Category Archives: Animal experiments

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 21, 2016

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Skin microbiome and cutaneous function, gut microbiota of children in Brazil, donor effects in FMT, how the gut prevents inflammation through PGE2, airborne microalgae and fungi, and bugs hiding in fruits and vegetables.

General microbiome

Review: Investigating a holobiont: Microbiota perturbations and transkingdom networks – Renee Greer – Gut Microbes

Pregnancy and birth

The effect of neutral oligosaccharides on fecal microbiota in premature infants fed exclusively with breast milk: A randomized clinical trial – Amir-Mohammad Armanian – Journal of Research in Pharmacy Practice

Perinatal Microbiomes Influence on Preterm Birth and Preterms’ Health: Influencing Factors and Modulation Strategies – Ruiz, Lorena – Journal of Pediatric Gastroenterology & Nutrition

Review: Probiotics in early life: a preventative and treatment approach
Askhan Hashemi – Food & Function

Human skin microbiome

Review: Shaping of cutaneous function by encounters with commensals – Emma Barnard – The Journal of Physiology

Human respiratory microbiome

Relevant for CF research: Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus – Benoit Briard – mBio

Human gut microbiome

Exclusive enteral nutrition in active pediatric Crohn disease: Effects on intestinal microbiota and immune regulation – Tobias Schwerd – Journal of Allergy and Clinical Immunology

Does the donor matter? Donor vs patient effects in the outcome of a next-generation microbiota-based drug trial for recurrent Clostridium difficile infection –
Arnab Ray – Future Microbiology

Gut microbiota differences in children from distinct socioeconomic levels living in the
same urban area in Brazil – Carolina Santos Mello – Journal of Pediatric Gastroenterology and Nutrition

Review: Practical Considerations and the Intestinal Microbiome in Disease: Antibiotics for IBD Therapy – Fedorak R.N. – Digestive Diseases

Editorial: Dietary metabolism, gut microbiota and acute heart failure – WH Wilson Tang – Heart

Animal models

Prostaglandin E2 constrains systemic inflammation through an innate lymphoid cell–IL-22 axis – Rodger Duffin – Science

Detection of peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis – Christopher B. Hergott – Blood

Intestinal Interleukin-17 Receptor Signaling Mediates Reciprocal Control of the Gut Microbiota and Autoimmune Inflammation – Pawan Kumar – Immunity

Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism – Thomas C. Fung – Immunity

Rhubarb extract prevents hepatic inflammation induced by acute alcohol intake, an effect related to the modulation of the gut microbiota – Audrey M. Neyrinck – Molecular Nutrition & Food Research

Impact of Ethanol and Saccharin on Fecal Microbiome in Pregnant and Non-Pregnant Mice – Matthew T Labrecque – Journal of Pregnancy Child Health

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community – Ilma Tapio – PLOS ONE

Review: The mouse gut microbiome revisited: From complex diversity to model ecosystems – Thomas Clavel – International Journal of Medical Microbiology

Review: Reversing Gut Damage in HIV Infection: Using Non-Human Primate Models to Instruct Clinical Research – Rosalie Ponte – EBioMedicine

Animal microbiome

Variability of the Sheep Lung Microbiota – Laura Glendinning – Applied and Environmental Microbiology

Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform – Si Hong Park – PLOS ONE

The Bacterial Community of Entomophilic Nematodes and Host Beetles – Sneha L. Koneru – Molecular Ecology

Plant, root, and soil microbiome

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub’ al Khali (the Empty Quarter), United Arab Emirates – Christopher P. McKay – PLOS ONE

Effects of long term rice straw application on the microbial communities of rapeseed rhizosphere in a paddy-upland rotation system – Caijuan Peng – Science of the Total Environment

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits –
L Bordez – Molecular Ecology

Arbuscular mycorrhizal fungi in Mimosa tenuiflora (Willd.) Poir from Brazilian semi-arid – Tancredo Augusto Feitosa de Souza – Brazilian Journal of Microbiology

The impact of tropical forest logging and oil palm agriculture on the soil microbiome – Binu M. Tripathi – Molecular Ecology

Drivers of phosphorus limitation across soil microbial communities – Petr Čapek – Functional Ecology

