Category Archives: Animal experiments

October 16, 2015

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Chronic wound microbiota of almost 3000 patients, two periodontitis papers, biography among Agave microbiotas, and microbial ecology of Antarctic aquatic systems.

Pregnancy and birth

Commentary: Metaproteomic analysis adds a functional glimpse into host–microbe succession in an infant’s GI – Joshua E. Elias – Proteomics

Editorial: Microbiomes – Embracing complexity – Pratik Jagtap – Proteomics

Human oral microbiome

Oral Microbiota, Periodontal Status and Osteoporosis in Postmenopausal Women – Scarlette Hernández-Vigueras – Journal of Periodontology

Relationship between periodontitis-associated subgingival microbiota and clinical inflammation by 16S pyrosequencing – A Camelo-Castillo – Journal of Clinical Periodontology

Plastic teeth that don’t allow bacteria to grow on them: 3D-Printable Antimicrobial Composite Resins – Jun Yue – Advanced Functional Materials

Human skin microbiome

Analysis of the chronic wound microbiota of 2,963 patients by 16S rDNA pyrosequencing – Randall D. Wolcott – Wound Repair and Regeneration

Human gut microbiome

A Gut Odyssey: The Impact of the Microbiota on Clostridium difficile Spore Formation and Germination – Aimee Shen – PLOS Pathogens

Review: Gut microbiota and obesity – Philippe Gérard – Cellular and Molecular Life Sciences
Animal microbiome

Evaluation of feed grade sodium bisulfate impact on gastrointestinal tract microbiota ecology in broilers via a pyrosequencing platform – Si Hong Park – Poultry Science

Birds: Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans – Kazunari Ushida – Journal of Veterinary Medical Science

First Evidence of an Important Organic Matter Trophic Pathway between Temperate Corals and Pelagic Microbial Communities – J. A. Fonvielle – PLOS ONE

Plant, root, and soil microbiome

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species – Devin Coleman-Derr – New Phytologist

Diversity of Bacterial Communities in a Profile of a Winter Wheat Field: Known and Unknown Members – Aurore Stroobants – Soil Microbiology

Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation tests – Noël J. Diepens – Environmental Science & Technology

Letter to the Editor: Plant microbiota: implications for human health – Leena von Hertzen – British Journal of Nutrition

Water microbiome

Impact of multiple anthropogenic stressors on freshwater: how do glyphosate and the invasive mussel Limnoperna fortunei affect microbial communities and water quality? – Haydée Pizarro – Ecotoxicology

Bacterial and protist community changes during a phytoplankton bloom – John K. Pearman – Limnology and Oceanography

Research Highlight: Wired communities – Denise Waldron – Nature Reviews Microbiology

Extremophile microbiome

Review: Microbial ecology of Antarctic aquatic systems – Ricardo Cavicchioli – Nature Reviews Microbiology

Built environment microbiome

Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area – Juanjuan Wang – Water Research

Microbes in the news

Crohn’s disease causes, symptoms, treatments and role of gut bacteria – Rebecca Bowslaugh – Bel Marra Health

Microbial Signatures Predict Post-op Recurrence in Crohn’s – David Wild – GastroEndoNews
Deep-sea corals in the Red Sea: reservoirs of hope – Sedeer El-Showk – Nature Asia

Guest Post — The Emergent Microbiome: A Revolution for the Life Sciences – Part III, Psychobiotics – Jessica Miles and Anthony D. Sabatelli – JD Supra

Researchers find an answer to invasive cheatgrass: Will this native bacteria finally thwart one of the most invasive weeds in North America? – Gloria Dickie – High Country News

Not a great title: 3D printed teeth to keep your mouth free of bacteria – Jacob Aron – New Scientist

Not for the faint of heart: Bacteria of maggots causes fatal septicemia in man – Chris Whitehouse – Outbreak News Today – Refers to this article in Emerging Infectious Diseases

Microbiology and Art

This is the Most Beautiful View of Poo You’re Ever Going to See – Jamie Condliffe – Gizmodo

Science, publishing, and career

How do we define and measure scientific literacy? – Joseph Timpona – Blogs at Plos

Your Data to Explore: An Interview with Anne Wojcicki from 23andMe – Jane Gitschier – PLOS Genetics
After sexual harassment reports, famed astronomer resigns from UC Berkeley – Rachel Feltman – Washington Post

Geoff Marcy incident indicative of larger problem – Ellen Simms – The Daily Cal

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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 14, 2015

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Gut microbes and the brain, transgenic goats, Salmonella infection of pigs, viral infection in honey bees, and a catalogue of microbial culture media.

