Category Archives: Human oral

September 30, 2016

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When does a probiotic stick around, microbial diversity in 12 French cheese varieties, effects of field conditions on fecal microbiota.

Events

Microbiome Drug Development Summit Europe – 24-26 January 2017, Paris, France

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – Jessica E. Koopman – Archives of Oral Biology

Review: Role of oral microbiome on oral cancers, a review – Pourya Gholizadeh – Biomedicine & Pharmatherapy

Human skin microbiome

Novel volatiles of skin-borne bacteria inhibit the growth of Gram-positive bacteria and affect quorum-sensing controlled phenotypes of Gram-negative bacteria – Marie Chantal Lemfack – Systematic and Applied Microbiology

Human gut microbiome

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome – María X. Maldonado-Gómez – Cell Host & Microbe

Press: A Probiotic That Actually Lasts. The bacteria in yogurts have largely failed to live up to their hyped health benefits, but there are other microbes that might – Ed Yong – The Atlantic

Animal microbiome

Consequences of coinfection with protective symbionts on the host phenotype and symbiont titres in the pea aphid system – Mélanie Leclair – Insect Science

Corals: Bacterial community diversity of the deep-sea octocoral Paramuricea placomus – Christina A. Kellogg – PeerJ

Plant, root, and soil microbiome

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps – Tommaso Bardelli – Science of the Total Environment

Food microbiology

Highlighting the microbial diversity of 12 French cheese varieties – Eric Dugat-Bony – International Journal of Food Microbiology

Microbial ecology and more microbiology

Macroecology for microbiology – Jay T Lennon – PeerJ Preprint

Review: Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Techniques

Effects of field conditions on fecal microbiota – Vanessa L. Hale – Journal of Microbiological Methods

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing – Henrik Krehenwinkel – Methods in Ecology and Evolution

Microbes in the news

The cost of cheap drugs? Toxic Indian lake is ‘superbug hotspot’ – Zeba Siddiqui – Reuters

Effects of maternal stress on newborn health: An Interview with Dr. Connie Mulligan of the University of Florida – DNA Genotek

Gene-engineered gut bacteria successfully treat sick mice — and could treat humans someday – Leah Samuel – STAT News

Microbiology retreat showcases research – Anamika Veeramani – Yale Daily News

Science, publishing, and career

Working life: Doing science while black – Edward J. Smith – Science

September 26, 2016

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Bifidobacteria, pathogens in oysters, root exudate cocktails.

Human mouth microbiome

Novel strategy to detect and locate periodontal pathogens: The PNA-FISH technique – Luzia Mendes – Microbiological Research

Human gut microbiome

Bifidobacteria—Insight into clinical outcomes and mechanisms of its probiotic action – Amrita Sarkar – Microbiological Research

Animal experiments

Response of germ-free mice to colonization with O. formigenes and altered Schaedler flora – Xingsheng Li – Applied and Environmental Microbiology

Animal microbiome

The contribution of marine aggregate-associated bacteria to the accumulation of pathogenic bacteria in oysters: an agent-based model – Andrew M. Kramer – Ecology and Evolution

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle – Sigmund Jensen – Microbial Ecology

Plant, root, and soil microbiome

Root exudate cocktails: the link between plant diversity and soil microorganisms? – Katja Steinauer – Ecology and Evolution

Wastewater and pollution microbiology
Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms – Lina Marcela Silva-Bedoya – Microbiological Research

Functional characterization and unique diversity of genes and microorganisms involved in arsenite oxidation from the tailings of a realgar mine – Xian-Chun Zeng – Applied and Environmental Microbiology

More microbes

Forum: Bacteria Are Smartphones and Mobile Genes Are Apps – J. Peter W. Young – Trends in Microbiology

Microbes in the news

How the Air Force Will Attack Its Tiniest Enemy: Plane-Corroding Bacteria – Eric Tegler – Popular Mechanics

