Category Archives: Metagenomics & Bioinformatics

March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

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

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 28, 2016

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Oral microbiome and smoking, a bacterial genome from a germ-free mouse isolate, semi-arid soils, jellyfish, OTU picking methods, and the best hypervariable regions in the 16S rRNA gene.

Human oral microbiome

Cigarette smoking and the oral microbiome in a large study of American adults – Jing Wu – The ISME Journal

Human gut microbiome

Persisting changes of intestinal microbiota after bowel lavage and colonoscopy – Drago, Lorenzo – European Journal of Gastroenterology & Hepatology

Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations – Rashmi Sinha – PLOS ONE

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India – Saurabh Kedia – Journal of Gastroenterology

Review: Gut Microbiota and Lifestyle Interventions in NAFLD – David Houghton – MDPI International Journal of Molecular Sciences

Review: Microbiota-gut-brain signalling in Parkinson’s disease: Implications for non-motor symptoms – Valeria D. Felice – Parkinsonism & Related Disorders

PhD Thesis: Development and analysis of molecular methods for functional metagenomics of the human gut microbiome – Kathy Lam – University of Waterloo

Animal models

Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease – Irina A. Kirpich – The American Journal of Pathology

Complete Genome Sequence of Turicibacter sp. Strain H121, Isolated from the Feces of a Contaminated Germ-Free Mouse – T. A. Auchtung – Genome Announcements

Animal microbiome

Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes – Daniel F. R. Cleary – FEMS Microbial Ecology

Review: Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases – Mikolaj M. Raszek – Frontiers in Genetics

Plant, root, and soil microbiome

Soil characteristics driving arbuscular mycorrhizal fungi communities in semiarid Mediterranean soils – Maria del Mar Alguacil – Applied and Environmental Microbiology

454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems – Elham A. Kazeeroni – Frontiers in Plant Science

Development of microbial community structure in vegetable-growing soils from open-field to plastic-greenhouse cultivation based on the PLFA analysis – Zhiyuan Yao – Journal of Soils and Sediments

Soil communities are affected by CO2 belowground emissions at a natural vent in Spain – I. Fernández-Montiel – Soil Biology and Biochemistry

No favorable effect of reduced tillage on microbial community diversity in a silty loam soil (Belgium) – Florine Degrune – Agriculture, Ecosystems & Environment

Bacteria play a more important role than nutrients in the accumulation of tetracycline resistance in manure-treated soil – Shuang Peng – Biology and Fertility of Soils

Review: Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism – Sofie Thijs – Frontiers in Microbiology

Water microbiome

Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids – Jean-Paul Baquiran – Frontiers in Microbiology

Streams: Regional and global elevational patterns of microbial species richness and evenness – Jianjun Wang – Ecography

Extremophile microbiome

Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes – Daniel R. Colman – Frontiers in Microbiology

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments – Alexander Crits-Christoph – Frontiers in Microbiology

Bioinformatics and metagenomics

Application of database-independent approach to assess the quality of OTU picking methods – Patrick D Schloss – BioRxiv

MG-Digger: an automated pipeline to search for giant virus-related sequences in metagenomes – Jonathan Verneau – Frontiers in Microbiology

MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices – Dinghua Li – Methods

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis – Bo Yang – BMC Bioinformatics

Absent words and the (dis)similarity analysis of DNA sequences: an experimental study – Mohammad Saifur Rahman – BMC Research Notes

Book chapter: Bidirectional Variable-Order de Bruijn Graphs – Djamal Belazzougui – LATIN 2016: Theoretical Informatics

Transcriptomics

Review: Translating RNA sequencing into clinical diagnostics: opportunities and challenges – Sara A. Byron – Nature Reviews Genetics

Techniques

Modification of a high- throughput automatic microbial cell enumeration system for ship board analyses – Christin M. Bennke – Applied and Environmental Microbiology

More microbiology

Rare-earth elements: Rare-earth separation using bacteria – William Bonificio – Environmental Science & Technology Letters

Expression of HIV-1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus – Angela Marcobal – AIDS Research and Human Retroviruses

Review: Studying Bacterial Multispecies Biofilms: Where to Start? – Henriette L. Røder – Trends in Microbiology

Microbes in the news

Osel scientists engineer vaginal lactobacillus to express neutralizing HIV-1 antibody fragments – EurekAlert

‘Good’ bacteria could save amphibians hit by fungal diseases – Adam Wernick – PRI

Forget Chocolate Rabbits: Microbiologists Celebrate Easter With Bacteria Bunny – ABC News

Psychobiotics Will Use Bacteria to Alter Your Brain Through Your Gut – Ben Guarino – Inverse

Low FODMAP diet may significantly improve IBS symptoms – Healio

Scientists to drill into dinosaur-killing blast – Eric Hand – Science

Rage Disorder Linked with Parasite Found in Cat Feces. Toxoplasmosis may alter brain chemistry is people exhibiting bouts of explosive anger – Christopher Wanjek – Scientific American

Bacteria Hysteria

Would you dare to bacteria-test your entire life? Katherine Keogh did … and the result will shock all house-proud readers – Katherine Keogh – Daily Mail

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March 24, 2016

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Two papers on antibiotics in early childhood and obesity, diabetic foot ulcers, vertebrate animal microbiomes, cattle hides, kimchi, human archaeological remains, and high inter-center variability in microbiome results.