Human gut microbiome

Feature: The tantalizing links between gut microbes and the brain – Peter Andrey Smith – Nature

Animal models

Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella enterica and Lawsonia intracellularis – Klaudyna A. Borewicz – PLOS ONE

The Effects of GH Transgenic Goats on the Microflora of the Intestine, Feces and Surrounding Soil – Zekun Bao – PLOS ONE

Research highlight: Culinary traditions—revealing the effect of travel and diet on gut microbiota and motility – Gillian Patman – Nature Gastroenterology & Hepatology

Animal microbiome

No apparent correlation between honey bee forager gut microbiota and honey production – Melissa A. Horton – PeerJ

Four Categories of Viral Infection Describe the Health Status of Honey Bee Colonies – Esmaeil Amiri – PLOS ONE

Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants – Clarissa S. Sit – PNAS

More microbes

Harnessing the landscape of microbial culture media to predict new organism–media pairings – Matthew A. Oberhardt – Nature Communications

Single-Cell Analysis of RNA Virus Infection Identifies Multiple Genetically Diverse Viral Genomes within Single Infectious Units – Marine Combe – Cell Host & Microbe

Microbes in the news

What does your gut microbiome look like? – Katherine Harmon Courage – Popular Science

Microbiome May Predict Colon Cancer Tumor Mutational Status – Neil Osterweil – Medscape

“Studying sanitation is not always the sexiest topic” Stanford study on the effects of toilet facilities on child health in rural Africa – Stanford News

NDSU researcher, students study how bacteria adapts to survive – North Dakota State University

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October 12, 2015

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A nice and short digest today. Happy Columbus Day!

Human gut microbiome

Relationship Between Microbiota of the Colonic Mucosa vs Feces and Symptoms, Colonic Transit, and Methane Production in Female Patients With Chronic Constipation – Gopanandan Parthasarathy – Gastroenterology

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa – Pål Trosvik and Eric Jacques de Muinck – Microbiome

Review: The Gut Microbiota as a Therapeutic Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors FXR and TGR5 – Annemarie Baars – Microorganisms

Review: Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy
Is It All About Diet? – Daniela Elena Serban – Nutrition in Clinical Practice

Review: Role of the Gut Microbiome in Obesity and Diabetes Mellitus – Gillian M. Barlow – Nutrition in Clinical Practice

Animal models

Functional analysis of the relationship between intestinal microbiota and the expression of hepatic genes and pathways during the course of liver regeneration – Hui-Xin Liu – Journal of Hepatology

Metagenomics and Bioinformatics

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data – Genivaldo Gueiros Z. Silva – Bioinformatics

Viruses and phages

Research Highlight: Phages’ box of tricks for CRISPR – Naomi Attar – Nature Reviews Microbiology

Microbes and art

Microbial masterpieces! Scientists ‘paint’ detailed works of art by growing bacteria from human skin and even faeces in petri dishes – Victoria Woollaston – Daily Mail
http://www.dailymail.co.uk/sciencetech/article-3269542/Microbial-masterpieces-Scientists-paint-detailed-works-art-growing-bacteria-petri-dishes.html

Microbes in the news

University of New Haven professor’s research focuses on ‘horrible’ Lyme disease – Mark Zaretsky – New Haven Register

Repeat from earlier podcast: The Bacterial Cloud We All Carry Could Be As Unique As A Fingerprint – Rob Stein – NPR

Antibiotics ban: California first state to outlaw routine use of bacteria-fighting drugs in livestock – Jessica Calefati – Mercury News

Desperate Families in Delhi as Dengue Overwhelms Hospitals – Nida Najar – New York Times

Novel mathematical method may help reduce development of antibiotic-resistant bacteria – News Medical

Bacteria Hysteria

Concerned about germs on shopping trolley handles? Cleaning gadget beats bacteria – Hannah Bouckley – BT

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October 10, 2015

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The Eukaryome of the human gut, core microbiome in rumen, overweight kitties, and viral metagenomics of a hot spring.

