Quite a few articles today especially in the plant/soil and water/extremophile sections. Plus: a new zebrafish model of the human gut microbiome, fiber and bifidos protect against north american diet-induced increased gut permeability in mice, prebiotics from the Morinda plant not only alter the gut microbiome but improve Alzheimers-like symptoms in a rat model, micro-eukaryotes may be an important factor in a deadly skin fungus infection in the Cascades Frog, and a new Leaf-FISH technique to visualize bacterial communities on plants. Happy Holidays!
Human oral microbiome
The oral microbiome—the relevant reservoir for acute pediatric appendicitis? – Carlotta Blod – International Journal of Colorectal Disease
Differences in carbon source usage by dental plaque in children with and without early childhood caries – Yan Zhao – International Journal of Oral Science
Review: Task Force on Design and Analysis in Oral Health Research: Host-Microbiome Interactions in Dysbiosis – T.E. Van Dyke – JDR Clinical & Translational Research
Human gut microbiome
Review: Probiotics and necrotizing enterocolitis – Ravi Mangal Patel – Seminars in Pediatric Surgery
*****************************
Animal experiments
Fusimonas intestini gen. nov., sp. nov., a novel intestinal bacterium of the family Lachnospiraceae associated with diabetes in mice – Hiroyuki Kusada – Scientific Reports
*Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota – Arias-Jayo Nerea – Zebrafish
*Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration – Bjoern O. Schroeder – Cell Host & Microbe
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host – William A. Bryant – Frontiers in Microbiology
*Prebiotic Effect of Fructooligosaccharides from Morinda officinalis on Alzheimer’s Disease in Rodent Models by Targeting the Microbiota-Gut-Brain Axis – Diling Chen – Frontiers in Aging Neuroscience
Animal microbiome
Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish – Anti Vasemägi – mSphere
*Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis – Jordan G. Kueneman – Frontiers in Microbiology
Plant, root, and soil microbiome
Chemical investigation of metabolites produced by an endophytic fungi Phialemonium curvatum from the leaves of Passiflora edulis – G. R. Nalin Rathnayake – Natural Product Research
Novel hydrocarbonoclastic metal-tolerant Acinetobacter and Pseudomonas strains from Aconcagua river oil-polluted soil – Valentina Méndez – Journal of soil science and plant nutrition
Spatial patterns of enzyme activities in the rhizosphere: Effects of root hairs and root radius – Xiaomin Ma – Soil Biology and Biochemistry
The rhizosphere microbial community response to a bio-organic fertilizer: finding the mechanisms behind the suppression of watermelon Fusarium wilt disease – Jia Zhao – Acta Physiologiae Plantarum
Efficiency of two inoculation methods of Pseudomonas putida on growth and yield of tomato plants – Luis G. Hernández-Montiel – Journal of soil science and plant nutrition
Rhizospere yeasts improve P uptake of a maize arbuscular mycorrhizal association – Marcela Sarabia – Applied Soil Ecology
Ammonia-oxidizing microorganisms: key players in the promotion of plant growth – Adenike Eunice Amoo – Journal of soil science and plant nutrition
Review: Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects A review – H. Etesami – Journal of soil science and plant nutrition
Long-term phosphorus fertilization effects on arbuscular mycorrhizal fungal diversity in Uruguayan grasses – Silvina García – Journal of soil science and plant nutrition
Alcaligenes faecalisassociated with Mimosa calodendron rizhosphere assist plant survival in arsenic rich soils – Érica Barbosa Felestrino – Journal of soil science and plant nutrition
Functional land-use change effects on soil fungal communities in Chilean temperate rainforests – César Marín – Journal of soil science and plant nutrition
Probiotic strain Stenotrophomonas acidaminiphila BJ1 degrades and reduces chlorothalonil toxicity to soil enzymes, microbial communities and plant roots – Qingming Zhang – AMB Express
Low light availability alters root exudation and reduces putative beneficial microorganisms in seagrass roots – Belinda C. Martin – Frontiers in Microbiology
Effects of biochar on nutrients and the microbial community structure of tobacco-planting soils – Gao Lin – Journal of soil science and plant nutrition
Root-associated bacterial and fungal community profiles of Arabidopsis thaliana are robust across contrasting soil P levels – Chanz Robbins – Phytobiomes
Water and extremophile microbiome
Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments – M.R. Mora-Ruiz del – Systematic and Applied Microbiology
Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology – Vijayakumar Somalinga – The American Biology Teacher
Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns – Clara López-Hermoso – Systematic and Applied Microbiology
Genome sequencing and heterologous expression of antiporters reveal alkaline response mechanisms of Halomonas alkalicola – Lei Zhai – Extremophiles
Benthic phototrophic community from Kiran soda lake, south-eastern Siberia – Ekaterina I. Burganskaya – Extremophiles
Enhancing the adaptability of the deep-sea bacterium Shewanella piezotolerans WP3 to high pressure and low temperature by experimental evolution under H2O2 stress – Zhe Xie – Applied and Environmental Microbiology
Fungal community structure at pelagic and littoral sites in Lake Biwa determined with high-throughput sequencing – Peixue Song – Limnology
Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula – Camila N. Signori – Deep Sea Research Part II: Topical Studies in Oceanography
Microbial Ecology
Dissertation: The Macroecology of Microorganisms: From Pattern to Process – David Clark – University of Essex
Review: Using metabolic networks to resolve ecological properties of microbiomes – Emilie E.L. Muller – Current Opinion in Systems Biology
Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose – Martina John – Scientific Reports
Built environment
Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers – Anna C. Llewellyn – PLOS one
Food microbiology
Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas – Kai-Yao Huang – BMC Systems Biology
Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks – Aaron M. Walsh – Applied and Environmental Microbiology
*****************************
Probiotics / prebiotics
Review: Recent Development of Prebiotic Research—Statement from an Expert Workshop – Giorgio La Fata – Nutrients
Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial – T. Nagino – Beneficial Microbes
Phages and viruses
Novel ssDNA viruses detected in the virome of bleached, habitat-forming kelp Ecklonia radiata – Douglas Beattie – Frontiers in Marine Science
Bioinformatics
Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples – Jake Lin – BMC Genomics
Techniques
*Leaf-FISH: Microscale imaging of bacterial taxa on phyllosphere – Elena L. Peredo – Frontiers in Microbiology
A new suite of plasmid vectors for fluorescence-based imaging of root colonizing pseudomonads – Rosemarie Wilton – Frontiers in Plant Science
Synthetic microbial consortia enable rapid assembly of pure translation machinery – Fernando Villarreal – Nature Chemical Biology
*****************************
Microbes in the news
Essential science: Link between gut microbes and despair – Tim Sandle – Digital Science
Enjoy the holidays, but don’t forget your fiber – Tim Sandle – Digital Science