Decreasing Nitrogen Fertilizer Input Had Little Effect on Microbial Communities in Three Types of Soils – Hailing Yu – PLOS ONE

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups – Sarah Piché-Choquette – PeerJ

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and extremophile microbiome

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics – Shangjin Tan – Journal of Phycology

More, smaller bacteria in response to ocean’s warming? – Xosé Anxelu G. Morán – Proceedings of the Royal Society B

All of these are 16S rRNA gene amplicon based:
Profiling of microbial community of Odisha hot spring based on metagenomic sequencing – Archana Singh – Genomics Data
Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data
Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing – Archana Singh – Genomics Data
Metagenomic exploration of the bacterial community structure at Paradip Port, Odisha, India – Arnab Pramanik – Genomics Data

Air microbiome

Review: Airborne Microalgae: Insights, Opportunities, and Challenges – Sylvie V. M. Tesson – Applied and Environmental Microbiology

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices – Loïc Pellissier – Applied and Environmental Microbiology

Waste and pollution microbiology

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments – Emine Ertekin – Environmental Science & Technology

Managing microbial risks from indirect wastewater reuse for irrigation in urbanizing watersheds – Matthew Eric Verbyla – Environmental Science & Technology

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress – Daiana Lima-Morales – Applied and Environmental Microbiology

Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome – Daniel E. Ross – PLOS ONE

Sediment Bacterial Communities Associated with Anaerobic Biodegradation of Bisphenol A – Yuyin Yang – Microbial Ecology

Bioreactor microbiology

Nitrification at different salinities: Biofilm community composition and physiological plasticity – Blanca M. Gonzalez-Silva – Water Research

In vitro extraction and fermentation of polyphenols from grape seeds (Vitis vinifera) by human intestinal microbiota – Li Zhou – Food & Function

Food microbiology

Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers – Zahra S. Al-Kharousi – International Journal of Microbiology

Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food – Peng Chen – Genomics Data

More microbiology

Multispecies Swarms of Social Microorganisms as Moving Ecosystems – Eshel Ben-Jacob – Trends in Microbiology

A Deadly Path: Bacterial Spread During Bubonic Plague – Rodrigo J. Gonzalez – Trends in Microbiology

Correspondence: Bacterial Persistent Infection at the Interface between Host and Microbiota – Min Yue – Clinical Infectious Diseases

Microbes in the news

Immune study shows how gut keeps deadly infections at bay – Science Daily

Bacteria’s Achilles heel uncovered by single molecule chemistry – Phys.org

Tiny algae could block Metro Vancouver’s Roberts Bank container expansion. Migrating sandpipers depend on biofilm secreted by microscopic diatoms for fuel – Larry Pynn – Vancouver Sun

Systemic Antibody Responses To Oral Bacteria With Aging, University of Kentucky Study – BioSpace
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March 20, 2016

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Back in the PDT, so catching up with the literature.

Pregnancy and birth

In mice: The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Review: New techniques to characterise the vaginal microbiome in pregnancy – George L. Mendz – AIMS Microbiology

Perspective: The Placental Microbiome: A New Site for Policing Women’s Bodies – Saray Ayala – International Journal of Feminist Approaches to Bioethics

Review: Building a Beneficial Microbiome from Birth – Esther Castanys-Muñoz – Advances in Nutrition

Human oral microbiome

Microbiome associated with severe caries in Canadian First Nations children – EurekAlert

Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

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

FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial – Keith McIntosh – Gut

Tumour-associated and non-tumour-associated microbiota in colorectal cancer – Burkhardt Flemer – Gut
Review: Microbiota and lifestyle interactions through the lifespan – Simone Rampelli – Trends in Food Science & Technology

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanism and Application of Metabolomics – Xuyun He – Int J Mol Sci

Animal models

Effect of artesunate supplementation on bacterial translocation and dysbiosis of gut microbiota in rats with liver cirrhosis – Yun-Xia Chen – World Journal of Gastroenterology

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

Animal microbiome

Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure – Carl N. Keiser – Current Zoology

Review: Microbial diversity associated with ascidians: a review of research methods and application – Lei Chen – Symbiosis