Tiny Bacteria Are Eating America’s Fighter Jets – David Tracy – Foxtrotalpha

Body fat link to bacteria in faeces – BBC

Prof Emphasizes Importance of Microbiomes in Regulating Human Health – Shruti Juneha – The Cornell Daily Sun

Does this 25 year-old hold the key to winning the war against superbugs? – Nicola Smith – Telegraph.co.uk

Kissing chickens is bad for your health, CDC warns – Karin Brulliard – Washington Post

September 18, 2016

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Gut fermentation bubbles might promote decompression sickness in divers, corals of the Tropical Eastern Pacific, and a new microbiome book: Let Them Eat Dirt.

General microbiome

Review: Transitioning From Descriptive to Mechanistic Understanding of the Microbiome: The Need for a Prospective Longitudinal Approach to Predicting Disease – Victoria J. Martin – The Journal of Pediatrics

Pregnancy and early life

Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool-age asthma – Leah Stiemsma – Clinical Science

Human oral microbiome

Review: The role of bacteriophages in periodontal health and disease – Graça Pinto – Future Medicine

Human urinary tract microbiome

A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms – Asha Rani – Scientific Reports

Human vaginal microbiome

Neither vaginal nor buccal administration of 800 μg misoprostol alters mucosal and systemic immune activation or the cervicovaginal microbiome: a pilot study – Spyros A. Kalams – The European Journal of Contraception & Reproductive Health Care

Human gut microbiome

Gut fermentation seems to promote decompression sickness in humans – Sébastien de Maistre – Journal of Applied Physiology

Review: Role of gut microbiota and nutrients in amyloid formation and pathogenesis of Alzheimer disease – Francesca Pistollato – Nutrition Reviews

Review: Enteric immunity, the gut microbiome, and sepsis: Rethinking the germ theory of disease – Javier Cabrera-Perez – Experimental Biology and Medicine

Review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Structural modulation of the gut microbiota and the relationship with body weight: compared evaluation of liraglutide and saxagliptin treatment – Lin Wang – Scientific Reports

Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice – Ningwen Tai – Journal of Experimental Medicine

Press: Yale study shows that gut microbes could trigger type 1 diabetes – Jack Woodfield – Diabetes.co.uk

Intestinal immune maturation is accompanied by temporal changes in the composition of the microbiota – G. Den Hartog – Beneficial Microbes

Animal microbiome

First deep screening of bacterial assemblages associated with corals of the Tropical Eastern Pacific – Joicye Hernández-Zulueta – FEMS Microbiology Ecology

Bioinformatics

Reference point insensitive molecular data analysis – M. Altenbuchinger – Bioinformatics

Microbes in the news
New book: Let Them Eat Dirt – B. Brett Finlay and Marie-Claire Arrieta

September 17, 2016

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Metabolic interactions between a 4-species community, captive and wild red-crowned cranes, microbial life around a coal mine fire that’s been burning for over 50 years.

Pregnancy and early life

Associations between EBV and CMV Seropositivity, Early Exposures, and Gut Microbiota in a Prospective Birth Cohort: A 10-Year Follow-up – Claudia Carvalho-Queiroz – Frontiers in Pediatrics

Human oral microbiome

The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health – Andres Gomez – Microbial Ecology

Human gut microbiome

Gut microbiota, metabolome and immune signatures in patients with uncomplicated diverticular disease – Giovanni Barbara – Gut

Faecal Concentrations of Short-chain Fatty Acids and Selected Bacteria in Healthy and Celiac Children – Maša Primec – International Journal of Celiac Disease

Animal and in vitro experiments

Impact of Gluten-Friendly Bread on the Metabolism and Function of In Vitro Gut Microbiota in Healthy Human and Coeliac Subjects – Antonio Bevilacqua – PLOS ONE

Protocol: Intestinal Organoids as a Novel Tool to Study Microbes–Epithelium Interactions – Giulia Nigro – Methods in Molecular Biology

The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community – Xiaokan Guo – PLOS Computational Biology

