Category Archives: Events and jobs

July 27, 2015

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Microbiome webinar tomorrow, female urinary microbiota, listening to our gut, bacteria on plastic in the North Sea, quantifying food spoilage, and “less is more” when it comes to dog poop.

Events

Tomorrow: Microbiome, Antibiotics and Human Disease – Cell Press Webinar July 28, at noon EST

Genome Science 2015 – September 7-9, University of Birmingham, UK

Human urinary tract microbiome

The Female Urinary Microbiota in Urgency Urinary Incontinence – Meghan M. Pearce – American Journal of Obstetrics and Gynecology

Human gut microbiome

Low urinary indoxyl sulfate levels early after ASCT reflect a disrupted microbiome and are associated with poor outcome – Daniela Weber – Blood

Review: Listening to Our Gut: Contribution of Gut Microbiota and Cardiovascular Risk in Diabetes Pathogenesis – Daniel Li – Current Diabetes Reports

Animal microbiome

Less is More—Optimization of DNA Extraction from Canine Feces – Christina D. Lindquist – Journal of Forensic Sciences

Review: Prebiotics and gut microbiota in chickens – Mohsen Pourabedin – FEMS Microbiology Letters

Topographical mapping of the rainbow trout (Oncorhynchus mykiss) microbiome reveals a diverse bacterial community in the skin with antifungal properties – Liam Lowrey – Applied and Environmental Microbiology

Plant, root, and soil microbiome

PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response – Jinyu Hou – Chemosphere

Water microbiome

Bacterial community profiling of plastic litter in the Belgian part of the North Sea –
Caroline A. De Tender – Environmental Science & Technology

The Dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing – Maria J. Rodriguez-Mora – FEMS Microbiology Ecology

Characterization of para-nitrophenol degrading bacterial communities in river water using functional markers and stable isotope probing – Agnieszka Kowalczyk – Applied and Environmental Microbiology

Review: Slow Microbial Life in the Seabed – Bo Barker Jørgensen – Annual Review of Marine Science

Food microbiology

Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores – Paulo de Boer – Microbiome

Microbes in the news

Microbial Me: Interview with Jack Gilbert – Lydialyle Gibson – The University of Chicago Magazine

We Want the Funk: The Ups and Downs of Wild Microbes in Beer – Kaitlyn Keller – PLOS Blogs

Chinese scientists discover therapy to child obesity – XinhuaNet

Is your milk off? This 3D-printed ‘smart’ bottle cap will know – Duncan Geere – TechRadar

The Bacteria Solution: A cosmetics startup knows that live microbes are the secret to healthier skin. Will anyone believe that? – Caroline Winter – Bloomberg Businessweek

Bacteria Hysteria

With “shocking” video (but I was entertained): How clean is YOUR car? Deadly bugs such as E.coli and found lurking on steering wheels and handbrakes caused by people eating and drinking on the move – Kate Pickles – Daily Mail

Microbes and Art

Video: Invisible You – The Human Microbiome: Rogan Brown tells the story behind his work ‘Cut Microbe’, an intricate paper sculpture based on a single bacteria form. – On permanent display at Eden Project in Cornwall, UK.

Bik’s Picks

Increasing prevalence of autism is due, in part, to changing diagnoses – Penn State Science

Oil droplets turn cells into tiny lasers. Injecting single cells with spheres of fluorescent dye could open new research and treatment avenues using light – Allie Wilkinson – Nature

Why Lake Tahoe is so blue (and how to measure it) – Kelsey Warner – CS Monitor

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July 24, 2015

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A review about small molecules produced by human microbiota, layers of microbial life in Dead Sea sediments, fungus making “hair ice”, exploring deep microbial life in the sea, and bacterial diversity at the North Pole.

Events

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

WAO Symposium on Food Allergy & the Microbiome – 5-6 December 2015, Miami, FL

Microbiome reviews

Small molecules from the human microbiota – Mohamed S. Donia, Michael A. Fischbach – Science

Editorial: Microbiota-induced T cells block allergic inflammation – Yvonne Bordon – Nature Reviews Immunology

Perspective: Promise and pragmatism in clinical microbiome research – Nadim J. Ajami – Mini-Reviews in Medicinal Chemistry

Review: The Role of Intestinal Microbiota in Graft versus Host Disease – no authors listed – Mini-Reviews in Medicinal Chemistry

Editorial: Protective role of gut microbial SCFAs – Ellen F. Carney – Nature Reviews Nephrology

Human oral microbiome

In vitro work: Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

Human gut microbiome

Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial – Hannah D Holscher – Journal of Nutrition

Plant, root, and soil microbiome

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea – C. Thomas – Geobiology

Evidence for biological shaping of hair ice – D. Hofmann – Biogeosciences

Water and extremophile microbiome

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor – F. Inagaki – Science

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs – Samia Amarouche-Yala – Extremophiles

