Category Archives: Human gut

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 5, 2015

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Context and the human microbiome, review about respiratory tract, gut microbiome in UC patients, arsenic effects on mouse microbiome, and microbiome of a river-to-ocean transition.

Jobs

3 PhD fellowship in Evolutionary and Ecological Metagenomics – Natural History Museum of Denmark

General microbiome

Review: Context and the human microbiome – Daniel McDonald, Amanda Birmingham and Rob Knight – Microbiome

Pregnancy and birth

Breastfeeding and the risk of dental caries: a systematic review and meta-analysis – R Tham – Acta Paediatrica

Breastfeeding and asthma and allergies: a systematic review and meta-analysis – CJ Lodge – Acta Paediatrica

Human respiratory microbiome

Review: The Microbiome and the Respiratory Tract – Robert P. Dickson – Annual Review of Physiology

Human gut microbiome

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis – David Kevan – Journal of Crohn’s and Colitis

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition – Christopher Quince – American Journal of Gastroenterology

Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung’s associated enterocolitis – Holger Till – Frontiers in Microbiology

eBook chapter: Human GI Tract Microbiota in Health and Disease: A Focus on Inflammatory Bowel Diseases – Clarissa Santos Rocha – Innovative Immunology

Review: Factors determining colorectal cancer: the role of the intestinal microbiota – Esther Nistal – Frontiers in Oncology

Animal models

In cattle: Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function – Shengyong Mao – Scientific Reports

In cattle: Manipulating rumen microbiome and fermentation through interventions during early life: a review – David R. Yáñez-Ruiz – Frontiers in Microbiology

 

In mice: Administration of defined microbiota is protective in a murine Salmonella infection model – Sarah-Lynn E. Martz – Scientific Reports

In mice: Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism – Rishu Dheer – Toxicology and Applied Pharmacology

Drosophila: Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – BioRxiv

In rats: The microbiota-gut-brain axis as a potential therapeutic approach for HIV-1+ cocaine abuse – Steven B. Harrod – Drug and Alcohol Dependence

In mice: Alteration of the intestinal microbiota by short-time antibiosis protects mice from CNS-specific autoimmunity – C. Gödel – Journal of the Neurological Sciences

 

Plant, root, and soil microbiome

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

Caffeine fostering of mycoparasitic fungi against phytopathogens – Akifumi Sugiyama – Plant Signaling & Behavior

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes – Kathryn M. Docherty – PLOS ONE

Fungal association and utilization of phosphate by plants: success, limitations, and future prospects – Atul K. Johri – Frontiers in Microbiology

Thesis: Manipulating the soil microbiome to increase plant health and productivity – Chaparro, Jacqueline Michelle – Colorado State University

Water and extremophile microbiome

Bacterial responses to environmental change on the Tibetan Plateau over the past half century – Yongqin Liu – Environmental Microbiology

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient – Caroline S. Fortunato – PLOS ONE

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea –
André Antunes – Genomics, Proteomics & Bioinformatics

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment – Salvador Mirete – Frontiers in Microbiology

Research topic and call for papers: Microbiology of the rapidly changing polar environments – Frontiers in Microbiology

Food microbiology

The diversity and evolution of microbiota in traditional Turkish Divle Cave cheese during ripening – Sebnem Ozturkoglu Budak – International Dairy Journal

More microbes

Ion channels enable electrical communication in bacterial communities – Arthur Prindle – Nature

Bioinformatics

De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L Westcott, Patrick Schloss – PeerJ Preprint

Unpublished manuscript: Improving De Novo Metatranscriptome Assembly via Machine Learning Algorithms – Hussein Mohsen – not published

Microbes in the news

eBook: Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You – Rob DeSalle, Susan L. Perkins – eBook

Fighting Cancer With Microbes, Flagship Bets on a $35M Startup– Luke Timmerman – Forbes

Toxin Taints Crabs and Kills Sea Mammals, Scientists Warn – Jonah Bromwich – The New York Times
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November 4, 2015

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Lots of upcoming workshops and seminars, genome-wide association of the human gut microbiota, contamination of cord blood units, and bacteria with the rRNA genes on a plasmid, not on their chromosome.

Events

Webinar: The ageing microbiota by Gemma Walton and Annie-Rose Harrison-Dunn – November 17, 2015 – 10AM Paris

Mothur 3-day workshop organized by Pat Schloss – December 16-18, Detroit.

2nd Microbiome R&D and Business Collaboration Congress: Asia – February 29-March 1 2016, Kuala Lumpur, Malaysia

Early career workshop on Microbiology of the built environment (Chicago, IL) – Jack Gilbert lab – April 26-29 2016

Human oral microbiome

Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes – Meng Zhang – PLOS ONE

Human gut microbiome

In Hutterites: Genome-Wide Association Studies of the Human Gut Microbiota – Emily R. Davenport – PLOS ONE

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

Infection microbiology

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling – Luís França – PLOS ONE

More microbes

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome – Mizue Anda – PNAS

High-throughput 3D tracking of bacteria on a standard phase contrast microscope –
K.M. Taute – Nature Communications

Automated image analysis for quantification of filamentous bacteria – Marlene Fredborg – BMC Microbiology

Microbial ecology

Community rescue in experimental metacommunities – Etienne Low-Décarie – PNAS

Microbes in the news

Family dog lowers kids’ asthma risk, proving dirt and bacteria are good for children – Shelley Hazen – Inquisitr

Microbiome expert Martin Blaser to receive Georgetown’s Cura Personalis Award Nov. 3 – EurekAlert

Microbiomes could prove essential in various fields of science, study suggests – Kimberly Nielsen – The Daily Californian