Plant, root, and soil microbiome

Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity – Binu M. Tripathi – Frontiers in Microbiology

Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field – Muhammad Naveed – Applied Soil Ecology

Microbial community structure and nutrient dynamics in forest soils colonized by bracken fern (Pteridium aquilinum) – Manuel Aira – PeerJ Preprint

Evidence of horizontal gene transfer between obligate leaf nodule symbionts – Marta Pinto-Carbó – The ISME Journal

Bacteria-Soil-Plant Interaction: This Relationship to Generate can Inputs and New Products for the Food Industry – Jeremias Pakulski Panizzon – Rice Research

Microbial growth and community structure in acid mine soils after addition of different amendments for soil reclamation – R. Zornoza – Geoderma

Water and extremophile microbiome

Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy – Amy R. Smith – Geomicrobiology Journal

Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy – Emil S. Ruff – Frontiers in Microbiology

Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge – Xinxu Zhang – Frontiers in Microbiology

Built environment microbiology

Qualitative and Quantitative Analysis of Microbial Communities in Household Dishwashers in Germany – Britta Brands – Tenside Surfactants Detergents

Waste and pollution microbiology

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure – Halil Coban – Bioprocess and Biosystems Engineering

Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils – Santonu Kumar Sanyal

Techniques

Example used in this review paper: kombucha (?): DNA metabarcoding of microbial communities for healthcare – Zaets I. Ye – Biopolym Cell

Next-Generation Sequencing in the Mycology Lab – Jan Zoll – Current Fungal Infection Reports

Metagenomics

Identification of virulence factors and antibiotic resistance markers using bacterial genomics – Sofiane Bakour – Future Medicine

Microbes in the news

Gut health: Stanford researchers explain how what’s in our bellies affects myriad health issues – Martha Ross – Contra Costa Times

Inflamed, noninflamed mucosal microbiota differ between patients with Crohn’s disease, UC – Healio

Video: Six Strange Things Bacteria Eat – Wall Street Journal

Bacteria in your mom’s gut may have influenced the way you fight off infections today
Katherine Ellen Foley – Quartz

New technique for rapidly killing bacteria using tiny gold disks and light – Nanowerk

Bacteria-powered Bio-Bots Avoid Obstacles on Way to Target – MedGadget

Pneumonia, middle ear infections might be prevented by diverse bacteria in gut microbiome – Emily Lunardo – Belmarra Health

Going viral: IU Southeast student, teacher discover a new type of virus
Student, professor find new bacteriophage in Ohio River – Jerod Clapp – News and Tribune

Brucellosis-causing bacteria could be dropped from bioterrorism list – Helenair

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March 17, 2016

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Metagenomics of Necrotizing Enterocolitis, sinus irrigation, variation in mice in German facilities, and bacteria vs phage.

Pregnancy and birth

The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants – Doyle V. Ward – Cell Reports

Human respiratory microbiome

Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation – Leah J. Hauser – International Forum of Allergy & Rhinology

Human gut microbiome

Fecal Microbiota Transplantation in Children: A Brief Review – Suchitra K Hourigan – Pediatric Research

Forum: Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota – Tom Konikoff – Trends in Microbiology

Commentary: Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections – Richard L. Gallo – Journal of the American Academy of Dermatology

Review: Low calorie sweeteners and gut microbiota – Kristian Daly – Physiology & Behavior

Animal models

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities – Philipp Rausch – International Journal of Medical Microbiology

Plant, soil, and root microbiome

Plant versus microbial controls on soil aggregate stability in a seasonally dry ecosystem – Joseph C. Blankinship – Geoderma

Soil microbial communities following bush removal in a Namibian savanna – Jeffrey S. Buyer – Soil

Monitoring benthic microflora in river bed sediments: a case study in the Anllóns River (Spain) – Diego Martiñá Prieto – Journal of Soils and Sediments

Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States – Erin A. Tripp – Journal of Biogeography

Viruses and phages

Classic Spotlight: Bacteria versus Phage—the Battle Rages! – Tina M. Henkin – Journal of Bacteriology

Techniques

Review: Confocal Microscopy Imaging of the Biofilm Matrix – Sebastian Schlafer – Journal of Microbiological Methods