Bacterial diversity in snow on North Pole ice floes – Aviaja L. Hauptmann – Extremophiles

Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses – Heejung Kim – Science of the Total Environment

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages – Haiwei Luo – Molecular Biology and Evolution

Built environment microbiome

Microbiological characterization of 3193 French dwellings of Elfe cohort children – S. Rocchi – Science of The Total Environment

Metagenomics and bioinformatics

For plant/animal assemblages, but might be of interest: cati: an R package using functional traits to detect and quantify multi-level community assembly processes – Adrien Taudiere – Ecography

Metabolomics and proteomics

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation – Rafael Bargiela – Proteomics

Microbes in the news

‘It’s like going to Pluto and seeing McDonald’s: ‘These microbes live more than 2 kilometers below the sea floor off the coast of Japan – Mitch Leslie – Science

It takes a village… to ward off dangerous infections? New microbiome research suggests so – MedicalXpress

Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment – American Microbiome Institute

Rotting Fungus Creates Beautiful, Glistening ‘Hair Ice’ – Elizabeth Goldbaum – LiveScience

Not endorsing this one, full of errors and false claims: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan – BusinessWire

Science, publishing, and career

New life for old bones: inventing ways to apply the DNA sequencing revolution to tissues ravaged by time. – Elizabeth Culotta – Science

Songwriting and science: Pitching songs, however, has taught me a few practical lessons about pitching papers and grant proposals: – C. Neal Stewart Jr. – Science

Bik’s Picks

Comparisons of life-history parameters between free-ranging and captive killer whale (Orcinus orca) populations for application toward species management – Todd R. Robeck – Journal of Mammalogy

Kiwi genome provides insights into evolution of a nocturnal lifestyle – Diana Le Duc – Genome Biology

A medical-toxicological view of tattooing – Peter Laux – The Lancet

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July 20, 2015

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Transcriptomics in periodontitis, stool consistency, truffles, ginger and pigs, and salt deserts.

Events (repeat posts)

Free Cell Press Webinar: Microbiome, Antibiotics and Human Disease with human microbiome leaders Martin Blaser, Michael Fischbach and Julie Segre – July 28, 2015, noon EST

Multi-omics for Microbiomes Conference, September 14-16, 2015, Three Rivers Convention Center, Kennewick, WA
Human oral microbiome / transcriptomics

Small RNA transcriptome of the oral microbiome during periodontitis progression – Ana E. Duran-Pinedo – Applied and Environmental Microbiology

Human gut microbiome

Solid evidence: Stool consistency as a major confounding factor affecting microbiota composition: an ignored variable? – Jack A Gilbert – Gut

Review [PDF]: Beyond gut microbiota: understanding obesity and type 2 diabetes – Eva Lau – Hormones

Models of microbiome research

Ginger and inulin: Assessment of Fecal Microflora Changes in Pigs Supplemented with Herbal Residue and Prebiotic – Ashis Kumar Samanta – PLOS ONE

Plant, root, and soil microbiome (and extremophiles!)

The role of the microbiome of truffles in aroma formation: a meta-analysis approach -Maryam Vahdatzadeh – Applied and Environmental Microbiology

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes – Yayoi Takeuchi – Systematic and Applied Microbiology

A snapshot of microbial communities from the Kutch: one of the largest salt deserts in the World – Aanal S. Pandit – Extremophiles

Temporal patterns of prokaryotic abundance, community structure and microbial activity in glacier foreland soils – Katrin Hofmann – Antonie van Leeuwenhoek

Built environment microbiome

Winner of today’s Longest Title Award: Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – Journal of Hospital Infection

Waste treatment microbiology

High prevalence of type 41 and high sequence diversity of partial hexon gene of human adenoviruses in municipal raw sewage and activated sludge – Hsion-Wen Kuo – Journal of Applied Microbiology

Acute Gastrointestinal Illness Risks in North Carolina Community Water Systems: A Methodological Comparison – Nicholas B. DeFelice – Environmental Science & Technology

Metagenomics

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data – Jason W. Sahl – Genome Biology

Microbial Ecology

Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection – Nobuto Takeuchi – BMC Biology

Techniques

A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities – Anne W. Thompson – Journal of Microbiological Methods

Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in mouse feces – Yun-wen Yang – Applied and Environmental Microbiology

Antibiotics

Prevalence of Parental Misconceptions About Antibiotic Use – Louise Elaine Vaz – Pediatrics

Microbes in the news

Ginger and prebiotic promote good bacteria in pigs – All About Feed

How plants keep bad bacteria out – ZeeNews India

Parental Knowledge About Appropriate Antibiotic Use Still Poor – Diana Phillips – Medscape

Bik’s Picks

Can’t get Kylie out of your head? Blame the shape of your brain – Sam Wong – New Scientist

Seti: Search for alien life receives $100m boost – Clive Cookson – Financial Times

Remembering the Apollo 11 Moon Landing With the Woman Who Made It Happen – Lily Rothman – Time

Endangered dragonflies, raised in captivity over several years, being released – Dispatch Times

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July 15, 2015

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Microbiome and weight loss with genetic and “simple” obesity, gut microbiome in coffee beetle detoxifies caffeine,  and a plant-fungal-bacterial symbiosis.