General microbiome

Review: Stress as a Normal Cue in the Symbiotic Environment – Julia A. Schwartzman – Trends in Microbiology

Pregnancy and birth

Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity – Frank I. Scott – Gastroenterology

Antibiotic Exposure During the First 6 Months of Life and Weight Gain During Childhood – Jeffrey S. Gerber – JAMA

Editorial: From Bottles to Diapers: How Manipulating and Exploring the Microbiome Is Defining Newborn Care – Jill L. Maron – Clinical Therapeutics

Research highlight: Gut microbiota dysbiosis precedes NEC – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Human skin microbiome

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers – Karen Smith – BMC Microbiology

Human gut microbiome

Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents – R. Alan Harris – Journal of Immunology Research

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling – Nicholas Edward Ilott – The ISME Journal

Targeting colorectal cancer-associated bacteria: a new area of research for personalized treatments – T. Faïs – Gut Microbes

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study – Borgo Francesca – Childhood Obesity

Review: Can attention to the intestinal microbiota improve understanding and treatment of anorexia nervosa? – Jacquelyn Carr – Expert Review of Gastroenterology & Hepatology

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: FoMenTing Change? – Flaviano S. Martins – Digestive Diseases and Sciences

Review: Does the Microbiome Cause B27-related Acute Anterior Uveitis? – James T. Rosenbaum – Ocular Immunology and Inflammation

Microbes in blood

The prognostic significance of bacterial DNA in patients with decompensated cirrhosis and suspected infection – Tony Bruns – Liver International

Animal models

The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy – Gut Microbes

TLR4-Dependent Secretion by Hepatic Stellate Cells of the Neutrophil-Chemoattractant CXCL1 Mediates Liver Response to Gut Microbiota – Amélie E. Bigorgne – PLOS ONE

Animal microbiome

Vertebrate bacterial gut diversity: size also matters – Jean-Jacques Godon – BMC Ecology

Larval growth rate is associated with the composition of the gut microbiota in the Glanville fritillary butterfly – L. Ruokolainen – Oecologia

Host origin and tissue-microhabitat shaping the microbiota of the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – FEMS Microbiology Ecology

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides – Jessica Chopyk – Microbiome

Plant, root, and soil microbiome

High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – The Journal of Eukaryotic Microbiology

Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe – Jing Zhang – Scientific Reports

Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains – Manila Yadav – BMC Microbiology

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols – Huili Yu – Microbiology Open

Bioprospecting plant-associated microbiomes – Christina A. Müller – Journal of Biotechnology

Water and extremophile microbiome

Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters – Christoph Reitschuler – Antonie van Leeuwenhoek

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics – Alexandra Meziti – Environmental Microbiology

Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting – Dimitri Meier – Environmental Microbiology

Waste and pollution microbiology

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates – Vrutika Patel – BMC Microbiology

Built environment microbiology

Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system – Jenni Inkinen – Journal of Applied Microbiology

Forensic microbiology

Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains – Romy Müller – Journal of Archaeological Science

Food microbiology

Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable – Young Joon Oh – Antonie van Leeuwenhoek

Computational modeling

Host Selection of Microbiota via Differential Adhesion – Kirstie McLoughlin – Cell Host & Microbe

Techniques

The real cost of sequencing: scaling computation to keep pace with data generation – Paul Muir – Genome Biology

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability – Andreas Hiergeist –
International Journal of Medical Microbiology

Genotyping bacterial and fungal pathogens using sequence variation in the gene for the CCA-adding enzyme – Paul Franz – BMC Microbiology

Proteomics

Review: Tackling probiotic and gut microbiota functionality through proteomics – Lorena Ruiz – Journal of Proteomics

Microbes in the news

Can we model how viruses move between species? – Nancy Mendoza – Microbe Post

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More – Jon Palfreman – PBS

Report: Laminate wood flooring risk was underestimated by CDC – Jonathan Eisen – MicroBEnet

Microbiota profiles in patients with colorectal cancer differ from healthy individuals – Healio

Science, publishing and career

Set up a ‘self-retraction’ system for honest errors, says Daniele Fanelli – Nature

Incorporating Primary Scientific Literature in Middle and High School Education – Sarah C. Fankhauser – ASM Science

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March 23, 2016

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Today’s Microbiome Digest is dedicated to my sister Charlotte, who passed away last November. It would have been her birthday today.