Salivary microbiome of whitetail deer: Mature doe set the rut timetable – Oak Duke – Wellsville Daily Reporter

Finally! New germ exhibit opening at the American Museum of Natural History – Rebecca Rosenthal – North Jersey

Thank heavens, someone figured out which bacteria live on a donkey’s penis – Discover
http://blogs.discovermagazine.com/seriouslyscience/2015/11/03/thank-heavens-

How was the bacteria at York Hospital found?– Dylan Segelbaum – York Daily Record

Worms (and germs) may be the answer to preventing allergies – Jason Tetro – Popular Science

Two Million-Year-Old Bacteria Used Iron “Sunscreen” – Charlotte Ward – RedBrick

Bacteria infecting orange groves is driving up cost of juice; threatens nation’s supply – Sandy Miller – Fox2Now

Science, publishing, and career

EU urges science publishers to adapt to open access: European research commissioner Carlos Moedas has urged journal publishing companies to reshape their business models to an open access system. – LabNews

Supervision: Clear direction: Managing laboratory members as well as a research strategy can be difficult for early-career principal investigators, but help is at hand. – Boer Deng – Nature

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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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November 2, 2015

Posted on by

Overview of key players of the human microbiome in different sites, foals are born with a rich gut microbiome, biogeography of salmon microbiome, bacteria on Chinese glaciers, and the effect of X-rays on the mango microbiome.

General human microbiome

Diversity of key players in the microbial ecosystems of the human body – Ferenc Jordán – Scientific Reports

Pregnancy and birth

Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing – Hiroshi Murakami – Pediatric Surgery International

Review: Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics – Mohsin Khurshid – Future Microbiology

Review: Introduction : Microbiome in human reproduction – Jason M. Franasiak – Fertility and Sterility

Correspondence: Vaginal microbiota during pregnancy: Pathways of risk of preterm delivery in the absence of intrauterine infection? – Jeffrey A Keelan – PNAS

Reply to Keelan and Payne: Microbiota-related pathways for preterm birth – Daniel B DiGiulio – PNAS

Human oral microbiome

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation – Brenda P.F.A. Gomes – Journal of Endodontics

Oral microbiota in patients with atherosclerosis – Frida Fåk – Atherosclerosis

Review: Intermicrobial interactions as a driver for community composition and stratification of oral biofilms – Nicholas S. Jakubovics – Journal of Molecular Biology

Review: The Fungal Biome of the Oral Cavity – Jyotsna Chandra – Candida Species

Human respiratory microbiome

Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes – Alexandra Zimmermann – Journal of Medical Microbiology

Human gut microbiome

Donor species richness determines fecal microbiota transplantation success in inflammatory bowel disease – Severine Vermeire – Journal of Crohn’s and Colitis

Gut mucosal microbiome across stages of colorectal carcinogenesis – Geicho Nakatsu – Nature Communications

Review: Gut mycobiota and adenomas – Chunguang Luan – Gut Microbes

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Animal microbiome

Development of the faecal microbiota in foals – M. C. Costa – Equine Veterinary Journal

Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment – Saria Otani – Microbial Ecology

The biogeography of the atlantic salmon (Salmo salar) gut microbiome – Martin S Llewellyn – The ISME Journal

Exposure to West Nile Virus Increases Bacterial Diversity and Immune Gene Expression in Culex pipiens – Steven D. Zink – Viruses

Plant, root, and soil microbiome

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture – Linkun Wu – Scientific Reports

Drivers of bacterial beta diversity in two temperate forests –  Wang – Ecological Research

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing – Chris Munday – Aerobiologia

Review: Influence of soil microbiota in nurse plant systems – Susana Rodríguez-Echeverría – Functional Ecology

Review: The Role of Plant–Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants – Nele Weyens – International Journal of Molecular Sciences

Water and extremophile microbiome

Metagenomic analysis of the bacterial community of the Sea of Azov – D. G. Matishov – Marine Biology

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India – Jhasketan Badhai – Frontiers in Microbiology

High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing – Qing Liu – Systematic and Applied Microbiology

Review: Databases of the marine metagenomics – Katsuhiko Mineta – Gene

Waste microbiology

Changes in Microbial Composition of Wastewater During Treatment in a Full-Scale Plant – Marija Kaevska – Current Microbiology

Wastewater treatment and microbial communities in an integrated photo-bioelectrochemical system affected by different wastewater algal inocula – Li Xiao – Algal Research

Review: Microbial diversity in support of anaerobic biomass valorization – M. Jobard – Critical Reviews in Biotechnology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – Barakat S M Mahmoud – Letters in Applied Microbiology

Metagenomics and bioinformatics

Poster: Alignment-free methods for metagenomic profiling – Shanshan Gao – BMC Bioinformatics

Infection microbiology

Microbial diversity on intravascular catheters from paediatric patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Phages and viruses

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile – Pierre Boudry – mBio

Microbial Ecology

Do modern theories of biodiversity fail to predict commonness and rarity among microbes? – William R. Shoemaker – PeerJ

Strongly Deterministic Population Dynamics in Closed Microbial Communities – Zak Frentz – Physical Review

Microbes in the news

Scientists debate mega-microbiome initiatives: Research standards will advance the field, proponents say, but critics counter that they will stifle creativity – Rachel Becker – Nature

Foals born with rich microbial community in their gut – study – Horsetalk

Halloween: Monster Microbiology, 101: If werewolves and other ghouls existed, they’d surely have microbiomes – Rob Dunn – Science Friday

Bacteria in space – ‘You cannot just open the window’ – Interview with Ralf Möller about microbes found on the ISS – DW

New technique could prevent biofilms on catheters and medical implants – EurekAlert

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