Animal microbiome

Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis) – Yuwei Xie – Scientific Reports

Compartmentalization of microbial communities that inhabit the hindguts of millipedes – James B. Nardi – Arthropod Structure & Development

Plant, root, and soil microbiome

Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils – Luís França – Extremophiles

Niche filtering of bacteria in soil and rock habitats of the Colorado Plateau Desert, Utah, USA – Kevin Lee – Frontiers in Microbiology

The Centralia, PA, coal mine fire has been burning since 1962. Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – PeerJ Preprint

Water and extremophile microbiome

Functional ecology of soil microbial communities along a glacier forefield in Tierra de Fuego (Chile) – Miguel Angel Fernández-Martínez – Frontiers in Microbiology

Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia – John Paul Balmonte – Frontiers in Microbiology

Shifts in Microbial Community Structure and Activity in the Ultra-Oligotrophic Eastern Mediterranean Sea Driven by the Deposition of Saharan Dust and European Aerosols – Cui Guo- Frontiers in Marine Science

Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225) – Antje Lauer – Microorganisms

Built environment microbiome

Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants – Damien Costa – Pathogens and Disease

Techniques

Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction – Butler, Ross N. – Journal of Pediatric Gastroenterology and Nutrition

Microbes in the news

Get Your Children Good and Dirty – B. Brett Finlay and Marie-Claire Arrieta – Wall Street Journal

NASA Space Biology Fellowships to Study the Microbiome of the ISS as a Built Environment Research Announcement – SpaceRef

Intercontinental Plant Microbiome Research Earns UBiome Grant – Haverford.edu

Scientific research shows how corrugated stops bacteria – Packaging World

Bacterial Predators Surprise Scientists with Hidden Diversity – Jennifer Frazer – Scientific American

Bacteria Hysteria

Fear-mongering story sponsored by industry, performed by microbiology professor: Petri dishes you can wear: UA researchers study the bacteria on the bottoms of your shoes – Courtney Gallant – The Daily Wildcat

September 16, 2016

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Hadza fecal metabolome, phyllosphere of indoor plants, decoupling function and taxonomy in the ocean, and winners of the 2016 MoBio Microbiome Awards.

Events

The Swarm Inside: Making Sense of the Microbiome – September 27, 2016 – Kavli Conversations

Human oral microbiome / proteomics

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls – Daniel Belstrøm – PeerJ

Human reproductive tract microbiome

Inflammation, Microbiota, and Prostate Cancer – Martin Puhr – European Urology Focus

Human gut microbiome / metabolome

Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view – Silvia Turroni – Scientific Reports

Association of brain amyloidosis with pro-inflammatory gut bacterial taxa and peripheral inflammation markers in cognitively impaired elderly – Annamaria Cattaneo – Neurobiology of Aging

Minireview: Correlations of Host Genetics and Gut Microbiome Composition – Krystyna Dąbrowska – Frontiers in Microbiology

Animal and bioreactor experiments

Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity

In vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiotaIn vitro analysis of partially hydrolyzed guar gum fermentation on identified gut microbiota – Justin Carlsona – Anaerobe

Plant, root, and soil microbiome

The plant is crucial: specific composition and function of the phyllosphere microbiome of indoor ornamentals – Rocel Amor Ortega – FEMS Microbiology Ecology

Water microbiome

Decoupling function and taxonomy in the global ocean microbiome – Stilianos Louca – Science

Phages and viruses

The Expanding Virosphere – Edward C. Holmes – Cell Host & Microbe

From oil spills to barley growth – oil-degrading soil bacteria and their promoting effects – Annett Mikolasch – Journal of Basic Microbiology

More microbiology

Minimal Tool Set for a Prokaryotic Circadian Clock – Nicolas Schmelling – bioRxiv

Microbes in the news

I was in the jury! 2016 MoBio Microbiome Award Winners Announced – MoBio 

Oral infection outbreak appears linked to an Anaheim dental office, officials say – LA Times

