Category Archives: Extremophiles

October 17, 2015

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Fungal infection in brains of Alzheimer patients (already generating a lot of discussion on Twitter), solving a bloody mess in leeches, crosstalk in sewage cleaning plant roots, stromatolite microbiomes, halophilic viruses, and a new tool called Schmutzi.

General human microbiome

Different Brain Regions are Infected with Fungi in Alzheimer’s Disease – Diana Pisa – Scientific Reports

Human (and dog) oral microbiome

Microbiological Analysis of Anaerobic Bacteria Isolated from Periodontal
Pockets in Cases of Periodontal Disease in Dogs and Humans – Magdalena Gołyńska – Dentistry

Human gut microbiome

Review: Changes seen in gut bacteria content and distribution with obesity: causation or association? – David S. H. Bell – Postgraduate Medicine

Review: Obesity, Diet and the Gut Microbiota – Anthony R. Bird – Current Nutrition Reports

Animal models

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice – Adina Howe – The ISME Journal

Bacterial community response to changes in a tri-trophic cascade during a whole-lake fish manipulation – Jatta Saarenheimo – Ecology

Animal microbiome

Solving a bloody mess: B-vitamin independent metabolic convergence among gammaproteobacterial obligate endosymbionts from blood-feeding arthropods and the leech Haementeria officinalis – Alejandro Manzano-Marín – Genome Biology and Evolution

Plant, root, and soil microbiome

Beneficial Bacteria Isolated from Grapevine Inner Tissues Shape Arabidopsis thaliana Roots – Enrico Baldan – PLOS ONE

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest – Albert Barberán – Ecology Letters

Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis – Bin Luo – Scientific Reports

Impacts of root symbiotic associations on interspecific variation in sugar exudation rates and rhizosphere microbial communities: a comparison among four plant families – Atushi Okubo – Plant and Soil

Nitrogen fertilization directly affects soil bacterial diversity and indirectly affects bacterial community composition – Jun Zeng – Soil Biology and Biochemistry

Influence of Microbial Composition on the Carbon Storage capacity of the Mangrove soil at the land-ocean boundary in the Sundarban Mangrove Ecosystem, India – Subhajit Das – Geomicrobiology Journal

Extremophile microbiome

Analysis of metagenomic data reveals common features of halophilic viral communities across continents – S. Roux – Environmental Microbiology

Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis – Giorgio Casaburi – Environmental Microbiology

Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community – Surendra Vikram – Environmental Microbiology

Plants impact structure and function of bacterial communities in Arctic soils – Manoj Kumar – Plant and Soil

Novel and Unexpected Microbial Diversity in Acid Mine Drainage in Svalbard (78° N), Revealed by Culture-Independent Approaches – Antonio García-Moyano – Microorganisms

Waste treatment microbiology

Assessment of human virus removal during municipal wastewater treatment in Edmonton, Canada – Yuanyuan Qiu – Journal of Applied Microbiology

The change of microbial community from chlorinated solvent-contaminated groundwater after biostimulation using the metagenome analysis – Chih-Ming Kao – Journal of Hazardous Materials

Metagenomics and bioinformatics

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology – Peter D. Karp – Briefings in Bioinformatics

Jflow: a workflow management system for web applications – Jérôme Mariette – Bioinformatics

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA – Gabriel Renaud – Genome Biology

Microbes in the news

Inside the Grim World of the Phytoplasmas ‘Zombie’ Plant Bacteria – Michael Byrne – Motherboard

The Future of Dieting Is Personalized Algorithms Based on Your Gut Bacteria – Melissa Dahl – Huffington Post

From migraine to microbiome, 20 companies to watch at big BIO investor event – Ron Leuty – San Francisco Business Times

Microbial considerations in rosacea treatment: Greater understanding of that demodex mites play may uncover new therapeutic options – Lisette Hilton – Dermatology Times

Science, publishing, and career
Men set their own cites high: Gender and self-citation across fields and over time – Molly M. King
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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 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 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 7, 2015

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Human oral microbiome

The Microbiome in Populations with a Low and High Prevalence of Caries – I. Johansson – Journal of Dental Research

Human gut microbiome

Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children – S. M. Bahr – Translational Psychiatry

