Pregnancy and birth
Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity – Shaillay Dogra – mBio
Antimicrobial Protein and Peptide Concentrations and Activity in Human Breast Milk Consumed by Preterm Infants at Risk of Late-Onset Neonatal Sepsis – Stephanie Trend – PLOS ONE
Human oral microbiome
Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach – Toru Takeshita – Scientific Reports
Subgingival microbiota in health compared to periodontitis and the influence of smoking – A Camelo-Castillo – Frontiers in Microbiology
Human respiratory microbiome
Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis – Sébastien Boutin – PLOS ONE
Human gut microbiome
The networks of human gut microbe–metabolite associations are different between health and irritable bowel syndrome – Vijay Shankar – The ISME Journal
Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics
Animal microbiome
Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill – R.L. Simister – Deep Sea Research Part II: Topical Studies in Oceanography
Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms – J. Michael Day – PLOS ONE
Plant microbiome
Review: Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review – Youry Pii – Biology and Fertility of Soils
Soil microbiome
Changes in microbial properties and community composition in acid soils receiving wastewater from concentrated animal farming operations – Xiaoyan Ma – Applied Soil Ecology
Fine root decomposition, nutrient mobilization and fungal communities in a pine forest ecosystem – Ang Li – Soil Biology and Biochemistry
Experimental site and season over-control the effect of Pinus halepensis in microbiological properties of soils under semiarid and dry conditions – J. Hedo – Journal of Arid Environments
Water microbiome
Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – Limnology and Oceanography
Microbiome of the built environment
Pyrosequencing analysis of roof-harvested rainwater and river water used for domestic purposes in Luthengele village in the Eastern Cape Province of South Africa – Lizyben Chidamba, Lise Korsten – Environmental Monitoring and Assessment
Bioreactor microbiome
Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application – Valeria Ventorino – Scientific Reports
Food microbiology
Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches – Anna Greppi – International Journal of Food Microbiology
Techniques
PCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes – Shaun W. Lim – PLOS ONE
Bioinformatics, metagenomics
Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS – Martin S. Lindner, Bernhard Y. Renard – PLOS ONE
In peer-review: Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly – Priti Kumari – F1000Research
SFA-SPA: a suffix array based short peptide assembler for metagenomic data – Youngik Yang – Bioinformatics
A RESTful API for Accessing Microbial Community Data for MG-RAST – Andreas Wilke – PLOS Computational BIology
Review: New insight into the gut microbiome through metagenomics – Boyang Ji, Jens Nielsen – Advances in Genomics and Genetics
Book: Biocode: The New Age of Genomics
Phages and viruses
Rising to the challenge: accelerated pace of discovery transforms marine virology – Jennifer R. Brum & Matthew B. Sullivan – Nature Reviews Microbiology
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes – Joshua S Weitz – ISME Journal
The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae – Marine Henry – PLOS ONE
Microbes in the news
The Roots of Health – Episode 18: Microbiome Research & Applications with Dr. Embriette Hyde – Part 1 – WebTalkRadio
The Human Microbiome and Media Confusion – Science in the News – Harvard
Let’s Explore the World of Human Microbiome – Jason Carr – Wired Cosmos
Hospital Microbiome Project – Brent Stephens / Daniel Smith – Hospital Microbiome
Root of Lethal Bacterial Infection, Iron Overload Disease Link Identified – Jacquelyn Gray – HCP Live
Teaching phylogenetics with DUPLO – Erik Pelve – The Third Domain
How Can We Protect Mars From Earth, While Searching For Life? – Elizabeth Howell – AstroBio
Grape seed flour’s metabolic benefits linked to gut changes: Study – Stephen Daniells – NutraIngredients
Sell Your Poop For $13000 A Year And Help Save Lives: Here’s How You Can Do It – Jim Algar – TechTimes
Science, publishing, and career
From Scotland to Brazil: Making the decision (twice) – Julie Gould – Nature Jobs Blog
Los Alamos National Laboratory researcher gets 5 years in prison – Brooks Hays – UPI
A Future Segregated by Science? – Charles M. Blow – New York Times
Bik’s Picks
Walking on ice takes more than brains: ‘Mini-brain’ in spinal cord aids in balance – Science Daily
Surveying the Genomic Landscape of Modern Mammals
– Ricki Lewis – PLOS Blogs
Talking science with a doc, Hawkeye Pierce (with Alan Alda) – Sally Pollack – Burlington Free Press
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Microbiome Digest - Bik's Picks 