Human gut microbiome

Repertory of Eukaryotes (Eukaryome) in the Human Gastrointestinal Tract: Taxonomy and Detection Methods – Ibrahim Hamad – Parasite Immunology

Diversity of Duodenal and Rectal Microbiota in Biopsy Tissues and Luminal Contents in Healthy Volunteers – Gangping Li – Journal of Microbiology and Biotechnology

Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease – Bashar Aqel, John K. DiBaise – Nutrition in Clinical Practice

Review: Gut Microbiome: What We Do and Don’t Know – Gail A. Cresci and Emmy Bawden – Nutrition in Clinical Practice

Editorial: Contribution of Gut Bacteria to Lipid Levels Another Metabolic Role for Microbes? – Hooman Allayee, Stanley L. Hazen

Human vaginal microbiome

Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota – Kenetta L. Nunn – mBio

Models of microbiome research

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity
Denise Morais da Fonseca – Cell

Animal microbiome

Overweight and the feline gut microbiome – a pilot study – I. N. Kieler – Journal of Animal Physiology and Animal Nutrition

Bovine mastitis may be associated with the deprivation of gut Lactobacillus – C. Ma – Beneficial Microbes

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range – Gemma Henderson – Scientific Reports

Plant, root, and soil microbiome

Evaluating a multigene environmental DNA approach for biodiversity assessment
Alexei J. Drummond – GigaScience (via PMC)

Sheep grazing and soil bacterial diversity in shrublands of the Patagonian Monte, Argentina – Nelda L. Olivera – Journal of Arid Environments

Climatic conditions, soil fertility and atmospheric nitrogen deposition largely determine the structure and functioning of microbial communities in biocrust-dominated Mediterranean drylands – Raul Ochoa-Bon – Plant and Soil

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters – Amélia Bourceret – Microbial Ecology

Water and extremophile microbiome

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins – Dorina Seitaj – PNAS
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs – Sóley Ruth Gudbergsdóttir – Environmental Microbiology

Waste treatment microbiology

Characterization of microbial communities in water and biofilms along a large scale SWRO desalination facility: Site-specific prerequisite for biofouling treatments – Adi Levi – Desalination

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans – Massimo C Pernice – The ISME Journal

Metabolomics

A Global Metabolomic Analysis of a Mammalian Host Infected with Bacillus anthracis
Chinh T.Q. Nguyen – Infection and Immunity

Sequencing techniques

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
Tatsuya Unno – Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

Differential analysis of biological networks – Da Ruan – BMC Bioinformatics

SPINGO: a rapid species-classifier for microbial amplicon sequences – Guy Allard – BMC Bioinformatics

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection – Xiao Ding – BMC Bioinformatics

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology – Feng Ju and Tong Zhang – Environmental Science & Technology

A Comparison of Base-calling Algorithms for Illumina Sequencing Technology – Ashley Cacho – Briefings in Bioinformatics

Metabolomics

A Validated High Resolution Mass Spectrometry-based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype – Julie Vanden Bussche – Analytical Chemistry

Microbes in the news

Should We Bank Our Own Stool? – Moises Velasquez-Manoff – New York Times

Researchers use gut bacteria composition to genetically classify colorectal tumors – EurekAlert

Bacteria take on stinky problem in Kenner – Christie Walton – Fox8Live

MSU faculty member earns grant award for biofilm methodology research: Darla Goeres was recently awarded a Burroughs Wellcome Innovation in Regulatory Science Award. – Montana State University

Biotech of the week: Enterome, the Leading French Microbiome Start-up – LaBiotech

Conference Coverage: ID week: Drug Resistance: What Happens Inside the Nose? – HCP Live

Antibiotic use and cancer risk: Repeat exposure poses harm: interview with Ben Boursi – Healio

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October 9, 2015

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Microbes and midwives, gut-brain axis, gluten immunopathology, viruses from farm to fork, and handwashing in students.