Jobs

Tenure Track position Environmental Microbiology at Montana State University- Bozeman

Pregnancy and birth microbiome

Late-Onset Bloodstream Infection and Perturbed Maturation of the Gastrointestinal Microbiota in Premature Infants – Alexander G. Shaw – PLOS ONE

Human skin microbiome

Identification of axillary Staphylococcus sp. involved in the production of the malodorous thioalcohol 3-methyl-3-sufanylhexan-1-ol – Daniel Bawdon – FEMS Microbiology Letters

Human gut microbiome

Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children – Chenhong Zhang – EBioMedicine

Stool bacteriomic profiling in patients with metastatic renal cell carcinoma receiving vascular endothelial growth factor-tyrosine kinase inhibitors – Sumanta K. Pal – Clinical Cancer Research

Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial – Daniel E. Freedberg – Gastroenterology

Review: The bilateral responsiveness between intestinal microbes and IgA – Andrew J. Macpherson – Trends in Immunology

Animal models

Editorial: Medicinal mushroom reduces obesity by modulating microbiota – David Holmes – Nature Reviews Endocrinology

Bifidobacterium pseudocatenulatum CECT 7765 Reduces Obesity-Associated Inflammation by Restoring the Lymphocyte-Macrophage Balance and Gut Microbiota Structure in High-Fat Diet-Fed Mice – Angela Moya-Pérez – PLOS ONE

Animal microbiome

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee – Javier A. Ceja-Navarro – Nature Communications

Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians – Ana V. Longo – Royal Society Open Science

Most of the dominant members of amphibian skin bacterial communities can be readily cultured – Jenifer B. Walke – Applied and Environmental Microbiology

Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense) – Tzong-Der Tzeng – PLOS ONE

Potassium permanganate elicits a shift of the external fish microbiome and increases host susceptibility to columnaris disease – Haitham H. Mohammed – Veterinary Research

Microenvironment and Phylogenetic Diversity of Prochloron Inhabiting the Surface of Crustose Didemnid Ascidians – Daniel A. Nielsen – Environmental Microbiology

Deep Characterization of the Microbiomes of Calophya spp. (Hemiptera: Calophyidae) Gall-Inducing Psyllids Reveals the Absence of Plant Pathogenic Bacteria and Three Dominant Endosymbionts – Will A. Overholt – PLOS ONE

Plant, root, and soil microbiome

Review: What’s inside that seed we brew? A new approach to mining the coffee microbiome – Michael Joe Vaughan

A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment – Marcel GA van der Heijden – The ISME Journal

Terroir is a key driver of seed-associated microbial assemblages – Stephanie Klaedtke – Environmental Microbiology

Water microbiome

Enhanced salinities, as a proxy of seawater desalination discharges, impact coastal microbial communities of the eastern Mediterranean Sea – Natalia Belkin – Environmental Microbiology

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep silled fjord – Julia E. Storesund – FEMS Microbiology Ecology

Built environment microbiome

Using amplicon sequencing to characterize and monitor bacterial diversity in drinking water distribution systems – Jennifer L. A. Shaw – Applied and Environmental Microbiology

Microbes in the news

This Beetle is Ruining Your Coffee With the Help of Bacteria – Ed Yong- National Geographic
Gut microbes enable coffee pest to withstand extremely toxic concentrations of caffeine – Phys.org

Microbiologists Hold the Secrets to Making Perfect Cheese – Sophia Chen – Wired.com

About a study conducted in our lab: Citizen Science: How to be Your Own Research Project – Sally James – Seattle Mag

How To Make Better Health Predictions From Our Gut Microbes – Ed Yong – National Geographic

 

Microbiome Teams Up Against C. diff – Researchers build a mathematical model that can predict whether a mouse will be infected by Clostridium difficile based on the microbes found in its GI tract – Jef Akst – The Scientist

Research Finds Diversifying Your Diet May Make Your Gut Healthier – News Wise

Your Gut and Heart Health Connection – Carra Richling – Huffington Post

Prozac In The Yogurt Aisle: Can ‘Good’ Bacteria Chill Us Out? – Allison Aubrey – NPR

Bacteria could improve cancer detection: University lab is researching cancer utilizing intestinal microbial biomes – Sarah Thamer – MN Daily

Science, publishing, and career

Lifelong learning: Science professors need leadership training – Charles E. Leiserson & Chuck McVinney – Nature

PLOS Ecology Community Needs 2 Community Editors – PLOS

Bik’s Picks

Finally, here are the stunning pictures of Pluto NASA has waited a decade to capture – Rachel Feltman – Washington Post
Alzheimer’s Dementia Pathologies Differ by Race – Nancy A. Melville – Medscape

Oldest sperm ever is discovered in Antarctica, by accident – Will Greenberg – Washington Post

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July 13, 2015

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Trans-sialidases in human gut microbes, microbiome of the dairy cow’s uterus during metritis, and bacteria getting smaller because of ocean warming.