Pregnancy and birth

Note: no mentioning of extraction controls, many of the Salter contaminants found, figures hard to read. Proceed with caution: Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid – Maria Carmen Collado – Scientific Reports

Human skin microbiome

Effects of a New Emollient-Based Treatment on Skin Microflora Balance and Barrier Function in Children with Mild Atopic Dermatitis – Pascale Bianchi – Pediatric Dermatology

Human gut microbiome

Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults – Theresa Wan-Chen Yap – PLOS ONE

Review: Molecular Insight into Gut Microbiota and Rheumatoid Arthritis – Xiaohao Wu – MDPI International Journal of Molecular Sciences

Animal models

Lingonberries reduce atherosclerosis in Apoe-/- mice in association with altered gut microbiota composition and improved lipid profile – Chrysoula Matziouridou – Molecular Nutrition & Food Research

News and views: Barrier regulation: tolerance stops at cell death – Johanna Pott – Nature Immunology

Animal microbiome

Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species – Stephanie N. Lawler – Frontiers in Microbiology

Flow cytometry analysis of the microbiota associated with the midguts of vector mosquitoes – Tibebu Habtewold – Parasites & Vectors

Plant, root, and soil microbiome

Distribution and diversity of bacterial communities and sulfate-reducing bacteria in a paddy soil irrigated with acid mine drainage – Han Wang – Journal of Applied Microbiology

PhD thesis: The lichen-associated microbiome: taxonomy and functional roles of lichen-associated bacteria – Margrét Auður Sigurbjörnsdóttir – University of Iceland

Air microbiome

The effect of dust storms on the atmospheric microbiome in the Eastern Mediterranean – Yinon Mazar – Environmental Science & Technology

Water and extremophile microbiome

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton – Francisco M. Cornejo-Castillo – Nature Communications

More microbiology

Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose – Etienne G.J. Danchin – Molecular Biology and Evolution

Viruses and phages

Discovery of unfixed endogenous retrovirus insertions in diverse human populations – Julia Halo Wildschutte – PNAS

Virological factors that increase the transmissibility of emerging human viruses – Jemma L. Geoghegan – PNAS

Bioinformatics and metagenomics

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets – Sudhir Kumar – Molecular Biology and Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data – Jaime Huerta-Cepas – Molecular Biology and Evolution

Microbes in the news

Disease Detectives Find A Really Good Reason Not To Drink Date Palm Wine – Rae Ellen Bichell – NPR

Bacteria could be speeding up the darkening of Greenland’s ice – Tim Radford – The Guardian

Unlocking the Mechanics of the Urinary Tract Infection – Lina Zeldovich – The Atlantic

Transplant in training: Journey into the Microbiome! – Karen Gardner – The Frederick News-Post

Diversifying Your Microbiome – Academic Minute with Jack Gilbert – Inside Higher Ed

Methane-Eating Bacteria Could Be a Win-Win for Reducing Emissions, Impacts of Fish Farming – Hannah Furlong – Sustainable Brands

Artificial Sweeteners: A Wolf in Sheep’s Clothing? – David A. Johnson – Medscape

Paradigm shift: ‘We need to study lumps of bacteria’ – EurekAlert

Microbial diversity and ‘unique’ cheeses – Yufan Chen – Microbe Post

Old, deep and close to home: the places that scientists are looking for new drugs – Benjamin Thompson and Matt Hutchings- Microbe Post

The bacteria that grow better in SPACE: Tests reveal a certain strain develops faster in microgravity – but no-one knows why – Sarah Griffiths – Daily Mail

Windham schools to close for two days over intestinal bacteria – Jen Steer – Fox8 Cleveland

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March 22, 2016

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Eye microbiota and contact lenses, leaf-cutter ant dumps, bacteria help with platinum transformation, metagenomics from a Swedish cave, extreme habitats at home, bacteria on board the ISS, a special issue on Megaviromes, and a recipe for Poop Peeps.

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

Effect of Infant Formula Containing a Low Dose of the Probiotic Bifidobacterium lactis CNCM I-3446 on Immune and Gut Functions in C-Section Delivered Babies: A Pilot Study – L. Baglatzi – Clinical Medicine Insights: Pediatrics

Infection, immunology, and transplantion microbiology

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia – P. Gyarmati – Scientific Reports

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation – D Weber – Bone Marrow Transplantation

Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology

Crosstalk between microbiota, pathogens and the innate immune responses – Claudia Günther – International Journal of Medical Microbiology

Human oral microbiome

Commentary: Microbiota-derived metabolites modulate tissue homeostasis: relevance to the oral cavity? – Hervé Le Moual – Oral Diseases

Human eye and skin microbiome

Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio

Human vaginal microbiome

Improvement and automation of a real-time PCR assay for vaginal fluids – E. De Vittori – Forensic Science International