Metabolomics

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

Review: Challenges of metabolomics in human gut microbiota research – Kirill S. Smirnov – International Journal of Medical Microbiology

Microbes in the News

Subset of E. coli bacteria linked to deadly disease in pre-term infants – Medical Xpress

Our gut microbiome is always changing; it’s also remarkably stable – Science Codex

Meeting report: Microbes in the City: Mapping the Urban Genome – New York Academy of Sciences

Viral Infections May Affect Cystic Fibrosis Patients’ Respiratory Microbiome, Study Says – Daniela Semedo – Lung Disease News

Diverse diets enrich gut microbes – Catharine Paddock – Medical News Today

Mother’s Microbiome Shapes Offspring’s Immunity – The maternal gut microbiome guides neo- and postnatal immune system development, a mouse study shows – Anna Azvolinsky – The Scientist

How bacteria get their magnetic compass – Robert Sanders – Berkeley News

Science, publishing, and career

Blogging for beginners – Andrew David Thaler – Science

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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 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 12, 2016

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Microbiomes of farmland frogs and grape vine, and functional structures in acid mine drainage microbes.

Human oral microbiome

Ecological changes in oral microcosm biofilm during maturation – Young-Seok Kim – Journal of Biomedical Optics

Human gut microbiome

Review: Consequences of bile salt biotransformations by intestinal bacteria – Jason M. Ridlon – Gut Micobes

Review: The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder – Q. Li,- Neuroscience

Animal models

Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology – Qingqing Wang – PLOS ONE

Animal microbiome

Changes of diet and dominant intestinal microbes in farmland frogs – Chun-Wen Chang – BMC Microbiology

Plant, soil, and microbiome

Vitis vinifera microbiome: from basic research to technological development – Cátia Pinto – BioControl

Water and extremophile microbiology

Predicting taxonomic and functional structure of microbial communities in acid mine drainage – Jialiang Kuang – The ISME Journal

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences – Martin W Hahn – The ISME Journal

Waste and pollution microbiology

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing analyses – Yiwen Lin – Frontiers of Environmental Science & Engineering

Metabolomics

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease – Qiang Feng – Scientific Reports

Bioinformatics and metagenomics

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences – Alexey M Kozlov – BioRxiv

Microbial Ecology

Challenges in microbial ecology: building predictive understanding of community function and dynamics – Widder, S – White Rose Research Online

Microbes in the news

A cloud of distinction – Could the trails of microbes we leave behind be used to solve crimes? Julian Smith picks up the scent – Julian Smith  – New Scientist

Stick Out Your Tongue: Citizen science project draws up the first oral microbiome map for the youth: Over 4,000 people have taken part in this hands-on scientific project in Barcelona- EurekAlert

Biologicals in quest for 2050: BioConsortia is evaluating microbes that could help protect seedlings emerging in cold and wet conditions. – AgriView

Gut Microbiome Analysis for Detecting Colon Cancer Mutations – Univesrity of Minnesota

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March 11, 2016

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Posting from the airport – flying home to my folks for a week. I will try to keep you all updated, though! Fecal microbiota from dolphins (by another group!), microbes and Alzheimer’s, plastic-eating bacteria, and lead exposure.

Pregnancy and birth

State Scope of Practice Laws, Nurse-Midwifery Workforce, and Childbirth Procedures and Outcomes – Y. Tony Yang – Women’s Health Issues

Human oral microbiome

Characterization of a highly arginolytic Streptococcus species that potently antagonizes Streptococcus mutans – Xuelian Huang – Applied and Environmental Microbiology

The Microbiome of the Oral Mucosa in Irritable Bowel Syndrome – Nicolaas H. Fourie – Gut Microbes

Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus
Kun Wang – Scientific Reports

Human respiratory microbiome

Review: The lung microbiome and exacerbations of COPD – Dy, Rajany – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis – Hanneke Borgdorff – PLOS ONE

Human gut microbiome

The Microbiome, Intestinal Function, and Arginine Metabolism of Healthy Indian Women Are Different from Those of American and Jamaican Women – CC Kao – Journal of Nutrition

