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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Microbiome Digest - Bik's Picks 