Category Archives: Events and jobs

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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October 27, 2015

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Gut biogeography, soil transplants, donkey penises, Chicago public beaches, deep-sea mussels, dust particles in the International Space Station, and red pepper influence on kimchi microbiology

Events

About the world within us: This week, Penn Vet, Penn Medicine, and the Children’s Hospital of Philadelphia will host their second annual microbiome symposium – Sandy Bauers – Philly.com

Call for Volunteers: Gut Microbiota Samples – AGA is now recruiting volunteers to have their gut analyzed. Submit your name by Dec. 7 to be considered

General human microbiome

Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches – José E. Belizário – Frontiers in Microbiology

Pregnancy and birth microbiome

The Early Intestinal Microbiota of Healthy Korean Newborns – Eu Kyoung Lee – Iran J Pediatr

Human oral microbiome

Microbiome interaction with sugar plays an important role in relapse of childhood caries –
Jing Tian – Biochemical and Biophysical Research Communications

Human respiratory microbiome

The microbiome of the maxillary sinus and middle nasal meatus in chronic rhinosinusitis – O.A. Ivanchenko – Rhinology

Human skin microbiome

The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients – Charles W. Lynde – Journal of Cutaneous Medicine and Surgery

Human gut microbiome

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India – Anna Johnning – BMC Microbiology

Regulation of lung immunity and host defense by the intestinal microbiota – Derrick R. Samuelson – Frontiers in Microbiology

Intestinal Microbiota Profiles of Healthy Pre-School and School-Age Children and Effects of Probiotic Supplementation – Wang C. – Annals of Nutrition and Metabolism

Effect of Whole-Grain Barley on the Human Fecal Microbiota and Metabolome – Maria De Angelis – Applied and Environmental Microbiology

Microbiota studies in the bile duct strongly suggest a role for H. pylori in extrahepatic cholangiocarcinoma – Francisco Avilés-Jiménez- Clinical Microbiology and Infection

Review: A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes – Yueqiong Ni – mBio

Review: Gut biogeography of the bacterial microbiota – Gregory P. Donaldson – Nature Reviews Microbiology

Review: The Microbiome in Mental Health: Potential Contribution of Gut Microbiota in Disease and Pharmacotherapy Management – Stephanie A. Flowers – Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy

Review: Impact of Gut Microbiota on Obesity, Diabetes, and Cardiovascular Disease Risk – Luca Miele – Current Cardiology Reports

Editorial: Faecal transplants – Tim Spector, Rob Knight – British Medical Journal

Microbiome models

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection – Jason L. Kubinak

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model – Marisol Aguirre – Research in Microbiology

The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Frontiers in Microbiology

Review: Selective manipulation of the gut microbiota improves immune status in vertebrates – Ana Montalban-Arques – Frontiers in Immunology

Animal microbiome

With a picture of the sampling site! Bacterial and fungal microflora on the external genitalia of male donkeys (Equus asinus) – Carla L. Carleton – Animal Reproduction Science

Zoo animals: Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Insects: Microbial ecology-based methods to characterize the bacterial communities of non-model insects – Erica M. Prosdocimi – Journal of Microbiological Methods

Cattle: The nasopharyngeal microbiota of feedlot cattle – Devin B. Holman – Scientific Reports

Cattle: The rumen microbial metagenome associated with high methane production in cattle – R. John Wallace – BMC Genomics

Goose: Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing – Wen Wang – Microbiological Research

Bats: Bacterial diversity indicates dietary overlap among bats of different feeding habits – Sunil Banskar – Microbiological Research

Copepods: Biotransformation of petroleum hydrocarbons and microbial communities in seawater with oil dispersions and copepod feces – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Mussels: Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels – Lizbeth Sayavedra – eLIFE

Snail: Enrichment and Identification of Cellulolytic Bacteria from the Gastrointestinal Tract of Giant African Snail, Achatina fulica – Kiran D. Pawar – Applied Biochemistry and Biotechnology

Coral: Intraspecific diversity among partners drives functional variation in coral symbioses – John Everett Parkinson – Scientific Reports

Coral: Variations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system – Huda Mahmoud – Marine Pollution Bulletin

Coral: Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria – Julie L Meyer – The ISME Journal

