotenoid investment, nestling development and adult oxidative costs of reproduction in Great tits – Staffan Jacob – Functional Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12404/abstract

Review: Dietary fibre and the importance of the gut microbiota in feline nutrition: a review
Kristel Rochus – Nutrition Research Reviews
http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9534845&fileId=S0954422414000213

Plant microbiome

T Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time – Merete Wiken Dees – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1530.abstract

Soil, rock, and sediment microbiome

Long-term forest soil warming alters microbial communities in temperate forest soils – Kristen M. DeAngelis – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00104/abstract

This one was submitted in June 2013, but just published: Soil microbial community structure and activity in a 100-year-old fertilization and crop rotation experiment – Cancan Zhao – Journal of Plant Ecology
http://jpe.oxfordjournals.org/content/early/2015/01/28/jpe.rtv007.abstract

Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions – Jamie M. Johnson – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2014/12/24/femsec.fiu035.abstract

Short-term effects of soil amendment with meadowfoam seed meal on soil microbial composition and function – Suphannika Intanon – Applied Soil Ecology
http://www.sciencedirect.com/science/article/pii/S0929139315000104

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China – Yuan Wei – Journal of Environmental Sciences
http://www.sciencedirect.com/science/article/pii/S100107421500008X

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing – Michael Joe Vaughan – Microbial Ecology
http://link.springer.com/article/10.1007/s00248-014-0560-9

Effects of increasing precipitation on soil microbial community composition and soil respiration in a temperate desert, Northwestern China – Gang Huang – Soil Biology and Biochemistry
http://www.sciencedirect.com/science/article/pii/S003807171500019X

Review: Microbial ecology of hot desert edaphic systems – Thulani P. Makhalanyane – FEMS Microbiology Reviews
http://femsre.oxfordjournals.org/content/early/2015/01/23/femsre.fuu011.abstract

Water microbiome

Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-driven phytoplankton bloom – Emma K. Wear – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10042/abstract

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina) – María Sofía Urbieta – Extremophiles
http://link.springer.com/article/10.1007/s00792-015-0729-2

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) – Cassandre Sara Lazar – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12659/abstract

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – – Limnology and Oceanography
http://onlinelibrary.wiley.com/doi/10.1002/lno.10035/abstract

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton – Heba El-Swais – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12629/abstract

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America – Caroline Souffreau – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12692/abstract

Microbial Contamination of Drinking Water and Human Health from Community Water Systems
Nicholas J. Ashbolt – Current Environmental Health Reports
http://link.springer.com/article/10.1007/s40572-014-0037-5

Book Chapter: Microbial Bioprospecting in Marine Environments – Mariana Lozada, Hebe M. Dionisi – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_11

Bioreactor microbiome

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops – Rico Lucas – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/11/femsec.fiv004.abstract

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology
http://onlinelibrary.wiley.com/doi/10.1002/jctb.4649/abstract

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants – Qiao Ma – Microbiological Research
http://www.sciencedirect.com/science/article/pii/S0944501315000105

New steady-state microbial community compositions and process performances in
biogas reactors induced by temperature disturbances – Gang Luo – Biotechnology for Biofuels

Click to access s13068-014-0182-y.pdf

Archaea

Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers – Mark A. Lever and Andreas P. Teske – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1426.abstract

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter – WIlliam D Orsi – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014260a.html

Bioinformatics

Integrating Multi-omic features exploiting Chromosome Conformation Capture data – Ivan Merelli – Frontiers in Genetics
http://journal.frontiersin.org/Journal/10.3389/fgene.2015.00040/abstract

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach – Philippe Rocca-Serra – Database
http://database.oxfordjournals.org/content/2015/bau132.full

Koonkie: An Automated Software Tool for Processing Environmental
Sequence Information using Hadoop – Dongjae Kim – ASE360
http://www.ase360.org/bitstream/handle/123456789/164/P9.pdf?sequence=1&isAllowed=y

MetAmp: combining amplicon data from multiple markers for OTU analysis – Ilya Y. Zhbannikov,, James A. Foster – Bioinformatics

Click to access bioinformatics.btv049.full.pdf

MetaAB – A Novel Abundance-Based Binning Approach for Metagenomic Sequences
Van-Vinh Le – Nature of Computation and Communication
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering
http://link.springer.com/chapter/10.1007/978-3-319-15392-6_13

NCBI BLAST+ integrated into Galaxy – Peter J. A. Cock – BioRxiv

Click to access 014043.full.pdf

Metagenomics

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell
http://www.sciencedirect.com/science/article/pii/S0092867415000136

Integrated metagenomics and network analysis of soil microbial community of the forest timberline – Junjun Ding – Scientific Reports
http://www.nature.com/srep/2015/150123/srep07994/full/srep07994.html

Book Chapter: Marine Sponge Metagenomics – Valliappan Karuppiah, Zhiyong Li – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_17