Geriatric respondents and non-respondents to probiotic intervention can be differentiated by inherent gut microbiome composition – Suja Senan – Frontiers in Microbiology

Review: Intestinal microbiota and the innate immune system – a crosstalk in Crohn’s disease pathogenesis – Lea-Maxie Haag – Frontiers in Immunology

Review: The human gut virome: a multifaceted majority – Lesley A. Ogilvie – Frontiers in Microbiology

Review: Microbiota and host immune responses: a love-hate relationship –
Sarah Tomkovich – Immunology

Conference report: Gut microbiota and brain function: An evolving field in neuroscience – Jane A. Foster – International Journal of Neuropsychopharmacology

Animal microbiome

French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives – G. Minard – Frontiers in Microbiology

Plant, root, and soil microbiome

Deterministic processes vary during community assembly for ecologically dissimilar taxa – Jeff R. Powell – Nature Communications

A meta-analysis approach for assessing the diversity and specificity of belowground root and microbial volatiles – Denis Schenkel – Frontiers in Plant Science

Mining the phytomicrobiome to understand how bacterial coinoculations enhance plant growth – Maskit Maymon – Frontiers in Plant Science

Water microbiome

Contribution of cyanobacterial alkane production to the ocean hydrocarbon cycle
David J. Lea-Smith – PNAS

Review: Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities – BoonFei Tan – Frontiers in Microbiology

Extremophile microbiome

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential – Richard Allen White III – Frontiers in Microbiology

Built environment microbiology

Typo in title, some plagiarized text, and poor English but still including here: Metagenomic Human Repiratory Air in a Hospital Environment – Yi Yu Lai – PLOS ONE

Food microbiology

Lactic acid bacterium and yeast microbiotas of sixteen French traditional sourdoughs – Emilie Lhomme – International Journal of Food Microbiology

Waste microbiology

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry – Priyanka Kumari – PLOS ONE

Phages and viruses

Mammalian Host-Versus-Phage immune response determines phage fate in vivo – Katarzyna Hodyra-Stefaniak – Scientific Reports

Microbial Ecology

Review: Microbiomes: unifying animal and plant systems through the lens of community ecology theory – Natalie Christian – Frontiers in Microbiology

Metagenomics and bioinformatics

Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes
Sarah Temmam – PLOS ONE

Microbes in the news

“revolutionary poop platform”: Biomiic’s Platform Will Give People Microbiome Data From Crap: How Joseph Moon, Koji Yasuda and Soohong Kim are changing genomics Harvard iLab – Bostinno

Get To Know Your Poop Bacteria With This New iPhone App – Stephanie M. Lee – BuzzFeed

Could This Tough Bacteria Survive on Mars? – Irene Klot – Discovery

Bacteria in the world’s oceans produce millions of tonnes of hydrocarbons each year – Phys.org

Archaea: A headline on the front page of the New York Times for November 3, 1977, read “Scientists Discover a Way of Life That Predates Higher Organisms”. – Laura Eme, W. Ford Doolittle – Current Biology

The science of retweets – Science Daily
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October 4, 2015

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Pregnancy and birth

Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children – Jing Cheng – ISME Journal

Transplantation and infection microbiology

How’s your microbiota? Let’s check your urine. – Robert R. Jenq – Blood
Low urinary indoxyl sulfate levels early after transplantation reflect a disrupted microbiome and are associated with poor outcome – Daniela Weber – Blood

Next-Generation Sequencing for Infectious Disease Diagnosis and Management : A Report of the Association for Molecular Pathology – Martina I. Lefterova – The Journal of Molecular Diagnostics

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Human gut microbiome

The Intestinal Microbiota in Acute Anorexia Nervosa and During Renourishment: Relationship to Depression, Anxiety, and Eating Disorder Psychopathology – Kleiman, Susan C. – Psychosomatic Medicine

Interview: The Relationship Between the Gut Microbiota and Liver Disease – Jasmohan S. Bajaj – Gastroenterology & Hepatology

Animal models

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides – Meng Wu – Science

Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms: Part 2. Role of Gut Microorganisms – Yu Yang – Environmental Science & Technology