Human gut microbiome

Conference report: Talking about cross-talk: the immune system and the microbiome: A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, Feb 2016 – David Zeevi – Genome Biology

Review: An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? – Burman S. – Digestive Diseases

Review: Gut Microbiota: The Brain Peacekeeper – Chunlong Mu – Frontiers in Microbiology

Review [PDF]: The intestinal microbiota and its role in human health and
disease – Keiko Kataoka – The Journal of Medical Investigation

Editorial: The microbiome as a possible target to prevent celiac disease – Maureen M Leonard – Expert Review of Gastroenterology & Hepatology

Animal models

Mice: Arthritis-induced alveolar bone loss is associated with changes in the composition of oral microbiota – Jôice Dias Corrêa – Anaerobe

Chickens: Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens – Qin Luo – Biological Trace Element Research

Tilapia: Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis – Zhi Liu – Scientific Reports

Animal microbiome

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability – Gina R. Lewin – PLOS ONE

Plant, root, and soil microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity – Paul Carini – bioRxiv

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities – Megan A. Rúa – Frontiers in Microbiology

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert – Yan Gui Su – CATENA

The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests – Nicholas P. Rosenstock – New Phytologist

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass – Erin E. Nuccio – Ecology

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan – Shunsuke Matsuoka – FEMS Microbiology Ecology

Review: The Functioning of Rhizosphere Biota in Wetlands – a Review – Amir Neori – Wetlands

Water and extremophile microbiome

Experimental evidence that microbial activity lowers the albedo of glaciers – M. Musilova – Geochemical Perspectives Letters

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor – William D. Orsi – Environmental Microbiology Reports

Cave microbiome

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden – Marie Lisandra Zepeda Mendoza – PLOS ONE

Built environment microbiology

Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ preprint

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A. Coil – PeerJ

Food microbiology

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits – Wen Yi W. V – Letters in Applied Microbiology

Bioinformatics, techniques, and metagenomics

Strain-level microbial epidemiology and population genomics from shotgun metagenomics – Matthias Scholz – Nature Methods

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions – Shengqin Wang – Journal of Theoretical Biology

A framework for inferring biological communities from environmental DNA – Andrew Olaf Shelton – Ecological Applications

Review: Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money – Antony T. Vincent – Journal of Microbiological Methods

Metagenomics and viruses

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity – Yu-Nong Gong – PLOS ONE

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics – Daniel Wüthrich – Virology

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets – Oskar E. Karlsson – PLOS ONE

Special issue of Current Opinion in Microbiology: Megaviromes
Review: Giant viruses come of age – Matthias G Fischer
Review: Giant viruses and the origin of modern eukaryotes – Patrick Forterre

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life – Patrick Forterre – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

More microbiology

The mystery of plague in medieval Iceland – Chris Callow – Journal of Medieval History

Microbes in the news

HT: Tomer Altman: Poop Peeps: Today we’re going to make Poop Peeps. Marshmallow Peeps that are shaped like the poop emoji.– Matthew Cetta – Nomageddon

Elizabethkingia, the rare and deadly bacteria that’s sickening people in the Midwest, explained – Julia Belluz – Vox

Forest resilience; can microbes help combat climate change issues faster than genetic adaptations? – Armand Séguin

Controversial New Push to Tie Microbes to Alzheimer’s Disease. A journal article says herpes virus and Lyme disease bacteria are behind the mind-robbing illness, but not all researchers are convinced – Melinda Wenner Moyer – Scientific American

Bacteria Are Revolutionizing Biotech–Here’s Why We Need To Talk About It – Catherine Feuillet – Forbes

Contact Lenses Fill Your Eyes With Bacteria – Mandy Oaklander – Time

Killing Bacteria With Gold Nanodisks And Light – Jennifer Hicks – Forbes

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

Top Science Fair Projects Put Stream Data, Bacteria to Work – Dan Swanson – News Channel Nebraska

The Daily Startup: Startups Look to ‘New Frontier’ of Microbiomes to Fight Disease – Wall Street Journal

The Human Microbiome Handbook – Edited by Jason Tetro, Emma Allen-Vercoe

New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data – Genome Web

Ulcerative Colitis Improves in Multidonor Fecal Transplant Trial – Damian McNamara – MedScape

Blog posts by me:

New papers, March 22, 2016 – Elisabeth Bik – MicroBEnet

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 16, 2016

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Events

Strategies & Techniques for Analyzing Microbial Population Structures (STAMPS) Course 8/3-8/13 – MicroBEnet

Human skin microbiome

An in Vitro Model for the Human Cutaneous Microbial Ecosystem – Danique A. van der Krieken – Acta Dermato-Venereologica

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – I.M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory tract microbiome

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines – Chinelo Ebruke – BMC Microbiology

Human gut microbiome

Note: data segregate according to study: Gene expression profiling gut microbiota in different races of humans – Lei Chen – Scientific Reports