Zebrafish: Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine – W. Zac Stephens – mBio

Arthropod: The microbiome of Folsomia candida: an assessment of bacterial diversity in a Wolbachia-containing animal – V. Agamennone – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Dynamics of bacterial community structure on intertidal sandflat inhabited by the ghost shrimp Nihonotrypaea harmandi (decapoda: Axiidea: Callianassidae) in tomioka bay, amakusa, Japan – Minoru Wada – Gene

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest –
Dulce Flores-Rentería – Soil Biology and Biochemistry

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities – Francesco Vitali – Microbiological Research

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China – Weibing Xun – Environmental Microbiology

Microbial responses to southward and northward Cambisol soil transplant – Mengmeng Wang – Microbiology Open

Review: Incorporating the soil environment and microbial community into plant competition theory – Po-Ju Ke – Frontiers in Microbiology

Review: Root Microbiome Assemblage is Modulated by Plant Host Factors – Venkatachalam Lakshmanan – Advances in Botanical Research

Water microbiome

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats – Hon Lun Wong – Scientific Reports

Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches – Kema Malki – Data in Brief

Cyanobacterial reuse of extracellular organic carbon in microbial mats – Rhona K Stuart – The ISME Journal

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton – Sedimentology

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan – Takuro Nunoura – Environmental Microbiology

Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget? – Antony Meunier, Stéphan Jacquet – Biology Open

Active populations of rare microbes in oceanic environments as revealed by bromodeoxyuridine incorporation and 454 tag sequencing – Koji Hamasaki – Gene

Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment – Tao He – Applied Microbiology and Biotechnology

[Mini review] metagenomic studies of the Red Sea – Hayedeh Behzad – Gene

Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities and different biofilm 3D architectures – Ibtissem Doghri – BMC Microbiology

Genome-wide tuning of protein expression levels to rapidly engineer microbial traits – Emily F. Freed – ACS Synthetic Biology

Built Environment microbiology

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities – Aleksandra Checinska – Microbiome

Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing – Jing You – Applied Microbiology and Biotechnology

Food microbiology

The influence of red pepper powder on the density of Weissella koreensis during kimchi fermentation – Bo Kyoung Kang – Scientific Reports

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant – Maria Calasso – Food Microbiology

Extremophile microbiology

Hot spring deposits: Tracing Biosignature Preservation of Geothermally Silicified Microbial Textures into the Geological Record – Kathleen A. Campbell – Astrobiology

Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland – Hanna Miettinen – Frontiers in Microbiology

Bioinformatics and metagenomics

mBLAST: Keeping up with the Sequencing Explosion for (Meta) Genome Analysis – Curtis Davis – Journal of Data Mining in Genomics & Proteomics

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia – William C. Nelson – Applied and Environmental Microbiology

V-GAP: Viral genome assembly pipeline – Yoji Nakamura – Gene

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community – Robert M. Bowers – BMC Genomics

MinION Analysis and Reference Consortium: Phase 1 data release and analysis [version 1; referees: awaiting peer review] – Camilla L.C. Ip – F1000 Research

Review: Machine learning for metagenomics: methods and tools – Hayssam Soueidan, Macha Nikolski – Arxiv

Review: Novel Computational Technologies for Next-Generation Sequencing Data Analysis and Their Applications – Chuan Yi Tang – International Journal of Genomics

Microbes in the news

Potentially Dangerous Bacteria Thrive At The International Space Station, NASA Warns
– Katrina Pascual – Tech Times
What’s In The Microbiome Of Space? – Science 2.0

Decoding the DNA of lung bacteria to keep you healthy – Leah Cuthbertson – Imperial College London

US researchers delve into make-up of gut bacteria in horses – HorseTalk

Microbial engineering finds a home at SEAS: genetic engineering on biofilms – Adam Zewe – Harvard

Cultures: a small magazine tackling big issues – Special Kids Edition – ASM

Hurricane Patricia Victims Use Chlorine To Fight Bacteria – Operation Blessing

Bacteria can communicate like brain cells. This is a bacterial world. We just live in it. – Bradley J. Fikes – San Diego Union Tribune

Jessica Richman Wants People to Track Their Microbiomes – Wall Street Journal

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October 15, 2015

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Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyuan Fu – Circulation Research

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Mats Wedin – Environmental Microbiology

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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October 1, 2015

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October already! Today I’ve got two microbiome symposia for you, microbiome imaging, early antibiotics and asthma risk, and virome sequencing.