Animal microbiome

An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus – Joseph A. Hakim – Frontiers in Microbiology

Plant, root, and soil microbiome

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance – Hiromi Kato – DNA Research

Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica – Ying-wu Shi – Journal of Microbiology

Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan – Yu Fukasawa – Fungal Ecology

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities – Ye Deng – Global Change Biology

Waste microbiology

Contrasting microbial community composition and function perspective in sections of a full-scale coking wastewater treatment system – Shuang Zhu – Environmental Biotechnology

Microbial interactions and implications for oil biodegradation process in mangrove sediments – Adriana Daudt Grativol – PeerJ Preprint

Extremophiles

Subsurface Halophiles: An Analogue for Potential Life on Mars – Woolman, P. F – The Open University

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond – Addis Simachew – Microbiology of Aquatic Systems

Conference Abstract: Life on the frozen continent: diversity of RuBisCO, nifH and pufLM genes in soils around the Princess Elisabeth Station, Sør Rondane Mountains, Antarctica – Guillaume Tahon – Ghent University

Bioinformatics, mathematical models, metagenomics

Habitat Fluctuations Drive Species Covariation in the Human Microbiota – Charles K. Fisher – BioRxiv

Predicting Clinical Phenotype using OTU-based Metagenome Representation – Nathan LaPierre and Huzefa Rangwala – ICDM Workshop

Metabolomics, Proteomics

Video: An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis – David Colatriano, David A. Walsh – JoVE

Rumen microbial communities influence metabolic phenotypes in lambs – Diego P. Morgavi – Frontiers in Microbiology

Phages and viruses

The Tailocin Tale: Peeling off Phage Tails – Maarten G.K. Ghequire and René De Mot- Trends in Microbiology

Functional foods

Review: Prebiotics: why definitions matter – Robert W Hutkins – Current Opinion in Biotechnology

Microbes in the news

Microbiome Meals: Researchers identify a handful of genes that help bacteria in the mouse gut adapt to dietary changes – By Rina Shaikh-Lesko – The Scientist

Signature dishes: As people pass through life they leave a trail of bacteria in their wake – Economist

Chronic kidney disease and its effect on microbiome metabolism – American Microbiome Institute

Recap: Gut microbiome conference September 2015, Huntington Beach – UNC Center of Excellence for Eating Disorders

Nominations sought for NAS Committee on Microbiomes of the Built Environment – Jonathan Eisen – MicroBEnet

Legionnaires’ Bacteria Regrew in Bronx Cooling Towers That Were Disinfected – Benjamin Mueller – New York Times

NYU professor to chair presidential council on antibiotic bacteria resistance – Farhin Lilywala – Washington Square News

You say microbiota, I say microbiome: The 8 word guide to the microbiota – James Vitale – Taconic

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September 30, 2015

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Gut virome in infants, metabolome of Mediterranean diet, zebrafish gut assembly, antibiotic use and psoriasis risk, Roseobacter proteomics, and MetaPhlAn2.

Pregnancy and birth

The gut virome and bacterial microbiome—the early years – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Early life dynamics of the human gut virome and bacterial microbiome in infants –
Efrem S Lim – Nature Medicine

Human oral microbiome

Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis – Szymon P Szafrański – NPJ Biofilms and Microbiomes

Urease and Dental Plaque Microbial Profiles in Children – Evangelia Morou-Bermudez – PLOS ONE

High prevalence of colonization of oral cavity by respiratory pathogens in frail older patients with oropharyngeal dysphagia – O. Ortega – Neurogastroenterology & Motility

Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance – Ana Paula Vieira Colombo – Microbial Pathogenesis

Human gut microbiome

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome – Francesca De Fillippis – Gut

Review: Clinical and Pathophysiological Consequences of Alterations in the Microbiome in Cirrhosis – Jane Macnaughtan – American Journal of Gastroenterology

Animal models

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut – Sandi Wong – mBio

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis –
Peter Zanvit – Nature Communications

Plant, root, and soil microbiome

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Oily waste containing natural radionuclides: does it cause stimulation or inhibition of soil bacterial community? – Polina Galitskaya – Journal of Plant Nutrition and Soil Science