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman

Review: Gut Microbiota and Obesity: Potential Therapeutic Targets and Probiotic 
Nicole D. White – American Journal of Life Sciences

Animal models

Fuzhuan tea consumption imparts hepatoprotective effects and alters intestinal microbiota in high saturated fat diet-fed rats – Michelle T. Foster – Molecular Nutrition & Food Research

Long-term effects of early life microbiota disturbance on adaptive immunity in laying 
K. Simon – Poultry Science

Rapid evolution of microbe-mediated protection against pathogens in a worm host –
Kayla C King – ISME Journal

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Hongxing Han – Scientific Reports

Animal microbiome

Genomic Analysis of Companion Rabbit Staphylococcus aureus – Mark A. Holmes – PLOS ONE

Plant, root, and soil microbiome

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants – Tao Ding – PLOS ONE

Water and extremophile microbiome

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats – David Velázquez – Scientific Reports

Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters – Richard A. Haugland – Journal of Microbiological Methods

Built environment microbiome

Potentially harmful secondary metabolites produced by indoor Chaetomium species on artificially and naturally contaminated building materials – I. Došen – Indoor AIr

Food microbiology

Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties – Reza Ranjbar – BMC Microbiology

Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce – Ji Young Jung – PLOS ONE

Viruses and phages

The Formulation of Bacteriophage in a Semi Solid Preparation for Control of Propionibacterium acnes Growth – Teagan L. Brown – PLOS ONE

News & Views: Microbial oceanography: Viral strategies at sea – T. Frede Thingstad – Nature

Lytic to temperate switching of viral communities – B. Knowles – Nature

Microbial Ecology

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla – Judith Zimmerman – Molecular Ecology

Bioinformatics

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to 
Yanming Zhang – Nucleic Acids Research

Techniques

The US Culture Collection Network lays the foundation for progress in preservation of valuable microbial resources – Kevin McCluskey – Phytopathology

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

A modified micro chamber agar spot slide culture technique for microscopic examination of filamentous fungi – Peralam Yegneswaran Prakash – Journal of Microbiological Methods

Microbes in the news

uBiome is World’s First Company to Appoint Citizen-Scientist-in-Residence – PR Web

Incredible images reveal bacteria motor parts in unprecedented detail – Science Codex

Ancient Bacteria With Photosynthesis Were Much More Common Than Previously Thought, Study Finds – Catherine Griffin – HNGN

Viral Remnants Help Regulate Human Immunity: Endogenous retroviruses in the human genome can regulate genes involved in innate immune responses – Jyoti Madhusoodanan – The Scientist

Plastic That Mimics Insect Wings Kills Bacteria, University of California, Irvine Study – Biospace

Early heavy metal exposure can cause permanent changes to gut microbiome and cause a host of diseases – Dave Mihalovic – SOTT

Slice of PLOS: Bacteria’s Social Media – Lauren Richardson – PLOS ONE

“Unsurprisingly, Perlmutter has his critics.” Neurologist David Perlmutter gets to the guts of brain health with surprising advice – SMH.com

Opinion: A Mother’s Microbes: On “vaginal seeding” and the challenge of evidence-based parenting – Rob Knight and Jack Gilbert – The Scientist

Australian Scientists Discover How Gut Bacteria May Prevent Stomach Cancer – MSN

Reduction in dietary diversity impacts richness of human gut microbiota – Science Codex
http://www.nature.com/articles/srep23075

Press might be overinterpreting Mouse seminal microbiome study:
Scientists discover microbiome that may be responsible for male reproductive disorders – EurekAlert

Seminal work. How unruly data led MU scientists to discover a new microbiome – Roger Meissen – Decoding Science

Microbiome: This Type Of Bacteria May Increase Risk Of Reproductive Disorders – Kathleen Lees – HNGN

Science, publishing, and career

Handful of Biologists Went Rogue and Published Directly to Internet – Amy Harmon

Peer-Led Team Learning Helps Minority Students Succeed – Julia J. Snyder – PLOS Biology

Video parody: PloS ANNA VS ELSAvier – For The First Time – Luisa Hugerth -YouTube

Bik’s Picks

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

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March 15, 2016

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Intrapartum antibiotics and newborn gut microbiota, the seminal fluid microbiome, and xenobiotic metabolism by gut microbes.