Ecological and genetic interactions between cyanobacteria and viruses in a low-O2 mat community inferred through metagenomics and metatranscriptomics – Alexander A. Voorhies – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12756/abstract

Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream – Maria Liljeqvist – FEMS Microbiology Ecology
http://femsec.oxfordjournals.org/content/early/2015/01/27/femsec.fiv011.abstract

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics

Click to access s12864-014-1207-4.pdf

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking – Yuji Sekiguchi – PeerJ
https://peerj.com/articles/740/

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12668/abstract

Review: Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism – Sang Sun Yoon – Current Opinion in Microbiology
http://www.sciencedirect.com/science/article/pii/S1369527415000089

Book Chapter: Marine Metagenome and Supporting Technology – Tetsushi Mori – Hb25_Springer Handbook of Marine Biotechnology
http://link.springer.com/chapter/10.1007/978-3-642-53971-8_19

Transcriptomics, metabolomics

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen – Xin Dai – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1375.abstract

Genomic Potential for Polysaccharide Deconstruction in Bacteria – Renaud Berlemont and Adam C. Martiny – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1513.abstract

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor – Masaru K Nobu – ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014256a.html

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways – Philipp Engel – Applied Environmental Microbiology
http://aem.asm.org/content/81/4/1502.abstract

Transcriptome analyses to investigate symbiotic relationships between marine – Sergio Balzano – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00098/abstract

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism
http://www.sciencedirect.com/science/article/pii/S109671921500027X

Human metabolic, mineral, and microbiota fluctuations across daily nutritional intake visualized by a data-driven approach – Takuma Misawa – Journal of Proteome Research
http://pubs.acs.org/doi/abs/10.1021/pr501194k

Review: Prospects and challenges for fungal metatranscriptomics of complex communities – Cheryl R. Kuske – Fungal Ecology

Microbial Ecology

Disturbance opens recruitment sites for bacterial colonization – David Vuono – BioRxiv
http://biorxiv.org/content/early/2015/01/27/014456

Review: High-throughput DNA barcoding for ecological network studies – Hirokazu Toju – Population Ecology
http://link.springer.com/article/10.1007/s10144-014-0472-z

Book Chapter: For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
Jean-Claude Bertrand – Environmental Microbiology: Fundamentals and Applications
http://link.springer.com/chapter/10.1007/978-94-017-9118-2_4

Book Chapter: Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem- Muhammad Saleem – Microbiome Community Ecology
http://link.springer.com/chapter/10.1007/978-3-319-11665-5_1

More microbes

Introduction to a special issue of PLOS Pathogens: The Importance of Pathogen Load – Aubrey J. Cunnington – PLOS Pathogens
http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004563

Microbes in the news

Satire: Secret Microbiome Forensic Study Reveals DeflateGate Culprit – Megabiome.net

Secret microbiome forensic study reveals #deflategate culprit

Among gut microbes, strains, not just species, matter – MedicalXpress
http://medicalxpress.com/news/2015-01-gut-microbes-strains-species.html

Analysis Highlights Strain Diversity in Gut Microbiome – GenomeWeb
https://www.genomeweb.com/genetic-research/analysis-highlights-strain-diversity-gut-microbiome

Jonathan Eisen and Jessica Richman on the Microbiome – Kevin Bonham – Scientific American
http://blogs.scientificamerican.com/food-matters/2015/01/30/jonathan-eisen-and-jessica-richman-on-the-microbiome/

Part-Time Pooping: A New Way to Make an Extra $13,000 a Year – Everyday Health
http://www.everydayhealth.com/columns/daily-checkup/part-time-pooping-new-way-make-extra-money-year/

OpenBiome will pay for poo – Helen Clark – GizMag
http://www.gizmag.com/openbiome-fecal-transplant/35845/

January 2015 Update on American Gut, British Gut and Australian Gut Human Microbiome Projects – IBS Impact
https://ibsimpact.wordpress.com/2015/01/30/january-2015-update-on-american-gut-british-gut-and-australian-gut-human-microbiome-projects/

The Microbiome – New Research On Inflammatory Bowel Disease May Foreshadow Autism? – Teresa Conrick – Age of Autism
http://www.ageofautism.com/2015/01/the-microbiome-new-research-on-inflammatory-bowel-disease-may-foreshadow-autism.html

The microbiome of the upper airways: focus on chronic rhinosinusitis – 7th Space
http://7thspace.com/headlines/503056/the_microbiome_of_the_upper_airways_focus_on_chronic_rhinosinusitis.html

Germ Theory: What You May Not Know About The Bacteria Crawling Around Your Bathroom – Justin Caba – Medical Daily
http://www.medicaldaily.com/pulse/germ-theory-what-you-may-not-know-about-bacteria-crawling-around-your-bathroom-319884

Altered gut microbiota seen in patients with psoriatic arthritis – Healio.com
http://www.healio.com/rheumatology/psoriatic-arthritis/news/online/%7B0dd6068d-11b8-4e05-82f2-7713d4f28749%7D/altered-gut-microbiota-seen-in-patients-with-psoriatic-arthritis