Hundreds Of Children May Have Been Exposed To Infectious Bacteria At O.C. Dentist’s Office – CBSlocal.com

Transforming the Microbiology Laboratory to Address the Triple Aim in Healthcare – Irene Dusich – Health System Management

CSU professors hope to break ground in microbiology through RNA research – Allec Brust – Collegian

Increase in antibiotic-resistant bacteria hinders treatment of kidney infections– Phil Hampton – UCLA Newsroom

Bacteria Hysteria

Your water bottle has as much bacteria as your toilet – AOL

Science, publishing, and career

Universities failing to make best use of Twitter, researchers say – Chris Havergal – Times Higher Education

Science, a Deathbed Promise, and a Mother’s Gift – Jonathan Foley – The Macroscope

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

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Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff – Current Opinion in Pulmonary Medicine

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

August 27, 2016

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Gut microbiome in pre-Columbian mummies, spacecraft assembly cleanrooms, smokeless tobacco products, time series data, and a return of the Musical Microbes.

Human skin microbiome

Skin fungal community and its correlation with bacterial community of urban Chinese individuals – Marcus H. Y. Leung – Microbiome

Human oral microbiome

High-throughput quantitative method for assessing coaggregation among oral bacterial species – E. Levin-Sparenberg – Letters in Applied Microbiology

Human gut microbiome

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies – Tasha M. Santiago-Rodriguez – FEMS Microbiology Ecology

Note: unclear definition of “redemption”; means that a medication prescription was filled. Broad-Spectrum Antibiotic Treatment and Subsequent Childhood Type 1 Diabetes: A Nationwide Danish Cohort Study – Tine D. Clausen – PLOS ONE

Animal experiments

Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits – Y. Zhu – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Endolithic microbial diversity in sandstone and granite from the McMurdo Dry Valleys, Antarctica – Stephen D. J. Archer – Polar Biology

Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System – Rodrigo Gouvêa Taketani – Microbial Ecology

Review: Bacteria in decomposing wood and their interactions with wood-decay fungi – Sarah R. Johnston – FEMS Microbiology Ecology

Water microbiome

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution – Francisco J. R. C. Coelho – Molecular Ecology

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities – Anders Lanzén – Molecular Ecology

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification – Eric A. Dubinsky – Water Research

Spacecraft microbiome

Functional metagenomics of spacecraft assembly cleanrooms: Presence of virulence factors associated with human pathogens – Mina Bashir – Frontiers in Microbiology

Tobacco microbiome

Bacterial Populations Associated with Smokeless Tobacco Products – Jing Han – Applied and Environmental Microbiology

Bacteria in smokeless tobacco products may be a health concern – American Society for Microbiology
http://www.asm.org/index.php/journal-press-releases/94525-bacteria-in-smokeless-tobacco-products-may-be-a-health-concern
Proteomics

Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS – Jing Wu – Journal of Proteome Research

Bioinformatics, metagenomics, and statistics

Modeling time-series data from microbial communities – Benjamin J Ridenhour – bioRxiv

Improving ancient DNA genome assembly – Alexander Seitz – PeerJ Preprint

More microbiology

The Musical Microbes are back! Influence of a mono-frequency sound on bacteria can be a function of the sound-level – Vijay Kothari – bioRxiv

Microbes in the news

Focus: California drought reducing beach bacteria: Reduced runoff has meant fewer health advisories, data show – Daniel Wheaton – San Diego Union Tribune
Mystery Solved: How Lyme Disease Bacteria Spread Around the Body – Rachael Rettner – LiveScience

In sub-Saharan Africa, cancer can be an infectious disease – ScienceDaily

#BacteriaHysteria: You Should Never Ask For a Slice Of Lemon In Your Drink – Alice Sholl – Yahoo

Science, publishing, and career

There Was A Huge Outpouring Of Support For This Little Girl Who Got Bullied For Loving Bugs. Let Sophia play with her bugs! – Ishmael N. Daro – BuzzFeed

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science

August 19, 2016

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Gingivitis and periodontitis in Malawian cohort, gut Bifidobacteria during aging, picornaviruses in rats from 2 locations.