Jobs

Post-doctoral position is available in the laboratory of Lawrence David at Duke University: to help develop high-throughput microfluidic techniques for investigating bacterial interactions and ecology.

Conferences

Microbiome, Antibiotics and Human Disease, with Michael Fishbach, Martin Blaser, and Julie Segre – Cell Press Webinar July 28, 2015

11 speakers, only 1 woman: Meeting the Microbiome – 12 September 2015 – London, UK – CAM conferences

Microbiome of pregnancy and birth

High rates of Double-Stranded RNA Viruses and Mycoplasma hominis in Trichomonas vaginalis Clinical Isolates in South Brazil – Débora da Luz Becker – Infection, Genetics and Evolution

First Trimester Levels of BV-Associated Bacteria and Risk of Miscarriage Among Women Early in Pregnancy – Deborah B. Nelson – Maternal and Child Health Journal

Human oral microbiome

The impact of smoking and previous periodontal disease on peri-implant microbiota and health: a retrospective study up to 7-year follow-up – Quaranta A. – Annali Di Stomatologia

Human respiratory microbiome

Review: The Etiology and Pathogenesis of Chronic Rhinosinusitis: a Review of Current Hypotheses – Kent Lam – Current Allergy and Asthma Reports

Human gut microbiome

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation – Louise E. Tailford – Nature Communications

Viewpoint: Helicobacter pylori: enemy, commensal or, sometimes, friend? –  Michael B Whalen – The Journal of Infection in Developing Countries

Review: Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases – Nan Shen – Current Allergy and Asthma Reports

Review: Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection – Caroline Vincent – Antibiotics

Animal models

The microbiota regulates type 2 immunity through RORγt+ T cells – Caspar Ohnmacht – Science

Animal microbiome

Uterine microbiota progression from calving until establishment of metritis in dairy cows – Soo Jin Jeon – Applied and Environmental Microbiology

Preening as a Vehicle for Key Bacteria in Hoopoes – Ángela Martínez-García – Microbial Ecology

Variation in the Microbiota of Ixodes ticks with geography, species and sex – Will Van Treuren – Applied and Environmental Microbiology

The Host as Driver of the Microbiota in the Gut and External Environment of Drosophila melanogaster – Adam C-N Wong – Applied and Environmental Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Arsenophonus and Sodalis symbionts in louse flies: an analogy to the Wigglesworthia and Sodalis system in tsetse flies – Eva Nováková – Applied and Environmental Microbiology

Review: Microbial metagenomics in aquaculture: a potential tool for a deeper insight into the activity – Marcel Martínez-Porchas – Reviews in Aquaculture

Plant, root, and soil microbiome

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies ) Following Invasion of the Spruce Bud Scale (Physokermes piceae ) – Audrius Menkis – Microbial Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing – Youwei Hong – Canadian Journal of Microbiology

Communities of Cultivable Root Mycobionts of the Seagrass Posidonia oceanica in the Northwest Mediterranean Sea Are Dominated by a Hitherto Undescribed Pleosporalean Dark Septate Endophyte – Martin Vohník – Microbial Ecology

Precipitation modifies the effects of warming and nitrogen addition on soil microbial communities in northern Chinese grasslands – Naili Zhang – Soil Biology and Biochemistry

Long-term responses of plant growth, soil microbial communities and soil enzyme activities to elevated CO2 and neighbouring plants – Baoli Duan – Agricultural and Forest Meteorology

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils – Christopher R. Penton – Frontiers in Microbiology

Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways – Yu Dai – Applied Microbiology and Biotechnology

Water microbiome

More, smaller bacteria in response to ocean’s warming? – Xosé Anxelu G. Morán – Proceedings B

Microbial community changes along the active seepage site of one cold seep in the Red Sea – Huiluo Cao – Frontiers in Microbiology

Spatiotemporal dynamics and determinants of planktonic bacterial and microeukaryotic communities in a Chinese subtropical river – Yongming Wang – Applied Microbiology and Biotechnology

Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States – Yuyin Yang – Microbial Ecology

Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring – Anastasija Zaiko – Marine Environmental Research

A novel bacterial community index to assess stream ecological health – Kelvin E. M. Lau – Freshwater Biology

Bioreactor microbiome

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community – Orianna Bretschger – Bioresource Technology