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – PRNewsWIre
http://www.prnewswire.co.uk/news-releases/the-human-microbiome-biomedical-implications-and-birth-of-a-market—overview-290212581.html

Meet Dr. Armpit, changing body odor with bacteria – Fast Company
http://www.fastcompany.com/3041388/body-week/meet-dr-armpit-changing-body-odor-with-bacteria

Gut bacteria byproduct linked to chronic kidney disease for the first time – Medical Xpress
http://medicalxpress.com/news/2015-01-gut-bacteria-byproduct-linked-chronic.html

Does draft beer give you a worse hangover? We came across people from the beer industry and beer drinkers who claimed the bacteria in those lines contributes to a hangover. – Jace Larson – Click 2 Houston
http://www.click2houston.com/news/does-draft-beer-give-you-a-worse-hangover/31037044

Bik’s Picks

Face blindness predicted by structural differences in the brain, Stanford neuroscientists discover – Leslie Willoughby – Stanford News
http://news.stanford.edu/news/2015/january/face-blind-brain-013015.html

[hr]

January 26, 2015

Posted on by

Human oral microbiome

* 16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries – Sri Nisha Jagathrakshakan – European Journal of Dentistry

Human urinary tract microbiome

The microbiome of the urinary tract—a role beyond infection – Samantha A. Whiteside – Nature Reviews Urology

Human gut microbiome

* Association between specific mucosa-associated microbiota in Crohn’s disease at the time of resection and subsequent disease recurrence: A pilot study – Peter De Cruz – Journal of Gastroenterology and Hepatology

Enhanced vaccination effect against influenza by prebiotics in elderly patients receiving enteral nutrition – Hiroyasu Akatsu – Geriatrics & Gerontology International

Review: The small bowel microbiota – Carthage Moran – Current Opinion in Gastroenterology

Animal microbiome

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay – Riazuddin Mohammed – Frontiers in Microbiology

Plant microbiome

Mycorrhizal networks and coexistence in species-rich orchid communities – Hans Jacquemyn – New Phytologist

A 3-year field investigation of impacts of Monsanto’s transgenic Bt-cotton NC 33B on rhizosphere microbial communities in northern China – Yan-Jun Zhang – Applied Soil Ecology

Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration of Douglas-fir – J. Marty Kranabetter – New Phytologist

Review: Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism – Ariane C. Kemen – New Phytologist

Soil and sediment microbiome

Soil microbial community composition does not predominantly determine the variance of heterotrophic soil respiration across four subtropical forests – Hui Wei – Scientific Reports

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses – Fabio Stagnari – Frontiers in Microbiology

Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c – Hazel A. Barton – Frontiers in Microbiology

Diversity of Soil Microbial Communities Formed by Different Light Penetrations in Forests (article in Korean) – Jun Ho Park – DBpia

Bacterial community composition of sediments from a milkfish Chanos chanos Forsskål farm – Sheila Mae S Santander-de Leon – Aquaculture Research

Bacterial diversity and fatty acid composition of hypersaline cyanobacterial mats from an inland desert wadi – Raeid M.M. Abed – Journal of Arid Environments

Study of the succession of microbial communities for sulfur cycle response to ecological factors change in sediment of sewage system – Yanchen Liu – Environmental Science and Pollution Research

Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link – Pablo Souza-Alonso – Journal of Environmental Science and Health, Part B: Pesticides, Food Contaminants, and Agricultural Wastes

Fire alters vegetation and soil microbial community in alpine meadow – Changting Wang – Land Degradation & Development

Long-term oil contamination increases deterministic assembly processes in soil microbes – Yuting Liang – Ecological Applications

Reduced vertical stratification of soil bacterial community structure and composition is associated with Bromus tectorum invasion of sagebrush steppe – Carolyn F. Weber – Journal of Arid Environments

Water microbiome

Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes – Mylène Hugon – Environmental Microbiology Reports

Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary – L. F. Messer – Aquatic Microbial Ecology

Assessing impact of acid mine drainage on benthic macroinvertebrates: can functional diversity metrics be used as indicators? – Fengzhi He – Journal of Freshwater Ecology

Microbial community of the deep-sea brine Lake Kryos seawater–brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA – Michail M. Yakimov – Environmental Microbiology

Microbiome of the built environment
Aeromonas biofilm on stainless steel: efficiency of commonly used disinfectants – Sara Craveiro – International Journal of Food Science & Technology

Fungi and the like

An improved high throughput sequencing method for studying oomycete communities – Rumakanta Sapkota, Mogens Nicolaisen – Journal of Microbiological Methods

Metagenomics and bioinformatics

VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data – Cedric C Laczny – Microbiome

GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics – Deepak Nag Ayyala, Shili Lin – Bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metagenomics shows low energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene dissemination from domestic wastewater – Beate Christgen – Environmental Science & Technology

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes – Mikihiko Kawai – Environmental Microbiology Reports

