Category Archives: Animal microbiome

November 13, 2015

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Happy Friday the 13th! Today’s post features a gut-vascular barrier implicated in celiac disease, bison microbiota, 16S rRNA genes in metagenomics data, soil communities at neighboring sites, enriching microbial DNA, and lots of gut microbiota reviews.

Human gut microbiome

(humans and animal models; celiac disease) A gut-vascular barrier controls the systemic dissemination of bacteria – Ilaria Spadoni – Science

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella – Petia Kovatcheva-Datchary – Cell Metabolism

Effect of Antibiotics on Gut Microbiota, Gut Hormones and Glucose Metabolism – Kristian H. Mikkelsen – PLOS ONE

Review: The Enteric Microbiome in Hepatobiliary Health and Disease – James H. Tabibian – Liver International

Review: Microbiota and aging – Stephan C Bischoff – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The impact of gut microbiota on brain and behaviour: implications for psychiatry – Timothy G Dinan – Current Opinion in Clinical Nutrition & Metabolic Care

Review: The gut microbiota keeps enteric glial cells on the move; prospective roles of the gut epithelium and immune system – Panagiotis S. Kabouridis – Gut Microbes

Review: The joint power of sex and stress to modulate brain–gut–microbiota axis and intestinal barrier homeostasis: implications for irritable bowel syndrome – M. Pigrau – Neurogastroenterology & Motility

Review: Microbiome and Health in Past and Present Human Populations – Christina Warinner – American Anthropologist

Animal and bioreactor models

 

Individual Members of the Microbiota Disproportionately Modulate Host Innate Immune Responses – Annah S. Rolig – Cell Host & Microbe

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon – Sophie Fehlbaum – PLOS ONE

Animal microbiome

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison) – Gaddy T. Bergmann – PLOS ONE

Fecal contamination of echinoderms: first report of heavy E. coli loading of sea urchins from a natural growing area – M Bouchoucha – Letters in Applied Microbiology

Plant, root, and soil microbiome

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites – A. L. Gagliano – GeoBiology

Soil microorganisms behave like macroscopic organisms: patterns in the global distribution of soil euglyphid testate amoebae – Enrique Lara – Journal of Biogeography

Arsenic uptake, arsenite efflux and plant growth in hyperaccumulator Pteris vittata: Role of arsenic-resistant bacteria – Yong-He Han – Chemosphere

Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea – Hanin Alzubaidy – Gene

Review: Current trends in Bt crops and their fate on associated microbial community dynamics: a review – Amit Kishore Singh – Protoplasma

Built environment and waste treatment

Separate treatment of hospital and urban wastewaters: A real scale comparison of effluents and their effect on microbial communities – Teofana Chonova – Science of the Total Environment

Bioinformatics and metagenomics

Introducing REAGO: Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Techniques
Enriching microbial DNA: Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA – Angela Glassing – Journal of Microbiological Methods

The Sequence of Sequencers: The History of Sequencing DNA – James M. Heather – Genomics

Microbes in the news

Water Quality in Green Buildings – Katherine Dahlhausen – MicroBEnet

Video: Jonathan Eisen: Microbes in Food and Agriculture: Dr. Jonathan Eisen speaking at UC Davis’s Institute for Food and Ag Literacy round table about the impact the microbiome has made and potential relevance in health, food, and agriculture.

Want a Stronger Defense System against Diseases? Add Some Worms – Sheena Faherty – Scientific American

From garden to gut: New book from UW’s David Montgomery explores an unfolding scientific revolution – Hannah Hickey – University of Washington

Video in Dutch: How many bacteria do you exchange during French Kissing? A demonstration by microbiologist Remco Kort

Bacteria and bacteriophages collude in the formation of clinically frustrating biofilms – Phys.org

Extreme bacteria live in odd corners of the ecosystem – North Country Public Radio

Bacteria Hysteria

Sponsored report: Bacteria, Fecal Matter Found in Rain Puddles on Ground

Science, publishing, and career

In the eye of the Twitterstorm: Social media is shaking up how scientists talk about gender issues – Lauren Morello – Nature
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November 12, 2015

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Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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November 11, 2015

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Red-pigmented haloarchaea in flamingo feathers, cyanobacteria of the Western Himalaya, and read-filtering of HT amplicon reads.