Events

Second Annual Microbiome Symposium – October 28-29 – CHMI / Penn Vet Center for Host Microbial Interactions – Philadelphia, USA (click on tab “Symposium 2015 at the bottom part), featuring talks by Handelsman, Relman, Grice, Dominguez-Bello, Mills, and Gewirtz.

Second Microbiome R&D and Business Collaboration Congress: Asia – Feb 29-March 1, 2016 – Kuala Lumpur, Malaysia.

General microbiome

Review: Microbial Malaise: How Can We Classify the Microbiome? – Robert G. Beiko – Trends in Microbiology

Review: Early Life Adversity and Brain Development: Is the Microbiome a Missing Piece of the Puzzle? – S.M. O’ Mahony – Neuroscience

Review: American Diabetes Association and JDRF Research Symposium: Diabetes and the Microbiome – Clay F. Semenkovich – Diabetes

Pregnancy and birth

Editorial: Asthma: Undoing millions of years of coevolution in early life? – Maria Gloria Dominguez-Bello and Martin J. Blaser – Science Translational Medicine
Belongs to: Early infancy microbial and metabolic alterations affect risk of childhood asthma – Marie-Claire Arrieta – Science Translational Medicine

Human skin microbiome

Review: The intersection of microbiome and host at the skin interface: genomic- and metagenomic-based insights – Elizabeth A. Grice – Genome Research

Human gut microbiome

Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy – Tasha M. Santiago-Rodriguez – PLOS ONE

Review: The gut microbiome in NAFLD and ALD – Irina A. Kirpich – Clinical Liver Disease

Review: Prebiotic and Probiotic Regulation of Bone Health: Role of the Intestine and its Microbiome – Laura McCabe – Current Osteoporosis Reports

Animal models and bioreactors

Postnatal epigenetic regulation of intestinal stem cells requires DNA methylation and is guided by the microbiome – Da-Hai Yu – Genome Biology

Cultivation of stable, reproducible microbial communities from different fecal donors using minibioreactor arrays (MBRAs) – Jennifer M. Auchtung – Microbiome

Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Quantitative Imaging of Gut Microbiota Spatial Organization – Kristen A. Earle – Cell Host & Microbe

Increased Bacterial Load and Expression of Antimicrobial Peptides in Skin of Barrier-Deficient Mice with Reduced Cancer Susceptibility – Ken Natsuga – Journal of Investigative Dermatology

Animal Microbiome

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem – Susana Rodríguez-Marconi – PLOS ONE

Surveys for maternally-inherited endosymbionts reveal novel and variable infections within solitary bee species – Abiya Saeed – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Assessing the ecological status of seagrasses using morphology, biochemical descriptors and microbial community analyses. A study in Halophila stipulacea (Forsk.) Aschers meadows in the northern Red Sea – Astrid Y. Mejia – Ecological Indicators

The effects of exotic weed Flaveria bidentis with different invasion stages on soil bacterial community structures – Chaohe Huangfu – African Journal of Biotechnology

Water microbiome

Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific – Mark T. Price – Frontiers in Microbiology

Spatial–temporal variations and diversity of the bacterioplankton communities in the coastal waters of Kuwait – Awatef Almutairi – Marine Pollution Bulletin

Review: Substratum-Associated Microbiota: benthic algae and bacteria from a range of aquatic environments – Paula C. Furey – Water Environment Research

Waste and composting microbiology

Limited dissemination of the wastewater treatment plant core resistome – Christian Munck – Nature Communications

Neglected role of fungal community composition in explaining variation in wood decay rates – A. van der Wal – Ecology

Metagenomics

Enhanced virome sequencing through solution-based capture enrichment –
Todd N Wylie – Genome Research

Metabolic networks

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity – Tasia M. Taxis – Nucleic Acids Research

Microbes in the news

Missing Microbes Provide Clues About Asthma Risk – Rob Stein – NPR (see above)
Study Links Asthma to Low Levels of Gut Bacteria in Newborns – Gautam Naik – Wall Street Journal