Microbial community distribution and genetic analysis in a sludge active treatment for a complex industrial wastewater: a study using microbiological and molecular analysis and principal component analysis – Giulio Moretti – Annals of Microbiology

Bioinformatics and metagenomics

A reproducible approach to high-throughput biological data acquisition and integration – Daniela Börnigen – PeerJ

MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data – Xiaojun Wang – PeerJ

Good laboratory practice for clinical next-generation sequencing informatics pipelines –
Amy S Gargis – Nature Biotechnology

Transcriptomics, proteomics, and metabolomics

Mining microbial metatranscriptomes for expression of antibiotic resistance genes under natural conditions – Dennis Versluis – Scientific Reports

Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities – Fabian Kohrs – Proteomics

Combining Mass Spectrometric Metabolic Profiling with Genomic Analysis: A Powerful Approach for Discovering Natural Products from Cyanobacteria – Karin Kleigrewe – Journal of Natural Products

Microbial Ecology

Phylogenetic diversity analyses reveal disparity between fungal and bacterial communities during microbial primary succession – Shawn P. Brown – Soil Biology and Biochemistry

Editorial: Stopping superbugs, maintaining the microbiota – Victor Nizet – Science Translational Medicine

Biofilm Formation As a Response to Ecological Competition – Nuno M. Oliveria – PLOS Biology

Pawnobiome: Manipulation of the Hologenome Within One Host Generation and Beyond – Jameson D. Voss – Frontiers in Microbiology

Functional foods

Review: Towards microbial fermentation metabolites as markers for health benefits of prebiotics – Kristin A. Verbeke – Nutrition Research Reviews

Techniques

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities – Brett E. Arenz – Journal of Microbiological Methods

Microbes in the news

The role of the microbiota in preventing allergies – Medical Xpress

World’s largest steel company to use rabbit gut microbe to cut emissions – Emma Hartley – The Guardian

Paw Prints: Streptococcus bacteria a part of natural flora of cats and dogs – Niki Laviolette – Tribune Star

“I’m treating my son’s autism… with someone else’s faeces” – Liam Quinn – Daily Mail
This celebrity reckons autism can be treated with a poo transplant: is he right? – Clair Weaver – AWW

Navy Researchers Identify Bacteria in Human Serum – Christian Kotanen – Science DOD
surface enhanced Raman scattering (SERS) spectroscopy

Why you can’t just eat one french fry (or donut or slice of pizza) – Katherine Ellen Foley – SBS.com

Genetically Modified Bacteria Could Change Future Drug Treatments – Brandi – Clapway

Scientists at Brown University using federal grant to study mysterious fungus killing bats – The Sun Chronicle

Stop Kissing And Cuddling Chicken To Stop Salmonella Outbreak: CDC – Jill Arce – Tech Times

Bik’s Picks

New Horizons Science Update: Pluto Is The Biggest One Of All – Nadia Drake – National Geographic

Your last chance to see ‘Manhattanhenge’ sunset is tonight – Amanda Schallert – NJ.com

What’s in a name? For newborns, maybe fewer medical errors – Tara Haelle – MS News
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July 10, 2015

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Hacking B-theta’s genome, oral bacteria recycle nitrate, crustacean hemolymph microbiota, and extracting protist DNA from soil. Happy weekend!

Events

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

Jobs

Microbiome and NRI Faculty Scientist – UNC Nutrition Research Institute – North Carolina Research Campus

Human gut microbiome

Significant Differences in Fecal Microbiota are Associated With Various Stages of Glucose Tolerance in African-American Male Veterans – Irina Ciubotaru – Translational Research

Fecal microbiota transplantation restores dysbiosis in patients with methicillin resistant Staphylococcus aureus enterocolitis – Yao Wei – BMC Infectious Diseases

Perspective: Foodomics for personalized nutrition: how far are we? – Karani S Vimaleswaran – Current Opinion in Food Science

Animal models

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota – Mark Mimee – Cell Systems

The Gut Microbiota Regulates Intestinal CD4 T Cells Expressing RORγt and Controls Metabolic Disease – Lucile Garidou – Cell Metabolism

Got Worms? Perinatal Exposure to Helminths Prevents Persistent Immune Sensitization and Cognitive Dysfunction Induced by Early-Life Infection – Lauren L. Williamson –
Brain, Behavior, and Immunity

Dietary saponins from four popular herbal tea exert prebiotic-like effects on gut microbiota in C57BL/6 mice – Lei Chen – Journal of Functional Foods

Physiological recycling of endogenous nitrate by oral bacteria regulates gastric mucus thickness – Joel Petersson – Free Radical Biology and Medicine

Animal microbiome

Exceptionally low daily energy expenditure in the bamboo-eating giant panda – Yonggang Nie – Science

Review: Crustacean hemolymph microbiota: Endemic, tightly controlled, and utilization expectable – Xian-Wei Wang – Molecular Immunology