Human respiratory microbiome

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention – Leah Cuthbertson – ISME Journal

Human reproductive tract microbiome

Genital tract colonization with Ureaplasma spp. and its association with abnormal vaginal flora – Ellen Vancutsem – Journal of Medical Microbiology

Impact of Bacterial Vaginosis on Perineal Tears during Delivery: A Prospective Cohort Study – Vincent Letouzey – PLOS ONE

Human gut microbiome

Carriage of enterobacteria producing extended spectrum beta-lactamases and composition of the gut microbiota in an Amerindian community – María José Gosalbes – Antimicrobial Agents and Chemotherapy

Animal microbiome (and archaea)

Occurrence of viable, red-pigmented haloarchaea in the plumage of captive flamingoes – Kyung June Yim – Scientific Reports

DGGE: Effect of chemical stress and ultraviolet radiation in the bacterial communities of zebrafish embryos – Jacinta M.M. Oliveira – Environmental Pollution

Plant, root, and soil microbiome

Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya – Kateřina Čapková – Microbial Ecology

Phytostabilization of moderate copper contaminated soils using co-inoculation of Vicia faba with plant growth promoting bacteria – Imen Challougui Fatnassi – Journal of Basic Microbiology

Effects of Common Mycorrhizal Network on Plant Carbohydrates and Soil Properties in Trifoliate Orange–White Clover Association – Ze-Zhi Zhang – PLOS ONE

Distributions and compositions of old and emerging flame retardants in the rhizosphere and non-rhizosphere soil in an e-waste contaminated area of South China – Shaorui Wang – Environmental Pollution

Water microbiome

High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling – Tomàs Llorens-Marès – Microbial Ecology

Bioinformatics

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences – Vinita Deshpande – Mycologia

A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies – Fernando Puente-Sánchez – Nucleic Acids Research

Microbes in the news

One course of antibiotics disrupts gut microbiome for a year – Medical News Today

Science, publishing, and career

Public Data Archiving in Ecology and Evolution: How Well Are We Doing? – Dominique G. Roche – PLOS Biology
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November 10, 2015

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Oral and gut microbiomes respond differently to antibiotics, looking two gifted horses in the mouth, BMIs and Bifidos, Drosophila mating, gut microbes and tumorigenesis, microbial food webs in clay rocks, and don’t forget that Bonferroni correction.

Pregnancy and birth (Probiotics too!)

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit – J. M. Franasiak – Journal of Assisted Reproduction and Genetics

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study – Ulla Uusitalo – JAMA Pediatrics

Human oral microbiome

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces – Egija Zaura – mBio

Crossover clinical trial of different methods of removing a denture adhesive and the influence on the oral microbiota – Élen Massaro Nunes – The Journal of Prosthetic Dentistry

Human gut microbiome

Correlation between body mass index and fecal microbiota from children – A. Ignacio – Clinical Microbiology and Infection

Review: Clostridium difficile infection and intestinal microbiota interactions – C. Rodriguez – Microbial Pathogenesis

Animal and bioreactor models

A Statistical Error in: “Analysis of Caecal Microbiota in Rats Fed with Genetically Modified Rice by Real-Time Quantitative PCR” – Alexander Panchin – Journal of Food Science

In mice: Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis -Joseph P. Zackular – mSphere

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster – Devin Arbuthnott – Journal of Evolutionary Biology

Chemostat culture systems support diverse bacteriophage communities from human feces – Tasha M. Santiago-Rodriguez – Microbiome

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans – Nicholas A. Pudlo – mBio

Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass – Sharon A. Huws – FEMS Microbiology Ecology

Animal microbiome

In-depth snapshot of the equine subgingival microbiome – Wenling Gao – Microbial Pathogenesis

Occurrence and distribution of Malassezia species on skin and external ear canal of horses – Hojjatollah Shokr – Mycoses

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning – Microbiome

Plant, root, and soil microbiome

The effect of altitudinal gradient on soil microbial community activity and structure in moso bamboo plantations – Ed-Haun Chang – Applied Soil Ecology

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea – A Metagenomic Approach – Marta Filipa Simões – Genomics, Proteomics & Bioinformatics

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches – Pranitha S. Pandit – Environmental Microbiology

Effects of Sulfamethazine and Zinc on the Functional Diversity of Microbial Communities during Composting – Manli Duan – Environmental Microbiology

Evidence for duplication in title words: Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks – Michael Schloter – Frontiers in Microbiology

A minimalistic microbial food web in an excavated deep subsurface clay rock -Alexandre Bagnoud – FEMS Microbial Ecology

Water microbiome

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms – Sara Kleindienst – PNAS

Extremophile microbiome

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter – Evgeniya Matyugina – Chinese Journal of Oceanology and Limnology