New test detects all viruses that infect people, animals – EurekAlert (see above)

Your gut development during infancy can have lifelong implications – Baylor College of Medicine – EurekAlert

Biologists Say Breeding Better Soil Microbes Can Help Grow Bigger Plants – Kiona Smith-Strickland – Gizmodo

Diets Rich in Vegetables May Reduce Heart Disease Risk Through Microbiome Changes – Medical Research

TU Delft students win on world stage with 3D bacteria printer – Materia

The headlines are getting weirder and weirder, but here we go: Ancient bacteria could be ‘elixir of life’ after it makes elderly mice ‘begin to dance’ and produce offspring – Andrew Griffin – Independent

Better Gut Microbiota Shift With Bypass vs Sleeve Gastrectomy – Becky McCall – Medscape

Sounds like trying to find a radio station on the wrong band: Scientists synthesise sound of single bacterium swimming – Bernie Hobbs – ABC Australia

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September 10, 2015

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Plaque microbiome model to predict caries development, ocular microbiota and Sjögren’s, and aging  fungus cultivating termites.

Events

Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25 – Jonathan Eisen – Phylogenomics

Human skin and eye microbiome

TSP-1 Deficiency Alters Ocular Microbiota: Implications for Sjögren’s Syndrome Pathogenesis – Terzulli Marielle – Journal of Ocular Pharmacology and Therapeutics

Human oral microbiome

See “Telltale Mouth Microbes” article below, featuring yours truly: Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota – Fei Teng – Cell Host & Microbe

Human respiratory microbiome

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia – Xiao-Jun Yang – Drug Design, Development and Therapy

Bacteria in the CF Lung: Isolation Drives Diversity – Pablo Manfredi – Cell Host & Microbe

Human reproductive tract microbiome

Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier – H Borgdorff – Mucosal Immunology

Human gut microbiome

The Long-term Efficacy and Safety of Fecal Microbiota Transplant for Recurrent, Severe, and Complicated Clostridium difficile Infection in 146 Elderly Individuals – Agrawal, Manas – Journal of Clinical Gastroenterology

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery – Sylvia Becker-Dreps – Am J Trop Med Hyg

PhD Thesis: Impaired Gut Microbial Community Development in Undernourished Children – Sathish Subramanian – Washington University

Review: Frenemies: Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions – Elizabeth A. Cameron, Vanessa Sperandio – Cell Host & Microbe

Review: Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis – Ruben J. Colman – Journal of Crohn’s and Colitis

Review: Candida albicans commensalism in the gastrointestinal tract – B. Anne Neville – Yeast Research

Review: Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies – Vincent Thomas – Future Microbiology

Review: The interaction of commensal intestinal bacteria with helminth parasites – Mario M. Zaiss – Parasite Immunology

Animal microbiome

Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus – Hongjie Li – Environmental Microbiology

Diet is the primary determinant of bacterial community structure in the guts of higher termites – Aram Mikaelyan – Molecular Ecology

Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica – Guilherme L. Pinheiro – Frontiers in Microbiology

Plant, soil, and root microbiome

Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere – Bo Yan – Frontiers in Microbiology

Soil fungi for mycoremediation of arsenic pollution in agriculture soils – Manvi Singh
– Journal of Applied Microbiology

Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem – Allison M. Veach – Microbiology Ecology

Review: The role of microorganisms in the ecological functions of soils – T. G. Dobrovol’skaya – Eurasian Soil Science

Water microbiome

Studying composition of bacteriobenthic communities in the sediments of water ecosystems by fatty acid markers – N. G. Sherysheva – Aquatic Microbiology

Extremophiles

Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka -Nikolay A. Chernyh – Extremophiles

Microbes of the built environment

Metabolomic and high-throughput sequencing analysis – modern approach for the assessment of biodeterioration of materials from historic buildings – Beata Gutarowska – Frontiers in Microbiology

Metagenomics and bioinformatics

Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations – Rodrigo García-López – Frontiers in Bioengineering and Biotechnology

Tentacle: distributed quantification of genes in metagenomes – Fredrik Boulund – GigaScience

Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens –
Bastian Greshake – Molecular Ecology Resources