Pregnancy and birth

Conference abstract: Seeding the infant microbiome: The midwife’s role – Asha McCurley – Women and Birth

Human skin microbiome

Poor hand hygiene by college students linked to more occurrences of infectious diseases, medical visits, and absence from classes – Kayla J. Prater – American Journal of Infection Control

Human gut microbiome

Gut microbiota interacts with brain microstructure and function – José-Manuel Fernandez-Real – The Journal of Clinical Endocrinology & Metabolism

Microbiota–Gut–Brain Axis: Yeast Species Isolated from Stool Samples of Children with Suspected or Diagnosed Autism Spectrum Disorders and In Vitro Susceptibility Against Nystatin and Fluconazole – A. Serda Kantarcioglu

Animal models

Intestinal Microbiota Modulates Gluten-Induced Immunopathology in Humanized Mice – Heather J. Galipeau – American Journal of Pathology

Animal microbiome

Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation – Claudia Barelli – Scientific Reports

Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing – Michel Diouf – PLOS ONE

Built Environment microbiome

Microbial control of dental unit water: Feedback on different disinfection methods experience – Julie Lizon – American Journal of Infection Control

Food microbiology

Review: Fate of Foodborne Viruses in the “Farm to Fork” Chain of Fresh Produce – Dan Li – Comprehensive Reviews in Food Science and Food Safety

Metagenomics

Strain recovery from metagenomes – C Titus Brown – Nature Biotechnology

Science, publishing, and career

Peer Review Resources: tips and suggestions from experienced reviewers as well as externally prepared resources for the beginning peer reviewer – Publons

Funny and informative: So you think you want to run an environmental conservation meeting? Advice on the slings and arrows of outrageous fortune that accompany academic conference planning – E. C. M. Parsons – Journal of Environmental Studies and Sciences

Microbes in the news

UNC-Chapel Hill researchers reveal type of vaginal bacteria that protects women from HIV – EurekAlert

When Evolution Is Infectious – How “probiotic epidemics” help wildlife—and us—survive – Moises Velasquez-Manoff – Nautilus
It takes a village of bacteria to help frogs fight deadly disease, Virginia Tech researchers say – Augusta Free Press

Dirty hospital equipment causes 11 people to become infected with bacteria that could lead to pneumonia – Daily Mail

Cat poop coffee goes biotech – Nature Biotechnology

Bad times for good bacteria: how modern life has damaged our internal ecosystems – The Conversation

Gut microorganisms cause gluten-induced pathology in mouse model of celiac disease – MedicalXpress

Bacteria Hysteria

Sponsored by Dettol: Most teddy bears are covered in food poisoning bacteria, tests reveal – Plymouth Herald
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October 8, 2015

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Animal models

Impact of the gut microbiota on the neuroendocrine and behavioural responses to stress in rodents – Sylvie Rabot – OCL

Animal microbiome

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus – Jenifer B. Walke – PLOS ONE

Plant, root, and soil microbiome

Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands – Roberto A. Geremia – New Phytologist

Disentangling the ‘brown world’ faecal–detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Molecular Characterization and Assessment of Phylogenetic Relationship among Tomato Rhizospheric Bacterial Population – Rabaila Riaz – Biologia (Pakistan)

Metagenomic analysis of microbial community in uranium-contaminated soil – Xun Yan – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Periphytic and planktonic bacterial community structure in turbid and clear shallow lakes of the Pampean Plain (Argentina): a CARD-FISH approach – Sánchez, Laura María – Latin American Journal of Aquatic Research

Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring – S. Chen – Biogeosciences Discussions

Waste treatment microbiology

Molecular Assessment of Microbial Species Involved in the Biodegradation of Crude Oil in Saline Niger Delta Sediments Using Bioreactors – Chioma Blaise Chikere – Bioremediation & Biodegradation

Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants – An-Dong Li – Frontiers in Microbiology

Metagenomics and bioinformatics

Higher Classification Accuracy of Short Metagenomic Reads by Discriminative Spaced k-mers – Rachid Ounit, Stefano Lonardi – Algorithms in Bioinformatics

Microbes in the news

From Bacteria to Mold, Health Concerns Abound in Aftermath of South Carolina Flooding – Associated Press

Researchers team up with Illumina to speed-read your microbiome – Medical Xpress

I Sent a Sample of My Poop to uBiome – Sarah Scoles – Discover Magazine

Video: Where are The Most Bacteria-Filled Places In Your Life? – Discover

A ‘bacterial condom’ could help prevent HIV – Alexandra Ossola – Popular Science

Wrap up of talk by Norm Pace on “Metagenomics and the Tree of Life” – Jonathan Eisen – MicroBEnet

Frog Microbes May Help Fight Disease: Commensal skin bacteria adjusted their community structure when frogs were exposed to chytrid fungus in a recent study – Karen Zusi – The Scientist