Built environment microbiome

Differences in intertidal microbial assemblages on urban structures and natural rocky reef – Elisa L. Tan – Frontiers in Microbiology

Waste microbiology

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments – Lilian M. Guibert – Environmental Microbiology

Cultivating Microbial Dark Matter in Benzene-Degrading Methanogenic Consortia –
Fei Luo – Environmental Microbiology

Metagenomics and bioinformatics

DESM: portal for microbial knowledge exploration systems – Adil Salhi – Nucleic Acids Research

Techniques

Coupling dye-integrated polymeric membranes with smartphone detection to classify bacteria – Lígia Bueno – RSC Advances

Microbes in the news

9 Fascinating Facts About The Microbiome, The Trillions Of Microbes Hidden Inside Us — Jessica Leber – Fast Co.Exist

NTU scientists use dead bacteria to kill colorectal cancer – EurekAlert

Science, publishing, and career

(A)Historical Science: why scientists should care more about the history of science – Arturo Casadevall and Ferric C. Fang – Infection and Immunity

November 9, 2015

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Bronchial microbiome in COPD patients, tilapia pond systems, bacteria and fungi at the root tips of Pinus, and microbiome of an extreme Australian river.

Human respiratory microbiome

Influence of biofim on the bronchial microbiome in COPD patients colonized or infected by pseudomonas aeruginosa – Marian Garcia-Nuñez – European Respiratory Journal

Human gut microbiome

Review: Gut Microbiota and Host Reaction in Liver Diseases – Hiroshi Fukui – Microorganisms

Animal models

Repeated dose (28-day) administration of silver nanoparticles of varied size and coating does not significantly alter the indigenous murine gut microbiome – Laura A. Wilding – Nanotoxicology

Animal microbiome

Bacteria associated with Amblyomma cajennense tick eggs – Erik Machado-Ferreira – Genetics and Molecular Biology

Characterization of microbial communities in intensive GIFT tilapia (Oreochromis niloticus) pond systems during the peak period of breeding – Limin Fan – Aquaculture Research

Plant, root, and soil microbiome

Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes – Shin-Yi Lee Marzano – Virus Research

The local environment determines the assembly of root endophytic fungi at a continental scale – Kyriaki Glynou – Environmental Microbiology

Effects of vegetation and seasonality on bacterial communities in Amazonian dark earth and adjacent soils – Amanda Barbosa Lima – African Journal of Microbiology Research

Response of soil microbiota to nine-year application of swine manure and urea – Diana Morales – Ciencia Rural

Analysis of single root-tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi – Srisailam Marupakula – Environmental Microbiology

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use – E. A. Ivanova – Soil Biology

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of The Total Environment

Functional selections of soil metagenomes identify tolerance genes against lignocellulose-derived inhibitors – Kevin J. Forsberg – Applied and Environmental Microbiology

Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine – Letícia Bianca Pereira – Genetics and Molecular Biology
http://www.scielo.br/scielo.php?pid=S1415-47572015005050025&script=sci_arttext
Water / Extremophile microbiome

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia – Shipeng Lu – Environmental Microbiology Reports

Food microbiology

Impact of nisin-activated packaging on microbiota of beef burgers during storage – Ilario Ferrocino – Applied and Environmental Microbiology

Techniques

PacBio Sequencing and Its Applications – Anthony Rhoads – Genomics, Proteomics & Bioinformatics

Preservation of Uncultivated Microbial Cells for Single Cell Genomics and Cultivation in Future – Om Prakash – Single Cell Biology

Microbes in the news

Kangaroo farts won’t save the world – Their gut microbes really aren’t that special – Arielle Duhaime-Ross

Based on the data shown here, the title seems a stretch: 2015 American College of Rheumatology Annual Meeting: Microbiome Seems to Have a Role in Triggering Lupus – HCP Live

Bacteria looks to be promising in cheatgrass battle – Larry Meyer – The Argus Observer
http://www.argusobserver.com/news/bacteria-looks-to-be-promising-in-cheatgrass-

Veterinarians Warn Pet Owners About Bacteria After Flooding: increased chance of leptospirosis – TWC news
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November 7, 2015

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Human oral microbiome

Dental demineralization, radiation caries and oral microbiota in patients with head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: Bacterial interactions in pathogenic subgingival plaque – Hong Min Ng – Microbial Pathogenesis

Human gut microbiome

Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians – Fang Wang – Journal of Microbiology and Biotechnology