Techniques

Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities – Patrick K. H. Lee – Environmental Science & Technology

Infection and Immunity

Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection – Rodrigo J. Gonzalez – PLOS Pathogens

Hypotheses: Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space – Gerardo Suzán – Ecology and Evolution

Bacteria in the news

Immune System Promotes Digestive Health by Fostering Community of “Good” Gut Bacteria – University of Utah – LabManager

Breastmilk drug could fight resistant bacteria – The Local

Zombie bacteria in tuberculosis – Medical Express

Conversation Between “Good” Bacteria and Immune System Is Key to Digestive Health – Healthcare Utah

 

How Gut Bacteria Affect Brain Health – Sleep Review Magazine

Inflammatory Bowel Diseases Linked to Viruses – John Wilson – Utah People’s Post

Inflammatory bowel disease blamed on viruses – Regie Green – SMN Weekly

Oral Health Hack: Chewing Gum Removes Up To 100M Bacteria In 10 Minutes, Similar To Flossing – Lizette Borreli – Medical Daily

Understanding ‘Plant Microbiome’ Can Improve Farming And Plant Health – Elizabeth Bent – Science 2.0

Science Digested: A new mold species discovered on salami – Benjamin Wolfe – Microbial Foods

* Tricking Soil Bacteria to Grow in Lab: Discovering a Class of Antibiotics to Combat Drug-Resistant Bacteria – Kendra Witt – Daily Nexus

Bacteria Hysteria

How often do you change your pajamas? – Ali Berman – Mother Nature Network

Bik’s Picks

Wake no more – What if you could sleep 50 hours straight and still never feel truly awake? Welcome to the bizarre, distressing, and totally exhausting world of the hypersomniac – Virginia Hughes – Medium.com

Learning to Talk Like a Woman: For many transgender people, achieving a feminine voice can be difficult – Shivam Saini – The Atlantic

Is it OK to eat snow? Short answer: Yes, as long it’s fresh and white – Lydia Ramsey – Popular Science

[hr]

January 21, 2015

Posted on by

Today’s digest features the microbiome of chewing gum, infants of stressed-out moms, growing segmented filamentous bacteria, and a YouTube video with Jack Gilbert.

Chewing gum microbiome

Quantification and Qualification of Bacteria Trapped in Chewed Gum – Stefan W. Wessel – PLOS ONE

Human gut microbiome

Review: Gut microbial metabolism and colon cancer: Can manipulations of the microbiota be useful in the management of gastrointestinal health? – Antoaneta Belcheva – BioEssays

Microbiome of pregnancy and birth

Maternal Prenatal Stress is Associated with the Infant Intestinal Microbiota – Maartje A.C. Zijlmans – Psychoneuroendocrinology (which is a nice word for Scrabble or Hangman)

Animal and other models of microbiome research

Growth and host interaction of mouse segmented filamentous bacteria in vitro – Pamela Schnupf – Nature

Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology

Soil microbiome

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea – Jong-Shik Kim – Microbiology Open

Water microbiome

Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek’s watershed – A.L. Barkovskii – Journal of Applied Microbiology

Immunology

Reduced neonatal regulatory T cell response to microbial stimuli associates with subsequent eczema in high-risk infants – Intan H. Ismail – Pediatric Allergy and Immunology

Metagenomics

Biological interpretation of genome-wide association studies using predicted gene functions – Tune H. Pers – Nature Communications

Microbes in the news

YouTube video with Jack Gilbert: Invisible Influence: A Bacterial Guide to Your Health – Argonne OutLoud on YouTube

Commensal Defense: Beneficial gut bacteria have evolved resistance to antimicrobial peptides that hosts release to fight pathogens – Kate Yandell – The Scientist

GM microbes created that can’t escape the lab – Engineered bacteria kept in check with a designer diet – Elie Dolgin – Nature

SDSU Hosts the “Year of the Phage” – Jeneene Chatowsky and Michael Price – San Diego State University

Novel IBD microbiome drug advanced to phase 1 trial – Healio

Optibiotix unlocking the mysteries of the human microbiome – Ian Lyall – Proactive Investors

New bacterial ‘language’ discovered: Previously unknown communication pathway – Science Daily

Science, publishing and career

Turning point: Swati Padmaraj – Scott Kraft – Nature

Time management: Seize the moment – Jeffrey M. Perkel – Nature

How to recruit a good bioinformatician – Opiniomics

Science and Art

Micro Masterpiece: The artful science of Tom Deerinck, a micrographer who consistently places in Nikon’s Small World competition – Jef Akst – The Scientist

Bik’s Picks

The Science Behind Deflated Footballs – Erin Blakemore – Smithsonian

Science gets its moment in Obama’s 2015 State of the Union – David Malakoff – Science

The Namer: Carl Linnaeus’s lasting impact on biological science – Kerry Grens – The Scientist

[hr]

January 19, 2015

Posted on by

Thanks for all the encouraging comments here and per email! This blog appears to fill an important niche in the coverage of scientific microbiome research, in a wide range of hosts and environmental sources, so I will continue writing this. But please spread the word – 100 viewers per day is nice, but more is better!