General microbiome

Review: The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo – Therapeutic Advances in Gastroenterology

Pregnancy and birth

Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions – Irene Aloisio – Applied Microbiology and Biotechnology

Human respiratory microbiome

Neonatal Gastrointestinal and Respiratory Microbiome in Cystic Fibrosis: Potential Interactions and Implications for Systemic Health – Juliette C. Madan – Clinical Therapeutics

Review: Host-microbiome interactions in acute and chronic respiratory infections – Steven Taylor – Cellular Microbiology

Human reproductive tract microbiome

Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status – Angela B. Javurek – Scientific Reports

Human gut microbiome

Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection – Caroline Vincent – Microbiome

Upper Versus Lower Gastrointestinal Delivery for Transplantation of Fecal Microbiota in Recurrent or Refractory Clostridium difficile Infection: A Collaborative Analysis of Individual Patient Data From 14 Studies – Luis Furuya-Kanamori – Journal of Clinical Gastroenterology

Similar depletion of protective Faecalibacterium prausnitzii in psoriasis and Inflammatory Bowel Disease, but not in Hidradenitis Suppurativa – Hester Eppinga – Journal of Crohn’s and Colitis

Review: The role of the gastrointestinal tract and microbiota on uremic toxins and chronic kidney disease development – David Briskey – Clinical and Experimental Nephrology

Review: The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism – Peter Spanogiannopoulos – Nature Reviews Microbiology

Animal microbiome

Vertebrate hosts as islands: dynamics of selection, immigration, loss, persistence and potential function of bacteria on salamander skin – Andrew H. Loudon – Frontiers in Microbiology

Plant, root, and soil microbiome

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure – Felix Beulig – Nature Microbiology

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms – Jaejoon Jun – Scientific Reports

Bacterial Community Succession in Pine-Wood Decomposition – Anna M. Kielak – Frontiers in Microbiology

Cave microbiome

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot – Surajit De Mandal – Environmental Science and Pollution Research

Water microbiome

Bacterial diversity and distribution in seven different estuarine sediments of Poyang Lake, China – Ping Sheng – Environmental Earth Sciences

Built environment microbiology

Detection of Balamuthia mandrillaris DNA in the storage case of contact lenses in Germany – Carsten Balczun – Parasitology Research

Viruses and phages

Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus – Sarah Temmam – MDPI Viruses

Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa – Joshua O. Amimo – Archives of Virology

Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition – Matthieu Galtier – Environmental Microbiology

Review: Mutualistic viruses and the heteronomy of life – Thomas Pradeu – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

Microbial Ecology

Engineering microbial consortia for controllable outputs – Stephen R Lindemann – ISME Journal

Review: The Anthropocene: a conspicuous stratigraphical signal of anthropogenic changes in production and consumption across the biosphere – Mark Williams – Earth’s Future

Book, all chapters written by Thomas CG Bosch and David J Miller. Not free of plagiarism and self-citing: The Holobiont Imperative: Perspectives from Early Emerging Animals – Springer

Bioinformatics and metagenomics

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data – Melanie Schirmer – BMC Bioinformatics

Microbes in the news

Bacterial biofilms in hospital water pipes may show pathogenic properties – Phys.org

Developed in Prince William, ISOThrive feeds human microbiome – Potomac Local

The first Truth is already not true: 3 Truths and a Lie About the Microbiome. Stick to the science if you want a healthy gut. – Megan Meyer – US News

The microbial death clock – Kai Kupferschmidt – Science
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March 13, 2016

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General microbiome

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Pregnancy and birth / Human vaginal microbiome

Review: The vaginal microbiota, host defense and reproductive physiology – Steven B Smith – The Journal of Physiology

Human gut microbiome

Review: Brain-Gut-Microbiota axis: Challenges for Translation in Psychiatry – John R. Kelly – Annals of Epidemiology

Editorial: The microbiome in celiac disease: Beyond diet-genetic interactions – Jose U. Scher – Cleveland Clinic Journal of Medicine
Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Heat-treated high-fat diet modifies gut microbiota and metabolic markers in apoe−/− mice – Nittaya Marungruang – Nutrition & Metabolism

Animal microbiome

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee – Quinn S. McFrederick – Molecular Ecology

Plant, root, and soil microbiome

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season – Dinggang Zhou – Frontiers in Plant Science

Succession of soil microbial communities and enzyme activities in artificial soils – Franziska Ditteric – Pedobiologia

Effect of copper and zinc on microbial tolerance to triclosan in two soil types – Gerty J. H. P. Gielen – Journal of Soils and Sediments

Microbial enzymes as an early warning management tool for monitoring mining site soils – Mohammad Wahsha – CATENA

Water and glacier microbiome

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – FEMS Microbiology Ecology

The Differing Biogeochemical and Microbial Signatures of Glaciers and Rock Glaciers – Timothy S. Fegel – Journal of Geophysical Research

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon – Florent E. Angly – PeerJ

Infection microbiology

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans – Salah Zangena – Scientific Reports

Viruses

RNA viruses as major contributors to Antarctic virioplankton – Jaclyn A Miranda – Environmental Microbiology

Review: Giant viruses of amoebas: an update – Sarah Aherfi – Frontiers in Microbiology

Microbial Ecology

Review: Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts – George Hajishengallis – Trends in Microbiology

Metagenomics and bioinformatics

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly – Paola Bonizzoni – Journal of Computational Biology