Techniques

Effects of freezing storage on the DNA extraction and microbial evaluation from anaerobic digested sludges – Valeria Romanazzi – BMC Research Notes

Microbes in the news

Telltale Mouth Microbes- The composition of the plaque microbiome can reveal a child’s risk of dental caries months before the decay appears, according to a study. – Jyoti Madhusoodanan – The Scientist

Researcher Succumbs To Cystic Fibrosis, Leaves Unique Investigative Legacy – Charles Moore – Cystic Fibrosis News Today

uBiome Extends Reach of Microbiome Testing Through Global Ambassador Program – PR Web

Get the Poop on Organisms Living in Your Gut With a New Consumer Laboratory Test Offered by American Gut and uBiome – Dark Daily

“A diversity of gifts”: article about the MBL Microbial Diversity course – Jonathan Eisen – Microbe.net

Nanomesh dressings may draw bacteria from chronic wounds – Ben Coxworth – GizMag

Purple bacteria signal zinc deficiency – James Urquhart – Chemistry World

Professor pursues bacteria-to-fuel research abroad: Dr. Galyna Kufryk spent part of the summer studying cyanobacteria at the Institut Pasteur in Paris – Janie Magruder – Grand Canyon University

Bacteria in Overdrive: a key organism in the ocean’s food web will start reproducing at high speed as carbon dioxide levels rise – Robert Perkins – USC Dornsife

Bacteria Hysteria

The Most Bacteria-Infested Places on an Airplane – Rachael Schultz – Shape

Microbes and art

AMNH to present The Secret World Inside You exhibit, 11/4 – Broadway World

Science, publishing, and career

Q&A: The academic satirist: Jorge Cham wowed graduate students with The PhD Movie in 2011 – Zoë Corbyn – Nature

Gender balance: Women are funded more fairly in social science – Paul J. Boyle – Nature
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September 5, 2015

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Events

The Individual Microbe: Single-cell Analysis and Agent-based Modeling – ASM conference – March 18-20, 2016, Washington DC, USA

R workshop for microbial ecology – Pat Schloss – Nov 2-4, 2015, Detroit – No link but can email Pat at: pschloss@umich.edu

General microbiome

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – BioRxiv

Pregnancy and birth microbiome

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development – Federica Del Chierico – PLOS ONE

Human oral microbiome

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial – Jessica E. Koopman – PLOS ONE

Review: Oral Paleomicrobiology: study of the ancient oral microbiome – Namrata Dagli

Human gut microbiome

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children – M. Isabel Ordiz – Microbiome

Gastrointestinal Microbiome Modulator Improves Glucose Tolerance in Overweight and Obese Subjects: A Randomized Controlled Pilot Trial – Candida J. Rebello – Journal of Diabetes and its Complications

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis – Griet Debyser – Journal of Cystic Fibrosis

Review: Pathways and functions of gut microbiota metabolism impacting host physiology – Smitha Krishnan – Current Opinion in Biotechnology

Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases – Jose U. Scher – Arthritis & Rheumatology

Review: The human microbiome: opportunities and challenges for clinical care – G. B. Rogers – Internal Medicine Journal

Human respiratory microbiome (see also gut microbiome above)

MRSA Colonization and the Nasal Microbiome in Adults at High Risk for Colonization and Infection – Mary T. Bessesen – Journal of Infection

Review: Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection – Lindsay J. Caverly – Pediatric Pulmonology

Human other sites

In silico analyses of metagenomes from human atherosclerotic plaque samples – Suparna Mitra – Microbiome

Microbiome models

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Perspective: Metabolic labeling puts the microbiome under the microscope – Graham J Britton & Jeremiah J Faith – Nature Medicine

Animal microbiome

The composition of the zebrafish intestinal microbial community varies across development – W Zac Stephens – ISME Journal

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season – Jane Ludvigsen – Microbes and Environments

The genome of Aiptasia, a sea anemone model for coral symbiosis – Sebastian Baumgarten – PNAS

Special Issue: The Mammalian Microbiome and Its Importance in Laboratory Animal Research – André Bleich and James G. Fox – ILAR Journal

Plant, root, and soil microbiome

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling – Peter E. Larsen – PLOS ONE

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential – Asma Soussi – Plant and Soil