As one of the commenters suggested, I will try to mark Reviews as such, so they are easier to find (or skip).

Here we go with a new post. It’s Monday, so there is a lot to cover.

Human oral microbiome

Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile – Tacíria M Bezerra – Journal of Clinical Pathology

Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron – Pamela Vazquez-Gutierrez – BMC Microbiology

Review: Tuning the Brain-Gut Axis in Health and Disease – Rainbo Hultman – Current Stem Cell Reports

Microbiome of pregnancy and birth

Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques – Roberto Romero – Journal of Perinatal Medicine

Review: Relationship between periodontal diseases and preterm birth: Recent epidemiological and biological data – Moneet Walia, Navdeep Saini – International Journal of Applied and Basic Medical Research

Review: Viral Infections During Pregnancy – Michelle Silasi – American Journal of Reproductive Immunology

Review: Stress and the Commensal Microbiota: Importance in parturition and infant neurodevelopment – Tamar L. Gur – Frontiers in Psychiatry

Animal models of microbiome research

Commensal microbiota influence systemic autoimmune responses – Jens T Van Praet – The EMBO Journal

Modulation of the Intestinal Microbiota Is Associated with Lower Plasma Cholesterol and Weight Gain in Hamsters Fed Chardonnay Grape Seed Flour – Hyunsook Kim – J. Agric. Food Chem

Dysbiotic bacteria translocate in progressive SIV infection – Z Klase – Mucosal Immunology

Animal microbiome

Comparison of the gut microbiomes of 12 bony fish and 3 shark species – Carrie E. Givens – Marine Ecology Progress Series

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation – Jian Xue – Genome Biology

Review: Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota – Michael Poulsen – Environmental Microbiology

Plant microbiome

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root associated fungi mirrors plant succession in two glacial chronosequences – Marie Davey – Environmental Microbiology

Book: Beneficial Plant-Bacterial Interactions – Bernard R. Glick

Soil and sediment microbiome

Soil Bacterial Communities are Shaped by Temporal and Environmental Filtering: Evidence from a Long-Term Chronosequence – Zachary Freedman and Donald R. Zak – Environmental Microbiology

Abstract: Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois – Alexander B Faulkner – Proceedings, 19th Central Hardwood Forest Conference; 2014 March

Bacterial community composition at anodes of microbial fuel cells for paddy soils: the effects of soil properties – Ning Wang – Journal of Soils and Sediments

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Soil-Borne Microbiome: Linking Diversity to Function – Lucas W. Mendes – Microbial Ecology

Phytoextraction of nickel and rhizosphere microbial communities under mono- or multispecies hyperaccumulator plant cover in a serpentine soil – Marie Rue – Australian Journal of Botany

Methane-derived carbon flow through microbial communities in arctic lake sediments – Ruo He – Environmental Microbiology

Review: Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations – Sheree J. Finley – Applied Soil Ecology

Water microbiome

Book (open access): Subseafloor Biosphere Linked to Hydrothermal Systems
Some chapters of interest:
– Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor in the Back-Arc Hydrothermal System of the Southern Mariana Trough – Shingo Kato
– Microbial Cell Densities, Community Structures, and Growth in the Hydrothermal Plumes of Subduction Hydrothermal Systems – Michinari Sunamura, Katsunori Yanagawa
– Comparative Investigation of Microbial Communities Associated with Hydrothermal Activities in the Okinawa Trough – Ken Takai, Satoshi Nakagawa
– Quantification of Microbial Communities in Hydrothermal Vent Habitats of the Southern Mariana Trough and the Mid-Okinawa Trough – Katsunori Yanagawa

Microbiome of the built environment

Review: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome – Brent Stephens – Indoor Air

Food microbiology

Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese – Luana Faria Silva – Journal of Food Science

Metagenomics

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data – Xutao Deng – Nucleic Acids Research

Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology

Metabolomics, transcriptomics, and proteomics

Effects of high fructose and salt feeding on systematic metabonome probed via 1H NMR spectroscopy – Yongxia Yang – Magnetic Resonance in Chemistry

Also see above: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome – Florence Privé – Applied Microbiology and Biotechnology

Review: Proteomics of hosts and pathogens in cystic fibrosis – Karthik Shantharam Kamath – Proteomics – Clinical Applications

Bioinformatics

Book chapter: e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling – Fosso Bruno – RNA Bioinformatics / Methods in Molecular Biology

Book chapter: Deciphering Metatranscriptomic Data – Evguenia Kopylova – RNA Bioinformatics / Methods in Molecular Biology

Amplification and sequencing techniques

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples – Marta Pawluczyk – Analytical and Bioanalytical Chemistry

Probiotics

Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model – Tomohiro Kawahara – Microbiology and Immunology

Microbes in the news

* One Scientist’s Race To Help Microbes Help You – Katherine Harmon Courage – NPR Shots