Microbes in the news

Cool Citizen Microbiology Project in Spain With Great Engagement – David Coil – Microbenet

Podcast: The Bacteria Behind Your Favorite Blues, Bries, and More – Science Friday

Science, publishing and career

Scientists who tweet: 3 Fred Hutch researchers talk about getting #science out into the world, 140 characters at a time – Mary Engel – Fred Hutch

This Student Adds A Woman In Science To Wikipedia Every Time She’s Harassed Online – Kelly Oakes – BuzzFeed

Bik’s Picks

Neandertals’ large lower thorax may represent adaptation to high protein diet – Miki Ben-Dor – American Journal of Physical Anthropology

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March 10, 2016

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Signals within microbial communities, feeding the microbiome with milk, gut metagenomes of Japanese subjects, multiethnic cohorts, biogeography of viruses in the sea, and finding transcription start sites.

General human microbiome

Review: Signaling in Host-Associated Microbial Communities – Michael A. Fischbach and Julia A. Segre – Cell

Review: The microbiome systemic diseases connection – T.A. van der Meulen – Oral Diseases

Review: The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance – Melinda M. Pettigrew – Annals of Epidemiology

Pregnancy and birth

The placental microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis – Amanda L. Prince – American Journal of Obstetrics and Gynecology

It’s in the Milk: Feeding the Microbiome to Promote Infant Growth – Stavros Bashiardes – Cell Metabolism

The Microbiome in Necrotizing Enterocolitis: A Case Report in Twins and Minireview –
Suchitra K. Hourigan – Clinical Therapeutics

Comment: Gut microbiome and necrotising enterocolitis: time for intervention? –
Alessio Fasano – The Lancet

Human oral microbiome

Not sure if I agree with the goal of this paper: Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms – Lamprini Karygianni – Frontiers in Microbiology

Human urinary tract microbiome

The Urinary Microbiome Differs Significantly between Patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as between Patients with Different Clinical Phenotypes – Daniel A Shoskes – Urology

Human gut microbiome

The gut microbiome of healthy Japanese and its microbial and functional uniqueness – Suguru Nishijima – DNA Research

Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype – Tyler, Andrea D. – Inflammatory Bowel Diseases

Perspective: Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease – J. Schulberg – Internal Medicine Journal

FMT Happens: Regulating Fecal Microbiota Therapy in Canada; What You Need to Know – Shahad Salman – World Medical & Health Policy

Review: Characterization of the Gut Microbiome in Epidemiologic Studies: The Multiethnic Cohort Experience – Benjamin C. Fu – Annals of Epidemiology

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Animal models

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes – Chenhong Zhang – ISME Journal

Review: Viruses in Rodent Colonies: Lessons Learned from Murine Noroviruses – Stephanie M. Karst – Annual Review of Virology

Animal microbiome

Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals – Teresita de J. Bello González – Frontiers in Microbiology

Allows the consumption of toxic cabbage: SaxA-mediated isothiocyanate metabolism in phytopathogenic Pectobacteria – Cornelia U. Welte – Applied and Environmental Microbiology

Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-Throughput Sequencing of the V4 Region of the 16S rRNA Gen (sic) – Yiping Zhao – Asian Australian Journal of Animal Sciences

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

I really feel for horses who are sick of grass.  Abstract: Analysis of the large intestinal and faecal microbiota of horses with grass sickness using denaturing gradient gel electrophoresis – D. Nölkes – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Phyllosphere Fungal Communities Differentiate More Thoroughly than Bacterial Communities Along an Elevation Gradient – Corinne Vacher – Microbial Ecology

A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system – Hui Lin – Environmental Pollution

Water and extremophile microbiome

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi – József Geml – FEMS Microbiology Ecology

Review: Biogeography of Viruses in the Sea – Cheryl-Emiliane T. Chow – Annual Review of Virology

DGGE: Oil removal and effects of spilled oil on active microbial communities in close to salt‑saturation brines – Yannick Y. Corsellis – Extremophiles

Bioreactors and waste microbiology

Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures – Haifeng Geng – Microbial Ecology

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters – Arda Gülay – ISME Journal

Bacterial communities in different locations, seasons and segments of a dairy wastewater treatment system consisting of six segments – Kikue Hirota – Journal of Environmental Sciences

Food microbiology

Resistome diversity in cattle and the environment decreases during beef production – Noelle R Noyes – eLIFE

Inactivation of Salmonella on tainted foods: using blue light to disinfect cucumbers and processed meat products – J. Stephen Guffey – Food Science & Nutrition

Bioinformatics and metagenomics

Review: Recovering complete and draft population genomes from metagenome datasets – Naseer Sangwan – Microbiome

Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics – Leandro D. S. Duarte – Methods in Ecology and Evolution

Transcriptomics

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome – Laurence Ettwiller – BMC Genomics