Food microbiology

Understanding the bacterial communities of hard cheese with blowing defect – Daniela Bassi – Food Microbiology

Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential – Mario von Neubeck – International Journal of Food Microbiology

Metagenomics

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples – Jongin Lee – Journal of Microbiological Methods

Metabolic networks

Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community – Joshua J. Hamilton – PLOS Computational Biology

Techniques

Comparison of three DNA extraction methods for recovery of soil protist DNA – Susana S. Santos – Journal of Microbiological Methods

MALDI-TOF mass spectrometry for early identification of bacteria grown in blood culture bottles – Jean-Benoît Zabbe – Journal of Microbiological Methods

Assessment of four protocols for rapid bacterial identification from positive blood culture pellets by matrix-assisted laser desorption ionization-time of flight mass spectrometry (Vitek® MS) – Jean Thomin – Journal of Microbiological Methods

Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils – Glade Dlott – Journal of Microbiological Methods

Microbes in the news

How to Program One of the Gut’s Most Common Microbes – Ed Yong – National Geographic

Researchers develop basic computing elements for bacteria: Sensors, memory switches, and circuits can be encoded in a common gut bacterium – Helen Knight – MIT News

Pow! Bam! Seq! Uncovering the genomic secrets of superpowers – Illumina

TV One, International Gut Microbiome expert Dr Kathy McCoy returns to Malaghan Institute – Live News

Bacteria use DNA replication to time key decision – Phys.org

The Baby-Associated Built Environment (BABE) Microbiome Project – Zac Lewis – MicroBe.net

Microbial Communications and Mosquitoes: Changing the Message – Catherine Arnold – Nature World News

Science, publishing, and career

Controversial piece: Getting noticed is half the battle – Eleftherios P. Diamandis – Science

Book review: The Safety Dance. Book review of: The Ethics Police? The Struggle to Make Human Research Safe – Lainie Friedman Ross – Science

Bik’s Picks

Here’s What it Takes to Study Dolphin Vaginas – Diane Kelly – Throb Gizmodo

Giant Pandas’ Lazy Lifestyle Justified by Science – Laura Geggel – Discovery

With Sonar-Reflecting Leaves, Plant Lures Bats to Poo in it – Ed Yong – National Geographic

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July 9, 2015

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Microbiome in colicky infants, bacterial communities on seaweed, and viral communities in soil.

Events

Altering the Microbiome: Can it Impact Health? Sept 24, 2015. Call for Abstracts- Deadline August 3, 2015

Microbiome of pregnancy and birth

Probiotic Lactobacillus rhamnosus GG therapy and microbiological programming in infantile colic: a randomized, controlled trial – Anna Pärtty – Pediatric Research

Human respiratory microbiome
The Lung Microbiome: New Principles for Respiratory Bacteriology in Health and Disease – Robert P. Dickson – PLOS Pathogens

Human gut microbiome

Interactions between the intestinal microbiota and bile-acids in gallstones patients – Nirit Keren – Environmental Microbiology Reports

Plant, root, and soil microbiome

Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography – Ezequiel M. Marzinelli – Environmental Microbiology

Ecotoxicological assessment of soil microbial community tolerance to glyphosate – Marco Allegrini – Science of The Total Environment

Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation – Sharath Srinivasiah – FEMS Microbiology Ecology

Water microbiome

Zonation of bacterioplankton communities along aging upwelled water in the northern Benguela upwelling – Benjamin Bergen – Frontiers in Microbiology

Extremophile microbiome

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit – N. Diaby – Science of The Total Environment

 

Bioinformatics

Web Resources for Microbial Data – Qinglan Sun – Genomics, Proteomics & Bioinformatics

The unifrac significance test is sensitive to tree topology – Catherine A. Lozupone – BMC Bioinformatics

Microbes in the news

Researchers discover how bacteria sweet-talk their way into plants – Aarhus University – EurekAlert

Probiotics—for plants: Helpful bacteria promote growth, less fertilizer on crops – Phys.org

Designer microbiome: MIT biologists program common gut bacteria – Eryn Brown – LA Times

Certain species dominate oral microbiome in patients with Sjögren’s syndrome – Healio

Science, publishing, and career

How to fail better (and even succeed!) in the academic job market – Dr. Acclimatrix – Tenure She Wrote

Bik’s Picks

Science reveals how giant pandas survive on a bamboo diet – Karen Kaplan – LA Times

Patients can spot trouble with new dental implants – Lisa Rapaport – Reuters

This jumping, squishy robot looks like a tiny UFO – Rachel Feltman – Washington Post
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June 30, 2015

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Metabolomics and gut colonization of gnotobiotic mice, metabolomics of mice treated with antibiotics, inter-individual and temporal variation in human oral microbiotas, and several papers on microbes in agricultural-use soil.