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October 6, 2015

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Human gut microbiome

Intersections between Microbiome and Heart Failure: Revisiting the Gut Hypothesis –
Yuji Nagatomo – Journal of Cardiac Failure

Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects – Adriana Cuervo – Food and Function

Review: The Human Microbiota: Composition, Functions, and Therapeutic Potential – Rick Conrad, Alexander V. Vlassov – Medical Science Review

Models of microbiome research

Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection – Jason P. Mooney – Scientific Reports

Protocols for the Use of Gut Models to Study the Potential Contribution of the Gut Microbiota to Human Nutrition Through the Production of Short-Chain Fatty Acids –
Andrew J McBain – Springer Protocols Handbooks

Salami? Cecum microbial communities from steers differing in feed efficiency – P. R. Myer – Journal of Animal Science

Animal microbiome

Dholes are a species of wild dog: First report on the bacterial diversity in the distal gut of dholes (Cuon alpinus) by using 16S rRNA gene sequences analysis – Lei Chen – Journal of Applied Genetics

Plant, root, and soil microbiome

Diversity of fungi associated with plants growing in geothermal ecosystems and evaluation of their capacities to enhance thermotolerance of host plants – Wen-Na Zhou – Journal of Plant Interactions

Forage crops alter soil bacterial and fungal communities in an apple orchard – Sijun Qin – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Bacterial communities estimated by pyrosequencing in the soils of chinampa, a traditional sustainable agro-ecosystem in Mexico – Salvador Embarcadero-Jiménez – Journal of Soils and Sediments

Water microbiome

Bacterial diversity and community composition from seasurface to subseafloor – Emily A Walsh – The ISME Journal

Modelling the effects of hydrodynamic regimes on microbial communities within fluvial biofilms: combining deterministic and stochastic processes – Yi Li – Environmental Science & Technology

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect – Danny Ionescu – Scientific Reports

Book chapter: Protistan Diversity in Environmental Molecular Surveys – Ramon Massana – Marine Protists

Book chapter: Diversity of Microbial Eukaryotes in Deep Sea Chemosynthetic Ecosystems Illuminated by Molecular Techniques – Kiyotaka Takishita – Marine Protists

Extremophile microbiome

Metagenomic and metatranscriptomic analyses of Lake Vostok accretion ice – Yury M. Shtarkman – Bowling Green State University

Metabolic networks, proteomics

Gastrointestinal symptoms and altered intestinal permeability induced by combat-training are associated with distinct metabotypic changes – Lee Cheng Phua – Journal of Proteome Research

Review: Roles of Indole as an Interspecies and Interkingdom Signaling Molecule – Jin-Hyung Lee – Trends in Microbiology

Bioinformatics and metagenomics

Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ Preprints

MG-RAST, a Metagenomics Service for the Analysis of Microbial Community Structure and Function – Elizabeth M. Glass, Folker Meyer – Springer Protocols Handbook

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering – Oscar Franzén – Microbiome

Techniques

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms – Hooman Derakhshani – Journal of Basic Microbiology

More microbiology

This paper contains large amounts of plagiarism and confusing images, but here it is: Microbial Forensics in Legal Medicine – Pankaj Shrivastava – SAS Journal of Medicine

Microbes in the news

Georgia State Researcher Gets $1.35 Million to Study Effects of Common Food Additive on Body – Georgia State University
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October 5, 2015

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Characterizing and classifying the oral microbiome, homeostasis in the lung microbiome, collecting airborne microbes, and earthworms feeding on microbiomes.

Human oral microbiome

An accurate and efficient experimental approach for characterization of the complex oral microbiota – Wei Zheng – Microbiome

Phylogenetic approaches to microbial community classification – Jie Ning and Robert G. Beiko – Microbiome

DGGE: Stability of saliva microbiota during moderate consumption of red wine – Elvira Barroso – Archives of Oral Biology

Human respiratory tract microbiome

Review: Homeostasis and its Disruption in the Lung Microbiome – Robert P. Dickson – Am J Physiol Lung Cell Mol Physiol

Human gut microbiome

Faecalibacterium prausnitzii subspecies–level dysbiosis in the human gut microbiome underlying atopic dermatitis – Han Song – Journal of Allergy and Clinical Immunology