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Water microbiome

Anthropogenic activities drive the microbial community and its function in urban river sediment – Xu Zhang – Journal of Soils and Sediments

Built environment microbiome

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – Journal of Medical Entomology

Hospital’s Hidden Environmental Hazards: Probing the Microbiome – BioScience

Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China – Hongxing Ren – Applied Microbiology and Biotechnology

Food microbiology

The genomics of microbial domestication in the fermented food environment –
John G Gibbons – Current Opinion in Genetics & Development

Bioinformatics

Functional Basis of Microorganism Classification – Chengsheng Zhu – PLOS Computational Biology

ReproPhylo: An Environment for Reproducible Phylogenomics – Amir Szitenberg – PLOS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities – Dongwan D. Kang – PeerJ

More Microbiology

Evolution of coexistence in a crowded microplate well – J. Arjan G. M. de Visser – PNAS

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities – Tomáš Větrovský – Molecular Ecology Resources

Microbes in the news

Microbial diversity insights are often strongly biased – Suffield Times
Small advances: understanding the microbiome – Amanda Smith – ABC Australia

Science, publishing and career

When science fails a scientist – Kim Hunter-Schaedle – Science

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August 20, 2015

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Jobs

Jobs at Technical University of Denmark: Three PhD scholarships at the interface of synthetic biology, metagenomics and bacterial evolution

Pregnancy and birth

The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates – Jia Zheng – Nutrients

Impact of mode of delivery on the milk microbiota composition of healthy women – R. Cabrera-Rubio – Journal of Developmental Origins of Health and Disease

Human oral microbiome

Dental plaque as a biofilm and a microbial community – implications for treatment – P.D. Marsh – Journal of Oral Biosciences

Human gut microbiome

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis – Christopher J. Damman – PLOS ONE

The presence of Oxalobacter formigenes in the microbiome of healthy young adults – Clea Barnett – The Journal of Urology

The gut microbial community in metabolic syndrome patients is modified by diet – Carmen Haro – The Journal of Nutritional Biochemistry

Review: Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution? – María Carmen Cenit – Nutrients

Review: The intestinal microbiome in human disease and how it relates to arthritis and spondyloarthritis – Mary-Ellen Costello – Best Practice & Research Clinical Rheumatology

Editorial: Getting Healthier Through Microbiome Makeover – Duc Hong Le – EBioMedicine

Review: Nutritional Modulation of Gut Microbiota – The Impact on Metabolic Disease Pathophysiology – Patricia Ojeda – The Journal of Nutritional Biochemistry

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

IL-21 and probiotic therapy improve Th17 frequencies, microbial translocation, and microbiome in ARV-treated, SIV-infected macaques – A M Ortiz – Mucosal Immunology

Animal microbiome

The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls – JS Weese – Veterinary Microbiology

Bartonella Infection among Cats Adopted from a San Francisco Shelter, Revisited – Drew A. Fleischman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter – Lucia Žifčáková – Environmental Microbiology

Diversity and complexity of microbial communities from a chlor-alkali tailings dump – Cyril Zappelini – Soil Biology and Biochemistry

Different impacts of native and exotic earthworms on rhizodeposit carbon sequestration in a subtropical soil – Jinhua Huang – Soil Biology and Biochemistry

Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood – Stefano Covino – Journal of Hazardous Materials

Waste microbiology

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins – C. Hartard – Applied and Environmental Microbiology

Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater – Naim Montazeri – Applied and Environmental Microbiology

Metaproteomics of activated sludge from a wastewater treatment plant – A pilot study – Sebastian Püttker – Proteomics

Food microbiology

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains – M. van den Broek – Applied and Environmental Microbiology

Not sure why the title is between quotes: “Spoilage of vacuum-packed beef by the yeast Kazachstania psychrophila” – Jan Kabisch – Food Microbiology

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05 – Luana Martins Perin – International Journal of Food Microbiology

Microbes in the news

Does This Phylum Make Me Look Fat? – Katherine Harmon Courage – NPR

Stanford researchers find surprising level of tick-borne disease risk on local trails – Rob Jordan

What Gut Bacteria Can Teach Us About Eating Disorders: uBiome and University of North Carolina Launch Groundbreaking Study – Global News Wire

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August 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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