Jobs and events

QIIME 2 workshop Nov 4-5 (just prior to SSSA meeting) in Phoenix, AZ – Greg Caporaso – Microbe.net

Three postdoctoral researchers and one Ph.D. student: role of microbes in post-fire soil organic matter dynamics – University of Wisconsin-Madison

Human oral microbiome

Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: A Cross-Sectional Cohort Study in Malawi – Liam Shaw – Applied and Environmental Microbiology

Press: Investigators chart microbial ecology of gingivitis, periodontitis – EurekAlert

Association of metabolic syndrome and chronic periodontitis in Colombians – Adriana Jaramillo – Clinical Oral Investigations

Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism Revealed by Gene Meter Methodology – M Colby Hunter – bioRxiv

Human gut microbiome

Review: Gut Bifidobacteria Populations in Human Health and Aging – Silvia Arboleya – Frontiers in Microbiology

Review: Correlations of host genetic and gut microbiome composition – Krystyna Dabrowska – Frontiers in Microbiology

Review: Gut Microbiota: a contributing factor to obesity – Steve M. Harakeh – Frontiers in Cellular and Infection Microbiology

Animal microbiome

High diversity of picornaviruses in rats from different continents revealed by deep sequencing – Thomas Arn Hansen – Emerging Microbes & Infections

Composition of Ileal Bacterial Community in Grazing Goats Varies across Non-rumination, Transition and Rumination Stages of Life – Jinzhen Jiao – Frontiers in Microbiology

Spatial and temporal dynamics of Pacific oyster hemolymph microbiota across multiple scales – Ana Lokmer – Frontiers in Microbiology

Plant, root, and soil microbiome

Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes – Christopher J. Barnes – Frontiers in Microbiology

Fungal Assemblages in Different Habitats in an Erman’s Birch Forest – Teng Yang – Frontiers in Microbiology

Water microbiome

Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments – Mathilde Jeanbille – Frontiers in Microbiology

Microbes in space

The theory and application of space microbiology: China’s experiences in space experiments and beyond – Changting Liu – Environmental Microbiology

Bioreactor microbiology

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence – William Tottey – Journal of Neurogastroenterology and Motility

Bioinformatics

Resolving microbial membership using Abundance and Variability In Taxonomy (‘AVIT ) – Anirikh Chakrabarti – Scientific Reports

Microbes in the news

Trillions of Tiny Dictators. Microbes have taken over our bodies and maybe even our minds. What, exactly, are they? – Emily Willingham – The Wall Street Journal
With a little help from my friends. The microbiome gets a worthy biography – The Economist
Eating Yogurt Is Not Enough: Rebalancing The Ecosystem Of ‘The Microbes Within Us’ – Terry Gross – NPR Fresh Air (Transcript of interview with Ed Yong)

Prebiotics Take Front and Center Stage on the 700 Club – PR NewsWire

Uncovering the female body’s secret protection against HIV – Heather Boerner – PBS Newshour

Scientific Studies Using Mice May Be Hard to Replicate Due to Gut Microbes – Paul Ratner – BigThink

Scientists Investigate How Multidrug-Resistant Pathogens are Brought into Hospitals – SciCasts

MSU team shows biofilm and mineral-producing bacteria have potential for plugging oil and gas leaks – Marshall Swearingen – Montana State University

Montana Officials Close Yellowstone River To Fight Fish-Killing ParasiteMontana Officials Close Yellowstone River To Fight Fish-Killing Parasite – Richard Gonzales – NPR

Science, publishing, and career

Peer Review Week September 2016 #RecognizeReview – Alice Meadows – The Scholarly Kitchen

With Kate Rubins, a former PhD student in our lab: NASA Astronauts Successfully Install New Space Station Docking Port – Samantha Mathewson – Space.com