Gut colonization with methanobrevibacter smithii is associated with childhood weight development – Catherine A. Mbakwa – Obesity

Review: Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota – Paige V. Bauer – Cellular and Molecular Life Sciences

Animal and other models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Mice: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline – Jérôme Lluch – PLOS ONE

Sheep: Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium – David Collie – PLOS ONE

Human cells: The effect of short-chain fatty acids on human monocyte-derived dendritic cells – Claudia Nastasi – Scientific Reports

Review: Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? – E. Ringø – Aquaculture Nutrition

Animal microbiome

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions –
Katharina Burbach – Microbiology Open

Insects: Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis – Paul R. Johnston – PLOS Pathogens

Plant, root, and soil microbiome

Microbial immigration across the Mediterranean via airborne dust – Riccardo Rosselli – Scientific Reports

The herbaceous landlord: integrating the effects of symbiont consortia within a single host – Roo Vandegrift – PeerJ

Review: The plant microbiome explored: implications for experimental botany – Gabriele Berg- Journal of Experimental Botany

The influence of hydrogeological disturbance and mining on coal seam microbial communities – M. J. Raudsepp – Geobiology

Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards – Paula Baptista – Environmental Microbiology Reports

Water microbiome

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Metagenomics and bioinformatics

Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome – Tanudeep Bhattacharya – PLOS ONE

Kernel-Penalized Regression for Analysis of Microbiome Data – Timothy W. Randolph – ArXiv

Infection and microbial detection

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry – Aleksandra Jakovljev – BMC Microbiology

Copper surfaces are associated with significantly lower concentrations of bacteria on selected surfaces within a pediatric intensive care unit – Michael G. Schmidt – American Journal of Infection Control

Microbial ecology

An equilibrium theory signature in the island biogeography of human parasites and pathogens – Kévin Jean – Global Ecology and Biogeography

Microbes in the news

‘The Secret World Inside You’ Explores the Microbial Human – William Grimes – The New York Times
I Contain Multitudes: Microbiomes at the American Museum of Natural History –
Sean Hutchinson – Inverse
Exploring the Inner Universe. A new American Museum of Natural History exhibit introduces visitors to the microbes within their bodies – Ashley P. Taylor – The Scientist

Sexed-up beer – Nature Biotechnology

Microbes aid cancer drugs – Mitch Leslie – Science

Gut microbiota regulates antioxidant metabolism – EurekAlert

Kitchen utensils can spread bacteria between foods, UGA study finds – Sydney Devine – University of Georgia
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November 6, 2015

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Dog skin, kangaroo methane emissions, flea microbiome and ecology, domestication of wine yeast, and surface reflectance by roof microbes.

Events

11th International Meeting on Microbial Epidemiological Markers (IMMEM XI), March 2016, Portugal – Abstract submission deadline: November 10

General microbiome

Microbiomes in light of traits: A phylogenetic perspective – Jennifer B. H. Martiny – Science

The ecology of the microbiome: Networks, competition, and stability – Katharine Z. Coyte – Science

What makes the gut microbiome stable? – Caroline Ash – Science

Microbiome, a new dimension in cancer research – Antonio Galvao Neto – Annals of Translational Medicine

Human gut microbiome

Characterization of the salivary microbiome in patients with pancreatic cancer – Pedro J. Torres – PeerJ

Animal microbiome

What is living on your dog’s skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis – C.M. Smith – FEMS Microbial Ecology

Decreasing methane yield with increasing food intake keeps daily methane emissions constant in two foregut fermenting marsupials, the western grey kangaroo and red kangaroo – Catharina Vendl – Journal of Experimental Biology

Evaluation of the bacterial microbiome of two flea species using different DNA isolation techniques provides insights into flea host ecology  – Andrea L. Lawrence – FEMS Microbiology Ecology

The functional gene composition and metabolic potential of coral-associated microbial communities – Yanying Zhang – Scientific Reports

Plant, root, and soil microbiome

Can commercial soil microbial treatments remediate plant–soil feedbacks to improve restoration seedling performance? – Lora B. Perkins – Restoration Ecology

Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing – Hongmei Jing – Frontiers in Microbiology

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China –
Baiying Man – Frontiers in Microbiology

Review: Ongoing domestication of wine yeast: past, present and future – P.J. Chambers – Australian Journal of Grape and Wine Research

Built environment microbiology

Surface reflectance degradation by microbial communities – Meng-Dawn Cheng – Journal of Building Physics

Metagenomics and bioinformatics

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J Joseph – BioRxiv

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome – Yinfeng Zhang – International Journal of Molecular Sciences