Fecal Microbiota Transplantation Inhibits Multidrug-Resistant Gut Pathogens: Preliminary Report Performed in an Immunocompromised Host – Jarosław Biliński – Archivum Immunologiae et Therapiae Experimentalis

The Intersection of TNF, IBD and the Microbiome – Yava L. Jones-Hall – Gut Microbes

Review: Bacterial species involved in the conversion of dietary flavonoids in the human gut – Annett Braune – Gut Microbes

Review: Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism – Douglas J. Morrison – Gut Microbes

Microbiome models

Perinatal lead (Pb) exposure alters gut microbiota composition and results in sex-specific bodyweight increases in adult mice – Jianfeng Wu – Toxicological Sciences

Castration influences intestinal microflora and induces abdominal obesity in high-fat diet-fed mice – Naoki Harada – Scientific Reports

Animal microbiome

The bottlenose dolphin (Tursiops truncatus) fecal microbiota – Matteo Soverini – FEMS Microbiology Ecology

Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes – Moritz Buck – Scientific Reports

Resistance to antimicrobial agents among enterococci isolated from fecal samples of wild marine species in the southern coast of Brazil – Janira Prichula – Marine Pollution Bulletin

Targeting eukaryote mitochondrial 16S rRNA gene: Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing – Kyle Logue – PLOS Neglected Tropical Diseases

Characterization of caecum and crop microbiota of Indian indigenous chicken targeting multiple hypervariable regions within 16s rRNA gene – S. Saxena – British Poultry Science

Plant, root, and soil microbiome

Nitrogen-fixing bacterial communities in invasive legume nodules and associated soils are similar across introduced and native range populations in Australia – Christina Birnbaum – Journal of Biogeography

Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors? – José A. Siles – Microbial Ecology

Interactions between Bacteria And Aspen Defense Chemicals at the Phyllosphere – Herbivore Interface – Charles J. Mason – Journal of Chemical Ecology

Long-term effects of multi-walled carbon nanotubes and graphene on microbial communities in dry soil – Yuan Ge – Environmental Science and Technology

Air and space station microbiome

Airborne Bacterial Diversity from the Low Atmosphere of Greater Mexico City – Jaime García-Mena – Environmental Microbiology

Characterization of Fungi Isolated from the Equipment Used in the International Space Station or Space Shuttle – Kazuo Satoh – Microbiology and Immunology

Water, waste, and pollution microbiology

A bacterium that degrades and assimilates poly(ethylene terephthalate) – Shosuke Yoshida – Science

The occurrence of PAHs and faecal sterols in Dublin Bay and their influence on sedimentary microbial communities – Brian T. Murphy – Marine Pollution Bulletin

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

Microbial Ecology

Phylogenetic organization of bacterial activity – Ember M Morrissey – The ISME Journal

Infection and microbiology

Editorial: Microbes and Alzheimer’s Disease – Ruth F. Itzhaki – Journal of Alzheimer’s Disease

Treatment of in vitro enterohemorrhagic E. coli infection using phage and probiotics – Cecilia Dini _ Journal of Applied Microbiology

Microbes in the news

These plastic-eating bacteria could help cut down on waste – Rachel Feltman – Washington Post

Some bacteria think plastic is fantastic – Nicholas S. Wigginton – Science

Science: Newly Identified Bacteria Break Down Tough Plastic – Michelle Hampson – AAAS News

Scientists identify a virus and two bacteria that could be causing Alzheimer’s – Fiona MacDonald – Science Alert

Lead exposure changes gut microbiota, increases chance for obesity – Laurel Thomas Gnagey – University of Michigan

These newly discovered bacteria can help prevent cavities, and scientists want to put them in a pill – Peter Dockrill – Science Alert

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

Emollient Treatment Improves Skin Microbiome in Atopic Dermatitis: Interview with Sophie Seite – Medical Research

Science, publishing, and career

The Frequency of “Brilliant” and “Genius” in Teaching Evaluations Predicts the Representation of Women and African Americans across Fields – Daniel Storage – PLOS ONE

Papers with simpler abstracts are cited more, study suggests – Dalmeet Singh Chawla – Retraction Watch
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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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