Events

Free Cell Press webinar on Microbiome, Antibiotics and Human Disease: July 28th – Cell Press

Microbiome of pregnancy and birth

Book chapter: The Effect of Diet and Probiotics on the Human Gut Microbiome – Lorenzo Morelli – Metabolic Syndrome and Complications of Pregnancy

Human oral microbiome

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals – Yukuto Sato – PLOS ONE

Oral microflora of supragingival and subgingival biofilms in Algerian healthy adults – Sara Ziouani – African Journal of Microbiology Research

Human respiratory microbiome

Airway bacteria and respiratory symptoms are common in ambulatory HIV-positive UK adults – Camus Nimmo – European Respiratory Journal

Oral application of lactic acid bacteria following treatment with antibiotics inhibits allergic airway inflammation – Qiuxiang Zhang – Journal of Applied Microbiology

Human vaginal microbiome

Soluble Immune Mediators and Vaginal Bacteria Impact Innate Genital Mucosal Antimicrobial Activity in Young Women – Rebecca Pellett Madan – American Journal of Reproductive Immunology

Human gut microbiome

Fetal programming of overweight through the microbiome: boys are disproportionately affected – A. L. Kozyrskyj – Journal of Developmental Origins of Health and Disease

Impact of fluoroquinolones on human microbiota. Focus on the emergence of antibiotic resistance – Victoire de Lastours – Future Microbiology

Animal models

Metabolome progression during early gut microbial colonization of gnotobiotic mice – Angela Marcobal – Scientific Reports

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment – Yael R. Nobel – Nature Communications

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice – Joshua S. Son – PLOS ONE

Animal microbiome

Review: The use of probiotics in aquaculture – Ngo Van Hai – Journal of Applied Microbiology

Thesis: Roles of the symbiotic microbial communities associated with sponge hosts in the nitrogen and phosphorus cycles – Russell T Hill – University of Maryland

Master Thesis: Arsenic Exposure Alters the Microbiome of Larval Zebrafish: A Metagenomic Analysis – Dylan A. Dahan – Bard Digital Commons

Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi – Elizabeth Fahsbender – Archives of Virology

Sexual transmission of beneficial microbes – Chad C. Smith – Trends in Ecology & Evolution

Plant, root, and soil microbiome

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards – Ingrid H. Franke-Whittle – Plant and Soil

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers – Viia Kõiv – Scientific Reports

Maternal effects on tree phenotypes: considering the microbiome – Maria Vivas – Trends in Plant Science

Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature – Rafael Bargiela – Scientific Reports

Soil Microbial Communities are Shaped by Plant-Driven Changes in Resource Availability During Secondary Succession – Lauren C. Cline – Ecology

Warmer temperature accelerates methane emissions from the Zoige wetland on the Tibetan Plateau without changing methanogenic community composition – Mengmeng Cui – Scientific Reports

Water microbiome

Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake – Andrea Di Cesare – Molecular Ecology

Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater – Alexander L. Greninger – Genome Announcements

Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea – Sung-Suk Suh – PLOS ONE

Built environment / water treatment microbiology

Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system – Qi Hu – Research in Microbiology

Impact of disinfection on drinking water biofilm bacterial community – Zilong Mi – Journal of Environmental Sciences

Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – The Journal of Hospital Infection

A review of melanized (black) fungal contamination in pharmaceutical products – incidence, drug recall and control measures – Rajendran Vijayakumar – Journal of Applied Microbiology

Bioinformatics and metagenomics

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS – Bruno Fosso – BMC Bioinformatics

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial) – Adina Howe – Frontiers in Microbiology

Metabolomics

Human Urinary Composition Controls Antibacterial Activity of Siderocalin – Robin R. Shields-Cutler – The Journal of Biological Chemistry

Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli – Sarah E. Greene – mBio

New techniques

To Celebrate Marriage Equality, Illumina to Release “BiSeq” Genome Sequencer – The Allium

More microbiology

More than the sum of its parts – Julia Fahrenkamp-Uppenbrink – Science

Ecological communities by design – James K. Fredrickson – Science

The bacterial pangenome as a new tool for analyzing pathogenic bacteria – Laetitia Rouli – New Microbes and New Infections

Microbes in the news

Antibiotics and the Gut Microbiome: Antibiotics given to infant mice may have long-term effects on the animals’ metabolism and gut microbiota – Anna Azvolinsky – The Scientist

Study: Breast milk helps babies develop immunity-boosting gut bacteria – Deena Shanker – Quartz

Your Diet May Be Causing Your Urinary Tract Infections – Mandy Oaklander – Time

uBiome and OpenBiome Partner for Microbiome Study in FMT Patients – Study will provide new insights on mechanics of fecal microbiota transplantation in C. difficile patients – uBiome

Passive Aggressive: Drosophila microbiota influence behavior – Julie Wolf – mBioSphere

