Events
Bioinformatics for the Microbiome – Stanford Center for Genomics and Personalized Medicine – May 27, 2016
General microbiome
Microbiome sequencing: challenges and opportunities for molecular medicine – Thomas Clavel – Expert Review of Molecular Diagnostics
Human skin microbiome
An In vitro Model for Bacterial Growth on Human Stratum Corneum – Danique A. van der Krieken – Acta Dermato-Venereologica
Human respiratory microbiome
Launching into the Deep: Does the Pulmonary Microbiota Promote Chronic Lung Inflammation and Chronic Obstructive Pulmonary Disease Pathogenesis? – Marc A. Sze – American Journal of Respiratory and Critical Care Medicine
Human gut microbiome
Targeting the gut to protect the bladder: Oral Phage therapy approaches against urinary Escherichia coli infections? – Harald Brüssow – Environmental Microbiology
Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease – Takuo Emoto – Heart and Vessels
Review: Gut microbiota: an Indicator to Gastrointestinal Tract Diseases – Trupti Patel – Journal of Gastrointestinal Cancer
Review: Gut microbiome and kidney disease: a bidirectional relationship – Souhaila Al Khodor – Pediatric Nephrology
Animal models
Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice – Jin Li – Circulation
The effects of maternal and post-weaning diet on gut microbiota and glucose metabolism in mice offspring – Jia Zheng – Bioscience Reports
Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota – Brittany E. Harlow – PLOS ONE
Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows – Marija Kaevska – Canadian Journal of Microbiology
Molecular exploration of fecal microbiome in quinoa-supplemented obese mice – Jose F. Garcia-Mazcorro – FEMS Microbiology Ecology
Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice – Lovisa Heyman-Lindén – Food and Nutrition Research
The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems – Victor Schmidt – Applied and Environmental Microbiology
Insights into the biodiversity of the gut microbiota of broiler chickens – Leonardo Mancabelli – Environmental Microbiology
Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups – Wilma T. Steegenga – Molecular Nutrition & Food Research
Animal microbiome
Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan- Environmental Microbiology
Global microbialization of coral reefs – Andreas F. Haas – Nature Microbiology
Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria – Jan Hubert – Microbial Ecology
Review: Diagnosis and interpretation of intestinal dysbiosis in dogs and cats – Jan Suchodolski – The Veterinary Journal
Plant, root, and soil microbiome
Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea – Margrét Auður Sigurbjörnsdóttir – FEMS Microbiology Ecology
Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites – Frederic Mahe – bioRxiv
Edaphic properties override the influence of crops on the composition of the soil bacterial community in a semiarid agroecosystem – Luke D. Bainard – Applied Soil Ecology
Effects of land use change on the composition of soil microbial communities in a managed subtropical forest – Xiaoping Guo – Forest Ecology and Management
Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach – Nathaniel A. Lyngwi – PLOS ONE
Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems – Ian R Sanders – The ISME Journal
Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter – Thea Whitman – The ISME Journal
Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa – I. Moroenyane – Microbial Ecology
Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance – Cécile E. Thion – FEMS Microbiology Ecology
Ecological restoration alters microbial communities in mine tailings profiles – Yang Li – Scientific Reports
Water and extremophile microbiome
Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton – Mathias Milici – Frontiers in Microbiology
Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench – Jonathan Tarn – Frontiers in Microbiology
Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? – Mario Moreno-Pino – FEMS Microbiology Ecology
Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring – Zhou Jiang – Scientific Reports
Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – J. Goordial – Environmental Microbiology
Built environment microbiome
Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology
Food microbiology
Overlap of spoilage microbiota between meat and meat processing environment in small-scale vs large-scale retail distribution – Giuseppina Stellato – Applied and Environmental Microbiology
Fermentative capabilities and volatile compounds produced by Kloeckera/Hanseniaspora and Saccharomyces yeast strains in pure and mixed cultures during Agave tequilana juice fermentation – Ivonne Wendolyne González-Robles – Antonie van Leeuwenhoek
Pollution and waste microbiology
The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater – Scientific Reports – You-Wei Cui
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.– Alejandro Palomo – The ISME Journal
Bioinformatics and metagenomics
Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2 – Johan Bengtsson-Palme – Ecological Informatics
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data – Mohamed Mysara – BMC Bioinformatics
Minireview: Tracking strains in the microbiome: insights from metagenomics and models – Ilana L. Brito – Frontiers in Microbiology
Viruses and phages
Review: Endogenized viral sequences in mammals – Nicholas F. Parrish – Current Opinion in Microbiology
Probiotics
Probiotic Cream: Viability of Probiotic Bacteria and Chemical Characterization – Lutfiye Yilmaz-Ersan – Journal of Food Processing and Preservation
Transcriptomics
Use of Metatranscriptomics in Microbiome Research – Stavros Bashiardes – Bioinform Biol Insights
More microbiology
Complex molecular mixtures under cycling gradients as basis for lifes origins – Bert Poolman – bioRxiv
Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ – Laura Villanueva – Environmental Microbiology
Review: Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits – Kai Hillman – Current Opinion in Microbiology
Microbes in the news
Findings from the Gut—New Insights into the Human Microbiome – Karen Weintraub – Scientific American
What our gut tells us about the ‘hygiene hypothesis’ – Veronica Meade-Kelly – MedicalXpress
Russian scientists prove Antarctic bacteria brought from other continents – TASS
Beer made from belly button fluff has a bit of the brewer in every glass – Jenni Ryal – Mashable @7centBrewery
Yep, This Brewery Makes Beer Using Bacteria From People’s Belly Buttons: “7 cent Brewery” – Alec MacDonald – Elite Daily
Bacteria from Burning Tree mastodon survived 13,000 years – Laura Arenschield – Dispatch
Echo Bay woman caught harvesting bacteria at gardening event – Jeff Klassen – Soo Today
Weakened coral reefs are facing the threat of algae colonisation – Kemal Atlay – SBS Australia
Junk Food Is Bad For Plants, Too – How a steady diet of fertilizers has turned crops into couch potatoes – Anne Biklé and David R. Montgomery – Nautilus
From running shoes to carbon sinks: four surprising uses for algae – ABC Future Tense
Science, publishing, and career
“Everyone” Downloads Research Papers Illegally – Science magazine just published a great piece on the utility of Sci-Hub. Unfortunately, its defense of its own business model is flawed – Justin Peters – Slate
