Microbiota of migratory birds, blue fungus living in snow, migrating from SSU rRNAs to metagenomics.
Jobs
Awesome job at awesome institute: Postdoctoral Research Fellow, Microbiology – California Academy of Sciences
Human gut microbiome
Special issue of Trends in Food Science & Technology; several papers have appeared here before but worth checking out: Unravelling the role of the gut microbiome in energy balance and brain development and function: the European project MyNewGut
Review: Homeostasis of the Gut Barrier and Potential Biomarkers – Jerry M Wells – American Journal of Physiology, Gastrointestinal and Liver Physiology
Review: Challenges in simulating the human gut for understanding the role of the microbiota in obesity – M. Aguirre – Beneficial Microbes
Animal models
Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys – Xuan He – mSystems
Review: Dissecting the interplay between intestinal microbiota and host immunity in health and disease: Lessons learned from germfree and gnotobiotic animal models – Ulrike Fiebiger – European Journal of Microbiology and Immunology
Animal microbiome
* Changes in gut microbiota of migratory passerines during stopover after crossing an ecological barrier – William B. Lewis – The Auk
Plant, root, and soil microbiome
* Microbial Community Structure and Function of Soil following Ecosystem Conversion from Native Forests to Teak Plantation Forests – Vidya De Gannes – Frontiers in Microbiology
Drought tolerance of bioenergy grass Saccharum spontaneum L. enhanced by arbuscular mycorrhizae – P.P. Mirshad – Rhizosphere
Perspective: Microbiome selection could spur next-generation plant breeding strategies – Murali Gopal – Frontiers in Microbiology
Water and extremophile microbiome
Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean – Rene M. Boiteau – PNAS
Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments, Lake Baikal – S. M. Chernitsyna – Microbiology
Dampened copepod-mediated trophic cascades in a microzooplankton-dominated microbial food web: A mesocosm study – Bernadette Pree – Limnology and Oceanography
* Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica – Graciéle C. A. de Menezes – Extremophiles
Temporal variability of bacterial communities in cryoconite on an Alpine glacier – Andrea Franzetti – Environmental Microbiology Reports
Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP) – Michael Morando – Frontiers in Microbiology
Pollution microbiology
Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit – V. V. Kadnikov – Microbiology
Metagenomics and bioinformatics (viruses too)
MEGARes: an antimicrobial resistance database for high throughput sequencing – Steven M. Lakin – Nucleic Acids Research
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center – Alice R. Wattam – Nucleic Acids Research
Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences – Nathan A. Ahlgren – Nucleic Acids Research
* Crystal Ball: Migrating SSU rRNA gene surveys to the metagenomics era – Josh D. Neufeld – Environmental Microbiology Reports
Techniques
DNA extraction from benthic Cyanobacteria: comparative assessment and optimization – V. Gaget – Journal of Applied Microbiology
Microbial ecology
Microbial Community Coalescence for Microbiome Engineering – Matthias C. Rillig – Frontiers in Microbiology
More microbiology
How to Define Pathogenicity, Health, and Disease? – Mauno Vihinen – Human Mutation-Variation, Informatics, and Disease
Crystal Ball: Accessories make the microbe – Lisa Y. Stein – Environmental Microbiology Reports
Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data – Shiori Sagawa – bioRxiv
Microbes in the news
With my former Stanford co-worker Fiona Strouts: New farmers’ market baker knows art, science of bread-making. Stanford fellow brings baking know-how to Portola Valley farmers’ market – Dave Boyce – Mountain View Voice
New Mechanism to Control Human Viral Infections Discovered – Sean Nealon – University of California Riverside
Uterine microbiota play a key role in implantation and pregnancy success in in vitro fertilization – EurekAlert (see digest October 12)
Understanding microbiome impact on pig health – National Hog Farmer
Syphilis is coming back – Juha Wahlstedt – Clinical Laboratory Blogspot
Microbiome Digest - Bik's Picks 