Animal models

Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4 – Barbara U. Metzler-Zebeli – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Landscape Position Influences Microbial Composition and Function via Redistribution of Soil Water across a Watershed – Zhe Du – Applied and Environmental Microbiology

Waste treatment microbiology

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures – Manuel Aira – FEMS Microbiology Ecology

Food microbiology

Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques – Mia Ryssel – International Journal of Food Microbiology

Air / Built environment microbiome

Passive dust collectors for assessing airborne microbial material – Rachel I. Adams – Microbiome

Microbes in the news

Beating parasites wins three scientists Nobel prize for medicine: “I think the microbes might almost deserve it more than I do” – Reuters

Nobel Prize Doctors still spreading word of bacteria find – Cathy O’Leary – The West Australian

Intrapartum antibiotics associated with altered infant gut microbiome – Maren Shapiro and Leah Bressler – 2MinuteMedicine

L’eau de bacteria: A whiff of the future? Biotech firms explore using microorganisms to produce flavors, fragrances – Benjamin Plackett – The Charlotte Observer

uBiome Co-Founder Jessica Richman Scoops Top Prize At IVY Awards, uBiome Is Finalist In MedTech Innovator of 2015 – PR Web

Podcast: Our microbiome and our health. Guests: Gary Wu, Tracy Bale, Frederic Bushman – RadioTimes

Microbiome Monday: Animals and Their BFFs – American Museum of Natural History

Permafrost-eating bacteria: a new twist on thawing Arctic and global warming – Thomas S Bianchi – The Conversation

Microbes may play a major role in cloud formation and wet weather – Richard Gray – Daily Mail

Volkswagen: Diesel transplants reveal likely culprit behind DeiselGate: car microbiomes -featuring Jeferina Gordon, Josephine Candelsman, and Hands Dieter Poetsch – – Morten Blaser – The Megabiome

Bacteria Hysteria

Take care when reusing bags: Reusing carrier bags for a diverse range of contents puts consumers at risk of bacterial contamination – Worthing Herald

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October 2, 2015

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Human gut microbiome

Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease – Mireia Lopez-Siles – Applied and Environmental Microbiology

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection – Joshua S. Son – PLOS ONE

Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC – Kathleen Machiels – Gut

Review: The Intestinal Microbiome in Bariatric Surgery Patients – Christine M. Peat – European Eating Disorders Review

Human urinary tract microbiome

Incontinence medication response relates to the female urinary microbiota – Krystal J. Thomas-White – International Urogynecology Journal

Animal models

In rats: N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota – Matteo M. Pusceddu – PLOS ONE

Table grape consumption reduces adiposity and markers of hepatic lipogenesis and alters gut microbiota in butter fat-fed mice – Jessie Baldwin – The Journal of Nutritional Biochemistry

In mice: Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut – Jinbao Yin – Ecotoxicology

Review: Changes to the Intestinal Microbiome With Parenteral Nutrition – Review of a Murine Model and Potential Clinical Implications – Farokh R. Demehri – Nutrition in Clinical Practice

Plant, root, and soil microbiology

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis – Chen-hua Li – PLOS ONE

Water microbiology

The Ocean as a Global Reservoir of Antibiotic Resistance Genes – Stephen M. Hatosy – Applied and Environmental Microbiology

Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats – Mireia Fillol – FEMS Microbiology Ecology

DGGE: Bacterial Diversity in Bohai Bay Solar Saltworks, China – Jiaojiao Zhang – Current Microbiology

Techniques

Quantitative Microbial Ecology through Stable Isotope Probing – Bruce A. Hungate – Applied and Environmental Microbiology

Bioinformatics

Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Science, publishing, and career

Predatory publishers earned $75 million last year, study finds – John Bohannon – Science

‘Predatory’ open access: a longitudinal study of article volumes and market characteristics – Cenyu Shen and Bo-Christer Björk – BMC Medicine

Ten Simple Rules for Protecting Research Integrity – David M. Shaw, Thomas C. Erren – PLOS Computational Biology

Microbes in the news

How gut health affects cycling performance – Cycling Weekly

Microbial sampling starts in Cherokee Homes – Jordan Peccia – MicroBEnet

Why It Was Easier to Be Skinny in the 1980s – Olga Khazan – The Atlantic

How do we protect ourselves from Martian bacteria? – Anjana Ahuja – World Economic Forum
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