Researchers reveal link between the microbiome of young mice and later onset of autoimmune disease – News Medical

Podcast: Do Gut Bacteria Tell Us What To Eat? – Beth Anne Austein / The Food Guys – Montana Public Radio

The Fungus in Your Cheese Is Having Weird Sex – Rose Eveleth – Smithsonian.com

Disturbed gut microbiome linked to Parkinson’s disease – News Medical

#BacteriaHysteria

Honoring last week’s Law Enforcement Appreciation Day: Sheriff’s Office gets bacteria cleanse – Richard Goad – Cleveland Banner

Science, publishing, and career

7 Tips for Women at Science Conferences – Hilda Bastian – PLOS Blogs

Bik’s Picks

Do 80% of Americans not know there’s DNA in food? – Ben Lillie blog

Researchers Who Provided Key Evidence For Gluten Sensitivity Have Now Thoroughly Shown That It Doesn’t Exist – Jennifer Welsh – Business Insider

This whale might be old, but it does not look too happy (or it is swimming upside down?)
The Secret To Living 200 Years? Ask A Whale – Paul Rodgers – Forbes.com

[hr]

January 15, 2015

Posted on by

Human respiratory microbiome

Aging and the microbiome: implications for asthma in the elderly? – Sanjay H Chotirmall, and Conor M Burke – Expert Review of Respiratory Medicine

Human oral microbiome

Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity –
A.M. Richards – Molecular Oral Microbiology

Inhibitory effect of Lactobacillus salivarius on Streptococcus mutans biofilm formation – C.-C. Wu – Molecular Oral Microbiology

Animal models of microbiome research

Murine Gut Microbiota—Diet Trumps Genes – Jens Walter – Cell Host & Microbe

Animal microbiome

Effects of dietary synbiotic on growth, survival, lactobacillus bacterial count, blood indices and immunity of beluga (Huso huso Linnaeus, 1754) juvenile – R. Akrami – Aquaculture Nutrition

Plant microbiome

Short-term impact of two liquid organic fertilizers on Solanum lycopersicum L. rhizosphere Eubacteria and Archaea diversity – L. Canfora – Applied Soil Ecology

A review on weeds as source of novel plant growth promoting microbes for crop improvement – C. Sarathambal – Journal of Applied and Natural Science

Different mycorrhizal fungal strains determine plant community response to nitrogen and water availability – Laura B. Martínez – Journal of Plant Nutrition and Soil Science

Soil microbiome

Effects of wildfires on flora, fauna and physico-chemical properties of soil-An overview –
Manoj Kumar Jhariy* and Abhishek Raj – Journal of Applied and Natural Science

Cellulolytic potential under environmental changes in microbial communities from grassland litter – Renaud Berlemont – Frontiers in Microbiology

Water microbiome

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach – Melitza Crespo-Medina – Frontiers in Microbiology

Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India – Devanita Ghosh – Frontiers in Microbiology

Food microbiology

Isolation and Identification of Lactic Acid Bacteria in Winter Salad (Local Pickle) during Fermentation Using 16S rRNA Gene Sequence Analysis – Mansour Saeedi – Journal of Food Safety

Metagenomics

Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State – Melanie R. Mormile – Frontiers in Microbiology

Bioinformatics

The yearly Database Issue of Nucleic Acids Research is out. Just a selection:
–  rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development – Steven F. Stoddard
–  Update on RefSeq microbial genomes resources – Tatiana Tatusova

Scientific Meeting 2014 “NGS Data after the Gold Rush” Meeting, Norwich, UK – EMBnet.journal. Selection of 2 abstracts:
–  Analyzing RNA-Seq data with RNASeqGUI – Claudia Angelini, Francesco Russo – EMBnet.journal
–  NGS data management and analysis for hundreds of projects: Experiences from Sweden – Ola Spjuth – EMBnet.journal
Microbial Ecology

Perspective: Impact of spatial distribution on the development of mutualism in microbes – Ákos T. Kovács – Frontiers in Microbiology

Bacteria in the news

Cataloguing 10 million human gut microbial genes – Tim Sandle – Pharmamicroresources

Arctic bacteria could make life-saving drugs – Samantha Bresnahan – KSPR

Iron Overload Disease Causes Rapid Growth of Potentially Deadly Bacteria, UCLA Study Finds – Infection Control Today

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

Is Naya Rivera right about her ‘showering too often’ theory? – Hope Gillette – Voxxi

Science, publishing and career

Want To Be In STEM? Here Are The 10 Best Metro Areas – Hank Campbell – Science 2.0

Gender gap: Women welcome in ‘hard working’ fields, but ‘genius’ fields are male-dominated, study finds – Rachel Feltman – Washington Post

Bik’s Picks

Prolonging lifespan: Researchers create ‘Methuselah fly’ by selecting best cells – Science Daily

Proteins found in the brain may help speed up flu recovery while you sleep – Lydia Ramsey – Popular Science

What the history of dogs tells us about civilization in the Americas – Elahe Izadi – Washington Post