Fungi

Perspective: The invisible dimension of fungal diversity – David Hibbett – Science

Microbes in the news

At Stanford: Center launched to explore, exploit human microbiome – Bruce Goldman – Stanford Medicine

Columbia Expands Its Microbiome Research – Christopher Williams – Columbia University Medical Center

UT professor develops technique to enhance desirable traits of plants, animals through microbiology – Maluly Martinez Benavides – The Daily Texan

5th World Summit “Gut Microbiota For Health”: Media Information on Top Issues Ready for Download

Gut bacteria make cabbage poison harmless – Radboud University

Scientists developed a robust method for analysis of intestinal bacteria – Science Codex

Nukadoko: rich in beneficial bacteria: Nukadoko is made by fermenting rice bran, a byproduct of milling brown rice, with lactic acid bacteria and yeast. – Natsuko Tamaki – The Japan News

A mouse’s house may ruin experiments. Environmental factors lie behind many irreproducible rodent experiments – Sara Reardon – Nature

Viral infections may affect respiratory microbiome of patients with CF – Healio

Science, publishing, and career

German Defense Minister to keep doctoral degree – plagiarism found on 44% – Debora Weber-Wulff – Copy, Shake, and Paste

Bik’s Picks

How long can you chew on goat meat? Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans – Katherine D. Zink – Nature

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March 8, 2016

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A very special edition of Bik’s Picks on this International Women’s Day: Soil decomposition on Mount Kilimanjaro, genome of a Ruminococcus associated with IBS, survival of microbes during the digestion of cheese.

Human oral microbiome

Editorial: Oral Biofilm Architecture at the Microbial Scale – Maria D. Ferrer – Trends in Microbiology

Human reproductive tract microbiome

Cervical Microbiota Associated with Risk of Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses – Chandrika J Piyathilake – Cancer Prevention Research

Human gut microbiome

Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome – Ulla Hynönen – Anaerobe

Opinion: Gut microbiota impact on stroke outcome: Fad or fact? – Katarzyna Winek – J Cereb Blood Flow Metab

Review: Mechanisms linking the gut microbiome and glucose metabolism – Kristina M Utzschneider – J Clin Endocrinol Metab

Review: Gut Microbiome and Kidney Disease in Pediatrics: Does Connection Exist? – Tetyana L. Vasylyeva – Frontiers in Microbiology

Review: The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes – Mariia Taguer – Clinical Pharmacology & Therapeutics

Review: Obesity and Asthma: Microbiome-metabolome Interactions – Stephanie A Shore – American Journal of Respiratory Cell and Molecular Biology

Animal models

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens – Melody Y. Zeng – Immunity

Plant, root, and soil microbiome

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species – Christelle Lacroix – Applied and Environmental Microbiology

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis – Iris Bertani – Environmental Microbiology

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil-Associated Bacteria – Sachiko Masuda – Microbes and Environments

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil? – Minna Männistö – Soil Biology and Biochemistry

Temperature sensitivity and enzymatic mechanisms of soil organic matter decomposition along an altitudinal gradient on Mount Kilimanjaro – Еvgenia Blagodatskaya – Scientific Reports

Influence of pesticide seed treatments on rhizosphere fungal and bacterial communities and leaf fungal endophyte communities in maize and soybean – Rachel Nettles – Applied Soil Ecology

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum – Isabell von Rein – Global Change Biology

Water and extremophile microbiome

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean – Melinda P. Simmons – Applied and Environmental Microbiology

Metagenomic 16s rrna investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine – Oleksandra Bobrova – Acta Biochimica Polonica

Waste and pollution microbiology

Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing – Alison M. Cupples – Chemical Engineering & Technology

Food microbiology

Survival of lactic acid and propionibacteria in low- and full-fat Dutch-type cheese during human digestion Ex vivo – Aleksandra Martinovic – Letters in Applied Microbiology

Metagenomics and bioinformatics

Review: Targeted metagenomics of active microbial populations with stable-isotope probing -Sara Coyotzi – Current Opinion in Biotechnology

Infection and microbiology

Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach – Saskia Decuypere – PLOS Neglected Tropical Diseases

Microbes in the news

Fibre and protein enhance gut bacteria in children – Malene Sommer Christiansen – Science Nordic

Extreme Microbiome Project Aims to Characterize Microbes Living in Harsh Environments – Monica Heger – Genome Web

UTI bacteria use hooks to hang on inside you when you pee – Clare Wilson – New Scientist

Science, publishing and career

Statistical significance and its part in science downfalls – Hilda Bastian – PLOS Blogs

Microbiology and Nature in Video Games – Alex Alexiev – MicroBEnet

Tricon2016: The Microbiome: Sorting Out the Hype from the Hope – Bonnie Feldman – Storify

Leap day, giant viruses, and gene-editing – Dawn Field – Oxford University Press blog
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