Soil water, microbes influence carbon in world’s coldest desert, study finds – Phys.org

Invisible You: Art and Microbiology at the Eden Project – Microbe Post

Science, publishing, and career

The Myth of the Academic Lottery – Kelly J. Baker – Chronicle Vitae

Bik’s Picks

I saw this last night and it was so pretty: Venus and Jupiter to Put on ‘Best Backyard Sky Show of 2015’ – Alyssa Newcomb – ABC News

Say hello to the centipede from hell – Rachel Feltman – Washington Post

California governor signs strict law requiring vaccinations for most kids – Liz Szabo – USA Today

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June 21, 2015

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An upcoming workshop on bioinformatics and microbiome, lots of reviews about the intersection of gut microbiome and the immune system, and viruses in Arctic freshwater.

Events

NIMBioS Investigative Workshop: Computational Advances in Microbiome Research – July 27-28, 2015, University of Tennessee, Knoxville

Human oral microbiome

Salivary microbiota-immune profiling in cirrhosis: Could this be the noninvasive strategy that will revolutionize prognostication in hepatology? – Vishal C. Patel – Hepatology

Human gut microbiome

Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria – Weiwei Wang – Inflammatory Bowel Diseases

Review: Interactions between Innate Immunity, Microbiota, and Probiotics – GianMarco Giorgetti – Journal of Immunology Research

Review: Influence of the microbiome on response to vaccination – Amanda M. Jamieson – Human Vaccines & Immunotherapeutics

Review: How the Intricate Interaction among Toll-Like Receptors, Microbiota, and Intestinal Immunity Can Influence Gastrointestinal Pathology – Simona Frosali – Journal of Immunology Research

Review: The Interaction among Microbiota, Immunity, and Genetic and Dietary Factors Is the Condicio Sine Qua Non Celiac Disease Can Develop – D. Pagliari – Journal of Immunology Research

Review: Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions – Prem Prashant Chaudhary – Applied Microbiology and Biotechnology

Animal models

Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease – Marius Vital – Journal of Immunology Research

DGGE: Alteration of the Microbiota and Virulence Gene Expression in E. coli O157:H7 in Pig Ligated Intestine with and without AE Lesions – Bianfang Liu – PLOS ONE

Animal microbiome

The coral immune response facilitates protection against microbes during tissue regeneration – Jeroen A. J. M. van de Water – Molecular Ecology

Plant microbiome

DGGE: Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose – Andréa Cristina Bogas – Springer Plus

Plant root, soil, and sediment microbiome

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study – A. Peyton Smith – Global Change Biology

Oil Biodegradation and Oil-degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout – Ronald M Atlas – Environmental Science & Technology

Water microbiome

Biodiversity and distribution of polar freshwater DNA viruses – Daniel Aguirre de Cárcer – Science Advances

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data – Pedro M. Meirelles – PLOS ONE

Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification – Hai-Han Zhang – International Journal of Environmental Research and Public Health

Occurrence of Enterococcus species with virulence markers in an urban flow-influenced tropical recreational beach – Asmat Ahmad – Marine Pollution Bulletin

Microbes in the news

International Team Profiles DNA Viruses in Arctic Freshwater Lakes – Genome Web

Why is my hangover so bad? It’s not just the booze giving you a hangover – it’s the microbes in your stomach – Tim Spector

Israel Bets On Recycled Water To Meet Its Growing Thirst – Emily Harris – NPR

Science, publishing and career

Distraction Coefficients of Females in Biomedical Research Laboratories – Chi R. Ality – Significance

Bik’s Picks

Stanford researcher declares that the sixth mass extinction is here – Rob Jordan – Stanford University

A Periodic Diet that Mimics Fasting Promotes Multi-System Regeneration, Enhanced Cognitive Performance, and Healthspan – Sebastian Brandhorst – Cell Metabolism

Eating up to 100 g of chocolate daily linked to lowered heart disease and stroke risk – BMJ’s Heart
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May 18, 2015

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(Shorter posts this week because of international travel)

Events

Digestive Disease Week (DDW), May 16-19, Washington DC: Video: Hot topics at DDW 2015 include microbiome, new HCV treatments  –

Bioinformatics

phylogeo: an R package for geographic analysis and visualization of microbiome data -Zachary Charlop-Powers – Bioinformatics

Microbes in the news

Oddly Microbial: Honey Bee Gut Microbiomes — Queen vs. Workers –  Marcia Stone – Small Things Considered

Incredible ‘bioconcrete’ can heal itself thanks to limestone-producing bacteria – Brad Reed – BGR

NASA Hopes to Rely on Algae and Bacteria for Oxygen Production on Mars – Rachel K Wentz – Science Times

How Bacteria Break Through The Blood-Brain Barrier – Science 2.0

Ever wondered how milk becomes cheese? – Howard J. Bennett – Washington Post

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