Earth’s magnetic field guides sea turtles home – Julia Rosen – Science News

[hr]

January 13, 2015

Posted on by

Human oral microbiome

The Biofilm Community: Rebels with a Cause – A. Wilson Aruni – Current Oral Health Reports

Human respiratory microbiome

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age – J C Stearns – The ISME Journal

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection – Sophie E. Darch – Scientific Reports

Human gut microbiome

Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease – Nadeem O. Kaakoush – Clinical and Translational Gastroenterology

The intestinal microbiota: its role in health and disease – Luc Biedermann, Gerhard Rogler – European Journal of Pediatrics

Geographical patterns of the standing and active human gut microbiome in health and IBD – Ateequr Rehman – Gut

Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria – L. Nylund – Allergy

The influence of the microbiota on the immune response to transplantation – Bartman, Caroline – Current Opinion in Organ Transplantation

Animal models of microbiome research

The enduring importance of animal models in understanding periodontal disease – George Hajishengallis – Virulence

Animal microbiome

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors – Carmit Cohen – The ISME Journal

Molecular analysis of cecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic – Muhammad U. Sohail – Avian Pathology

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies – Karen E Sullam – The ISME Journal

Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes – Daniel F. R. Cleary – Antonie van Leeuwenhoek

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community – Pim Bongaerts – Scientific Reports

Soil microbiome

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach – Giovanni Bacci – Antonie van Leeuwenhoek

Role of RNase on microbial community analysis in the rice and wheat plants soil by 16S rDNA-DGGE – Md. Mizanur Rahman – Journal of Crop Science and Biotechnology

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils – Jing Li – Frontiers in Microbiology

Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil – Gaidi Ren – Frontiers in Microbiology

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach and Ralf Conrad – Frontiers in Microbiology

Biogeography and biophysicochemical traits link N2O emissions, N2O emission potential and microbial communities across New Zealand pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Formation of iron-rich shelled structures (IRSS) by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Effects of alkyl-imidazolium ionic liquid [Omim]Cl on the functional diversity of soil microbial communities – Pengpeng Guo – Environmental Science and Pollution Research

Cyanobacteria drive community composition and functionality in rock-soil interface communities – Angel Valverde – Molecular Ecology

Separation of soil microbial community structure by aggregate size to a large extent under agricultural practices during early pedogenesis of a Mollisol – Na Li – Applied Soil Ecology

Microbial community structure of anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454-pyrosequencing – Zhen Zhou – Chemical Engineering Journal

Conservation tillage positively influences the microflora and microfauna in the black soil of Northeast China – Shixiu Zhang – Soil and Tillage Research

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity – Zach Aanderud – Frontiers in Microbiology

Water microbiome

Drinking water microbiology — from measurement to management – Caitlin R Proctor, Frederik Hammes – Current Opinion in Biotechnology

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time – Guus Roeselers – Environmental Microbiology

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge – Håkon Dahle – The ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014247a.html

Metagenomics

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics – Tomàs Llorens-Marès – The ISME Journal

Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives – Vinay Kumar – Journal of The Institution of Engineers (India): Series A

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

Metagenomic Insights into the Effects of Fructo-oligosaccharides (FOS) on the Composition of Fecal Microbiota in Mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing – Samia N. Naccache – Clinical Infectious Diseases

Unbiased Next-Generation Sequencing and New Pathogen Discovery: Undeniable Advantages and Still-Existing Drawbacks – Arianna Calistri and Giorgio Palù – Clinical Infectious Diseases

Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA – Anisha Dayaram – Infection, Genetics and Evolution

Metabolomics

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology – Marco Fondi and Pietro Liò – BioRxiv

Techniques

Accounting for uncertainty in DNA sequencing data – Jason A. O’Rawe – Trends in Genetics

More microbes
3D-Printed Microfluidic Device for the Detection of Pathogenic Bacteria Using Size-based Separation in Helical Channel with Trapezoid Cross-Section – Wonjae Lee – Scientific Reports

Microbes in the news

UCSD hires star biologist Rob Knight – Gary Robbins – UT San Diego

Drug developed out of microbiome studies advances in phase I trial – Stephanie M. Lee – SF Gate
and
Second Genome’s gut check uncovers a possible drug for bowel disease – Ron Leuty – San Francisco Business Times

The Megabiome – It’s not micro anymore – Megabiome.net

Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (with Jessica Richman and Jonathan Eisen) – Tim Ferriss Show – Four Hour Workweek

Mounting Research Shows Gut-Brain Connection – Traci Pedersen – Psych Central

Microbiota organization influences colorectal cancers – Nicola Garrett – Family Practice News

“MyNewGut”: New project explores role of gut microbiota in preventing diet- and brain-related diseases – News-Medical.net

Joint Pain, From the Gut – David Kohn – The Atlantic

A Lamp Whose Light Comes From Bioluminescent Bacteria – Liz Stinson – Wired.com

Pieter Dorrestein Recognized by Pharmacology Society – Heather Buschman – UC San Diego