Fizzy: feature subset selection for metagenomics – Gregory Ditzler – BMC Bioinformatics

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities – Michael A. Peabody – BMC Bioinformatics

Microbes in the news

Our Dust, Ourselves – Emily Anthes – The New Yorker
Emily Anthes writes about Wildlife of Your Homes microbiome studies in the New Yorker – Jonathan Eisen – MicroBEnet

The Hottest New Cancer Drugs Depend on Gut Microbes – Ed Yong – The Atlantic
Gut bacteria may affect the success of cancer treatments – Sam Wong – New Scientist

This New Exhibition Is a Tour of the Human Body’s ‘Hidden Organ’ – Becky Ferreira – Motherboard

Podcast (20 min) We are a constellation of our microbiome and ourselves – Meg Tirrell and Luke Timmerman – Stat News

The strange case of the man infected with tapeworm cancer – Helen Branswell – StatNews

With a picture of human cells? 30 mind-blowing facts about the microbes that live inside of you – Julia Calderone – TechInsider
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November 3, 2015

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Dog exposure and childhood asthma, earthworm poop, thermally stressed corals, and cryospheric ecosystems.

General microbiome

From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology – Pierre-Edouard Fournier – Anaerobe

Study from Sweden with patients and dogs registries: Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma – Tove Fall – JAMA Pediatrics

Human gut microbiome

Plagiarism in intro and only CFU data for E. coli and lactic acid bacteria: A Comparative Study of Gut Microbiota Profiles of Children Living in Kulon Progo and West Lombok – Siti Helmyati – Pakistan Journal of Nutrition

Microbial Signatures in Post-Infectious Irritable Bowel Syndrome – Towards Patient Stratification for Improved Diagnostics and Treatment – Jonna Jalanka – Gut Microbes

Review: Genetic Variations in Vitamin D Metabolism Genes and the Microbiome, in the Presence of Adverse Environmental Changes, Increase Immune Dysregulation – Laing BB
and Ferguson LR – Austin Journal of Nutrition & Metabolism

Animal models

In mice: Gut microbe-derived extracellular vesicles induce insulin resistance, thereby impairing glucose metabolism in skeletal muscle – Youngwoo Choi – Scientific Reports

In mice: Influence of whole-wheat consumption on fecal microbial ecology of obese diabetic mice – Jose F Garcia-Mazcorro – PeerJ Preprints

Earthworms: Characterization of the bacterial communities of casts from Eisenia andrei fed with different substrates – Manuel Aira – Applied Soil Ecology

Animals

Viral and Bacterial Epibionts in Thermally-Stressed Corals – Hanh Nguyen-Kim – J Mar Sci Eng

Plant, root, and soil microbiome

Cross-biome comparison of microbial association networks – Karoline Faust – Frontiers in Microbiology

Response of microbial communities from an apple orchard and grassland soils to the first-time application of the fungicide tetraconazole – Sławomir Sułowicz – Ecotoxicology and Environmental Safety

A Chemical Perspective on Microalgal–Microbial Interactions – Erik F.Y. Hom – Trends in Plant Science

Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency – Laura Giagnoni – Applied Soil Ecology

Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change – Ellen L. Fry – Soil Biology and Biochemistry

Copper and temperature modify microbial communities, ammonium and sulfate release in soil – Rui Ferreira – Journal of Plant Nutrition and Soil Science

Review: Mitigating climate change through managing constructed-microbial communities in agriculture – Cyd E. Hamilton – Agriculture, Ecosystems & Environment

Extremophile microbiome

Editorial: Cryospheric ecosystems: a synthesis of snowpack and glacial research – Andy Hodson – Environmental Research Letters

Bioinformatics and metagenomics

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities – Anja Lange – PLOS ONE

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes – Mingjie Wang – Genome Biology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets – Yu-Wei Wu – Bioinformatics

Techniques

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms – Jeongan Choi – Scientific Reports

Microbes in the news

Microbesity: Obesity appears linked to the gut microbiome. How and why is still a mystery—but scientists have plenty of ideas – Jenny Rood – The Scientist

Science, publishing, and career

“There’s No Crying in Academia,” Acknowledging Emotional Labour in the Academy  – Margeaux Feldman – Gender and Society

2015 Life Sciences Salary Survey – Karen Zusi and Amanda B. Keener – The Scientist
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October 30, 2015

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Cave microbiome, vaginal bacteria in cute minipigs, and “disordered” home dust microbiome, and an update on the Beard Microbiome.