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Water microbiome

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

Extremophile microbiome

Perspective: The discovery of Antarctic RNA viruses: a new game changer – Ricardo Cavicchioli – Molecular Ecology

Metagenomics and bioinformatics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling – Duy Tin Truong – Nature Methods

Metabolomics, proteomics

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products – Chad W. Johnston – Nature Communications

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

CRISPRs

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins – Joseph Bondy-Denomy – Nature

Review: CRISPR-Cas immunity in prokaryotes – Luciano A. Marraffini – Nature

Microbes in the news

Study Links Skin Microbiome to Infections – Skin Inc

Ancient ‘Superman’ microbe’s ability to withstand damage to its DNA could be key to unlocking cancer cure, Chinese scientists say – Stephen Chen – South China Morning Post

Another Frontier in Microbiome Research: Preterm Birth – Julie A. Jacob – JAMA

Science, publishing, and career

A taxonomy of authorship roles – Credit Casrai

Bik’s Picks

What if everyone lived to 100? – Georgina Peters – London Business School Review

Gene-Edited “Micropigs” to Be Sold as Pets: The institute in Shenzhen, China, that creates the pigs quoted an initial price tag of $1,600 – David Cyranoski – Scientific American / Nature

1500-Year-Old Mosaic Map Found – Rossella Lorenzi – Discovery

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September 28, 2015

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Pregnancy and birth

Eczema susceptibility and composition of faecal microbiota at four weeks of age: A pilot study in Chinese infants – M.F. Tang – British Journal of Dermatology

Human skin microbiome

Prevalence and antibiotic susceptibility of bacteria from acute and chronic wounds in Malaysian subjects – Shin Yee Wong – The Journal of Infection in Developing Countries

Human respiratory microbiome

Induced sputum in young healthy children with cystic fibrosis – Julian Forton – Paediatric Respiratory Reviews

Human urinary tract microbiome

Assessment of the Lower Urinary Tract Microbiota during Symptom Flare in Women with Urologic Chronic Pelvic Pain Syndrome: A MAPP Network Study – J. Curtis Nickel – The Journal of Urology

Human gut microbiome

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer – Jun Yu – Gut

Animal microbiome

Abundance of ruminal bacteria, epithelial gene expression, and systemic biomarkers of metabolism and inflammation are altered during the peripartal period in dairy cows – A. Minuti – Journal of Dairy Science

Plant, root, and soil microbiome

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia – Alyssa A. Carrell and Anna C. Frank – Frontiers in Microbiology

Root isolations of Metarhizium spp. from crops reflect diversity in the soil and indicate no plant specificity – Bernhardt M. Steinwender – Journal of Invertebrate Pathology

DGGE: Biogas digestates affect crop P uptake and soil microbial community composition –
Sebastian Hupfauf – Science of The Total Environment

Water microbiome

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones – Jennifer B. Glass – Frontiers in Microbiology

Extremophile microbiome

Snow and ice ecosystems: not so extreme – Lorrie Maccario – Research in Microbiology

Metagenomics and bioinformatics

PanFP: pangenome-based functional profiles for microbial communities – Se-Ran Jun – BMC Research Notes

More microbes

The Out-of-the-Delta Hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen – Yan Boucher – Frontiers in Microbiology

Techniques

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities – Brett E. Arenz – Journal of Microbiological Methods

Microbes in the news

Infections in childhood could provide clues to disease development in later life – European Lung Foundation – EurekAlert

Harnessing The Hordes In The Microbiome: As researchers learn more about the connection between our bacteria and our health, companies are trying to develop therapies that exploit it – Lisa M. Jarvis – Chemical and Engineering News

Dried plums cuts risk of colon cancer, research reveals – Karla Tecson – International Business Times

Root microbiome engineering improves plant growth – EurekAlert

What could possibly go wrong? NASA Is Sending Bacteria to the Edge of Space to See if They Can Hitchhike to Mars – Maddie Stone – Gizmodo

Move over, Barry Marshall: 3.5-Million-Year Old Bacteria: Found To Boost Longevity In Lab Tests, Russian Scientist Injects Self – Aditi Simlai Tiwari – HNGN