Science, publishing and career

Post publication peer review comes of age – Emma Stoye – Chemistry World

What Tech Conferences Need to Stop for Women to Contribute More – Kellyn Pot’Vin-Gorman – LinkedIn

Bik’s Picks

Because our lab is close: Jeepers! New Look at ‘Creeping’ San Andreas Fault
by Becky Oskin – LiveScience
http://www.livescience.com/49435-san-andreas-fault-less-creepy.html

These scientists raised bot fly larvae in their own bodies — on purpose – Rachel Feltman – The Washington Post

Today in Adorable Science: Disney Has Created a L’il Turtle Robot to Draw Doodles in the Sand – Carolyn Cox – The Mary Sue

[hr]

January 12, 2015

Posted on by

Microbiome of pregnancy and birth

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome – Amanda L. Thompson – Frontiers in Cellular and Infection Microbiology

Human oral microbiome

Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population – Z Qi – International Endodontic Journal

Human gut microbiome
Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation – Mei San Tang – Gut Microbes

Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance – Thomas Clavel – Gut Microbes

Editorial: a simple faecal preparation protocol for faecal microbiota transplantation – C. R. Kelly – Alimentary Pharmacology & Therapeutics

Human skin microbiome

Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’ – Anne Spichler – BMC Medicine

Human urinary tract microbiome

The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

Animal microbiome

Normal bacterial conjunctival flora in the Huacaya alpaca (Vicugna pacos) – Goedele Storms – Veterinary Ophthalmology

Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla) – Miguel Carda Diéguez – Frontiers in Microbiology

Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome – Inna Rozman Grinberg – FEMS Microbiology Letters

Master Thesis: Predominant fecal microbiota of captive adult cheetahs housed in European zoos: a cross-sectional study – Niloufar Majdzadeh – Ghent University

Plant microbiome

Plant–microbe interactions: Microbiome remote control – Christopher Surridge – Nature Plants

Impact of plant development on the rhizobacterial population of Arachis hypogaea: a multifactorial analysis – Shyamalina Haldar and Sanghamitra Sengupta

Pyrosequencing Reveals Fungal Communities in the Rhizosphere of Xinjiang Jujube – Peng Liu – BioMed Research International

Soil, sediment, sludge microbiome

Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India – Gagandeep Kaur – 3 Biotech

Nitrogen and methanogen community composition within and among three Sphagnum dominated peatlands in Scandinavia – Magalí Martí – Soil Biology and Biochemistry

Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers – Feng Guo – Nature Scientific Reports

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra – Tatiana A. Semenova – Molecular Ecology

Microbial community composition of transiently wetted Antarctic Dry Valley soils – Thomas D. Neiderberger – Frontiers in Microbiology

Water microbiome

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity – Gourvendu Saxena – Environmental Science & Technology

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics – Shangjin Tan – Journal of Phycology

Phages and viruses

(also see above) The human urine virome in association with urinary tract infections – Tasha M. Santiago-Rodriguez – Frontiers in Microbiology

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells – Liana Fasching – Cell Reports

Probiotics

Systematic discovery of probiotics – Samuel C Forster & Trevor D Lawley – Nature Biotechnology

Microbes in the News

Prebiotics: Yeast Is Healthy, And So Are Bacteria That Help Us Break Down Bread And Beer – Science 2.0

Stop Killing the Good Guys! Protect Your Child’s Microbiome From Antibiotic Overuse – Aviva Romm – Huffington Post

Mounting research tightens gut microbial connection with the brain – MedicalXpress
http://medicalxpress.com/news/2015-01-mounting-tightens-gut-microbial-brain.html

Intestinal bacteria study uses Zingerman’s bread – Lea Giotto – The Michigan Daily

Are We Ruled by Our Microbiome? – Qiagen

Could Gut Microbes Help Us Treat Brain Disorders? – Kavli Foundation – Labmanager

Bacteria could contribute to development of wound-induced skin cancer – EurekAlert

Revenge of the bacteria? Earth Talk – August FreePress

Do viruses make us smarter? – Science Daily

The Doctor Who Championed Hand-Washing And Briefly Saved Lives – Rebecca Davis – NPR Morning Edition

Love your gut – and help your body shift those festive pounds – Kathie Swift – Daily Mail

Science, publishing, career

Life sciences workforce trends evolve with the industry – Kathy L Nugent & Lori Lindburg – Nature Biotechnology

12 Common Mistakes In Empirical Social Science – Fred Phillips – Science 2.0

How The War On Science Affects Us All – Greg Satell – Forbes

Bik’s Picks

Devil is in the detail: Evolution of color in plants and animals – Science Daily’

This cannot be statistically sound: Number Of Large Earthquakes Dropped 60 Percent In 2014 – Science 2.0

Why OCD Is ‘Miserable’: A Science Reporter’s Obsession With Contracting HIV – Shots/Fresh Air – NPR

[hr]