Human gut microbiome

Oatmeal porridge: impact on microflora-associated characteristics in healthy subjects – Jørgen Valeur – British Journal of Nutrition

Animal models

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle – Emma Lorenzen – Veterinary Research

Biofilm-associated bacterial amyloids dampen inflammation in the gut: oral treatment with curli fibres reduces the severity of hapten-induced colitis in mice – Gertrude O Oppong – NPJ Biofilms and Microbiomes

Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling – Alexandria M. Palaferri Schieber – Science

Cave microbiome

Microbial mediation of complex subterranean mineral structures – Nicola Tisato – Scientific Reports

Built environment microbiome

Home dust microbiota is disordered in homes of low-income asthmatic children – Christina E. Ciaccio – Journal of Asthma

Food microbiology

A Large Set of Newly Created Interspecific Saccharomyces Hybrids Increases Aromatic Diversity in Lager Beers – Stijn Mertens – Applied and Environmental Microbiology

T-RFLP: Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging – Mariasole Di Carli – FEMS Microbiology Letters

Viruses and phages

Virus Satellites Drive Viral Evolution and Ecology – Belén Frígols – PLOS Genetics

Bioinformatics and metagenomics

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Multi-view Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering – Y. Zhang – Computational Biology and Bioinformatics, IEEE/ACM Transactions

Bacteria in the news

The strain in metagenomics: Two computational tools extract strain-level information from reams of microbial sequence data. – Tal Nawy – Nature Methods

Bacteria found to play role in cow’s milk intolerance – SunCoast news

‘Superhero’ microbiome bacteria protect against deadly symptoms during infection – Salk Institute – EurekAlert

Can changes in the brain affect your microbiome? UB researchers are investigating – Ellen Goldbaum – University at Buffalo

BacteriaHysteria

Not news at all: I-Team: Everyday items we touch are loaded with bacteria – Ryan Walsh – WWLP

Beard microbiome

This was actually funny:  Will Forte (actor from “The Last Man on Earth”) has beard swabbed for bacteria test, fails, at Jimmy Fallon show – Yahoo Video

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October 28, 2015

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A global microbiome initiative, diversity of bumblebee gut microbes and rhizophere, and the microbiome of Brazilian banknotes.

General microbiome

Microbiology: Create a global microbiome effort – Nicole Dubilier, Margaret McFall-Ngai& Liping Zhao – Nature

A unified initiative to harness Earth’s microbiomes – A. P. Alivisatos – Science

Human gut microbiome

Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population – Carmen Haro – Journal of Clinical Endocrinology & Metabolism

Animal microbiome

Mollusk: Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod – Ajit Kumar Ngangbam – PLOS ONE

Bees: Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris) – Annelies Billiet – Insect Science

Plant, root, and soil microbiome

Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth – Mangal Singh – Scientific Reports

Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields – Li Bai – Microbiological Research

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity – Richard R. Rodrigues – PLOS ONE

Water microbiome

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing – Joel F. Gibson – PLOS ONE

Food microbiome

A Novel Bacteriophage Targeting Cronobacter sakazakii is a Potential Biocontrol Agent in Foods – Ju-Hoon Lee – Applied and Environmental Microbiology

Money microbiome

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces –
Tairacan Augusto Pereira da Fonseca – Int. J. Environ. Res. Public Health

Microbial Ecology, more microbes

Fungal communities as an experimental approach to Darwin’s naturalization hypothesis –
María Camila Morales – Research in Microbiology

Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses – Lu Han – Scientific Reports

Techniques

DNA Barcoding through Quaternary LDPC Codes – Elizabeth Tapia – PLOS ONE

Metagenomics

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life – Philippe Lopez – Biology Direct

Microbes in the news

Hey Obama, Can We Have a Unified Microbiome Initiative? Yours, the microbiologists – Ed Yong – The Atlantic

Intestinal Worms ‘Talk’ With Gut Bacteria – Talal Al-Khatib – Discovery

Intestinal Worms May Boost Our Immune System By Communicating With Gut Bacteria – Ed Cara – Medical Daily

Collecting dust from the International Space Station: an author Q+A – Sophie Marchant – BioMedCentral Blogs

Antarctic Bacteria Prove Resilient – Glacier Hub

Bacteria-Powered Shirts Vent When You Sweat – Glenn McDonald – Discovery

New Sherwin-Williams paint kills infection-causing bacteria – Nathan Bomey – USA Today

Bacteria Hysteria

Nasty Bacteria Found In Halloween Masks – MSN
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