Science, publishing, and career

High time for a common plagiarism detection system – Ivan Jarić – Scientometrics

It’s Peer Review Week: 28 Sep – 2 Oct 2015
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September 27, 2015

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General microbiome

Power Law Analysis of the Human Microbiome – Zhanshan Sam Ma – Molecular Ecology

Pregnancy and birth

Review: Probiotics and necrotizing enterocolitis – Paul Fleming – Pediatric Surgery International

Human oral microbiome

The efficacy of two oral hygiene regimens in reducing oral malodour: a randomised clinical trial – Magda Feres – International Dental Journal

Human respiratory tract microbiome

PhD Thesis: Investigating the host and bacterial factors in cystic fibrosis that promote persistence of infection in the lung – Daniel James Smith – University of Queensland

Human gut microbiome

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants – Roberto Berni Canani – The ISME Journal

Review: Reciprocal interaction of diet and microbiome in inflammatory bowel diseases – Monika Schaubeck – Current Opinion in Gastroenterology

Review: Resistant starches for the management of metabolic diseases – Laure B. Bindels – Current Opinion in Clinical Nutrition & Metabolic Care

Animal models

Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna – Martijn Callens – The ISME Journal

Animal microbiome

Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption – J. Stoops – Food Microbiology

Indigenous microbiota and Leishmaniasis – Mateus Eustáquio de Moura Lopes – Parasite Immunology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B Hadapad – Pest Management Science

Plant, root, and soil microbiome

Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes – Fabiola Miranda-Sánchez – Environmental Microbiology

Non-random species loss in bacterial communities reduces antifungal volatile production – W. H. Gera Hol – Ecology

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment – Mohammad Bahram – The ISME Journal

Plant and root-endophyte assembly history: interactive effects on native and exotic plants – Benjamin A. Sikes – Ecology

Review: Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach – Fernando Carlos Gómez-Merino – Acta Physiologiae Plantarum

Review: Engineering Microbiomes to Improve Plant and Animal Health – U.G. Mueller – Trends in Microbiology

Water microbiome

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River – Bonnie L. Brown – Standards in Genomic Sciences

Extremophile microbiome

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy – Judith M Klatt – The ISME Journal

Emerging spatial patterns in Antarctic prokaryotes – Chun Wie Chong – Frontiers in Microbiology

Waste microbiology

Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels – Maria Westerholm- Biotechnology for Biofuels

Food microbiology

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing – Ruo-si Fang – Journal of Food Sciences

Isolation and characterization of bacteriocinogenic lactic bacteria from M-Tuba and Tepache, two traditional fermented beverages in México – Norma M. de la Fuente-Salcido – Food Science & Nutrition

Built environment microbiology

Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel – Nahum Y. Shpigel – PLOS ONE

Microbial Ecology

Transient dynamics of competitive exclusion in microbial communities – Stilianos Louca – Environmental Microbiology

Metagenomics and bioinformatics

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

Review: Recovering full-length viral genomes from metagenomes – Saskia Smits – Frontiers in Microbiology

Editorial: The main challenges that remain in applying high-throughput sequencing to clinical diagnostics – Michael Loeffelholz & Yuriy Fofanov – Expert Review of Molecular Diagnostics

Microbes in the News

uBiome Supports Oral Disease Prevention with Donations and Study – PR Web

Probiotic Formula Reverses Cow’s Milk Allergies by Changing Gut Bacteria of Infants – Lab Manager

Microbes and art

Microbe artwork shows the limits of antibiotics – University of Oxford

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September 22, 2015

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Effect of hookworm infection on microbiome of celiac subjects, neutrophil ageing, altering the bone niche, and a personal microbial cloud.

Pregnancy and birth

Influence of a combination of probiotics on bacterial infections in very low birthweight newborns – Zlatka Kanic – Wiener klinische Wochenschrift

Microbiome of death

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses – Seung Hak Yang – Genetics and Molecular Biology

Human respiratory tract microbiome

Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics – Leah J. Hauser – International Forum of Allergy & Rhinology

Human oral microbiome

Comparison of Subgingival and Peri-implant Microbiome in Chronic Periodontitis – Zhang, Qian – Chinese Journal of Dental Research

The novel association between red complex of oral microbe and body mass index in healthy Japanese: a population based cross-sectional study – Kanae Matsushita – Journal of Clinical Biochemistry and Nutrition

Human gut microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects – I. Rangel – Alimentary Pharmacology & Therapeutics

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial – Hyuk Yoon – Journal of Clinical Biochemistry and Nutrition

Review: Improving healthspan via changes in gut microbiota and fermentation – Michael J. Keenan – AGE

Review: Gastric Microbiota – Gianluca Ianiro – Helicobacter

Thesis: High-resolution analysis of the human intestinal microbiota stability landscape – Tineka Blake – Aalto University

Animal models

An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea – Yemeng Li – RCS Advances

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche – Yubin Luo – Cell Metabolism

The levonorgestrel-releasing intrauterine system is associated with delayed endocervical clearance of Chlamydia trachomatis without alterations in vaginal microbiota – E.R. Liechty – Pathogens and Disease

Goldfish: Correlations of Gut Microbial Community Shift with Hepatic Damages and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure – Haifeng Kan – Environmental Science & Technology

Neutrophil ageing is regulated by the microbiome – Dachuan Zhang – Nature

Animal microbiome

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea – Qingsong Yang – Aquatic Ecosystem Health & Management

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease – Ermanno Federici – Microbes and Environments

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression –
Jia Y. Har – Frontiers in Microbiology

Plant, root, and soil microbiome

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage – Natalia Pimentel Esposito-Polesi – World Journal of Microbiology and Biotechnology

Endospores, prokaryotes, and microbial indicators in arable soils from three long-term experiments – Paulina Tamez-Hidalgo – Biology and Fertility of Soils

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities – Sandra Ronca – Frontiers in Microbiology

Responses of aromatic-degrading microbial communities to elevated nitrate in sediments –
Meiying Xu – Environmental Science & Technology

Climate change and physical disturbance cause similar community shifts in biological soil crusts – Scott Ferrenberg – PNAS

Water / Extremophile microbiome

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing – Jae-Ho Jung – Animal Cells and Systems

Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing – H. Jing – Biogeosciences Discussions

Built environment microbiome

Humans differ in their personal microbial cloud – James F. Meadow – PeerJ

Waste microbiology

Relationship between bacterial diversity and environmental parameters during composting of different raw materials – Xueqin Wang – Bioresource Technology

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination – Siobhan O’Brien, Angus Buckling – EMBO Reports

Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation – Marc A. Demeter – Frontiers in Microbiology

Microbial Ecology

Predicting microbial traits with phylogenies – Marta Goberna and Miguel Verdú – The ISME Journal

Bioinformatics and metagenomics

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories – Christine L Sun – The ISME Journal

CCLasso: correlation inference for compositional data through Lasso – Huaying Fang – Bioinformatics

Computational methodology for predicting the landscape of the human–microbial interactome region level influence – Edgar D. Coelho – Journal of Bioinformatics and Computational Biology

Techniques

Targeted single molecule mutation detection with massively parallel sequencing – Mark T. Gregory – Nucleic Acids Research

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures – Stefan A. Boers – Scientific Reports

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis – Thomas Briese – mBio

Microbes in the news

Wherever You Go, Your Personal Cloud Of Microbes Follows – Rob Stein – NPR

Former CEO knew about contamination, wrote “Just ship it”: 28 years for salmonella: Peanut exec gets groundbreaking sentence – Moni Basu – CNN

UGA microbiology researchers identify potential mechanism for neurodegenerative diseases – News Medical

Researchers find novel signature in the brains of children with cerebral malaria – EurekAlert

Science, publishing, and career

About annoying invitations to write papers in questionable journals and strategies how to handle those: You are invited to submit… – David Moher and Anubhav Srivastava – BMC Medicine

Bik’s Picks

8 trillion microbeads pollute U.S. aquatic habitats daily – Jareen Imam – CNN

Science Says This Is the Sound Giraffes Make – Alexandra Sifferlin – Time

I Am the Walrus: What 35,000 Walruses Tell Us About Our Future in Warming World – Miyoko Sakashita – Huffington Post

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