Self-tracking the microbiome (quantified self), a human gut-on-a-chip model, indoor air bacteria in residences in the San Francisco Bay Area, and using probiotics on corals during oil spills.
General microbiome
Biometrics’ new identity—measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts – Andrea Rinaldi – EMBO Reports
Commentary: Self-tracking the microbiome: where do we go from here? – Carine Gimbert – Microbiome
Conference abstracts: 3th ISM World Congress on Targeting Microbiota – Journal of International Society of Microbiota Volume 1 No. 1
Pregnancy and birth
Buccal administration of human colostrum: impact on the oral microbiota of premature infants – K Sohn – Journal of Perinatology
Human mouth/ear microbiome
Pathophysiology of sinusitis of odontogenic origin – Silvio Taschieri – Journal of Investigative and Clinical Dentistry
Human gut microbiome
Different sub-type strains of Akkermansia muciniphila abundantly colonize in southern China – Xianfeng Guo – Journal of Applied Microbiology
Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome – Vijay Shankar – Microbiome
Mucosal Barrier Depletion And Loss Of Bacterial Diversity Are Primary Abnormalities In Paediatric Ulcerative Colitis – Misagh Alipour – Journal of Crohn’s and Colitis
Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection – Y.-T. Li – Alimentary Pharmacology & Therapeutics
Microbiome models
Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip – Hyun Jung Kim – PNAS
Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record
Animal microbiome
Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces – Liping Ma – Environmental Science & Technology
The impact of rearing environment on the development of gut microbiota in tilapia larvae – Christos Giatsis – Scientific Reports
The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni – Katie A. Clayton – Parasites & Vectors
Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota – Henrique Fragoso ados Santos – Scientific Reports
Plant, root, and soil microbiome
Stronger warming effects on microbial abundances in colder regions – Ji Chen – Scientific Reports
Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe – T. I. Chernov – Eurasian Soil Science
Water and extremophile microbiome
Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W. Hugerth – Genome Biology
Similar microbial communities found on two distant seafloor basalts – Esther Singer – Frontiers in Microbiology
Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades – Michael D. Lee – Frontiers in Microbiology
Bacterioplankton dynamics within a large anthropogenically impacted urban estuary – Thomas C. Jeffries – Frontiers in Microbiology
Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing – Savvas Genitsaris – Marine Biology Research
Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths – Sarah Ben Maamar – Frontiers in Microbiology
Review: Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes – Virginia Helena Albarracín – Photochemistry and Photobiology
Food microbiology
Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations – Jinshui Zheng – Scientific Reports
Built environment microbiology
Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences – Marzia Miletto – Microbiome
Review: Antibiotic resistance in urban aquatic environments: can it be controlled? – Célia M. Manaia – Applied Microbiology and Biotechnology
Metagenomics, phages, and bioinformatics
Computational approaches to predict bacteriophage–host relationships – Robert A. Edwards – FEMS Microbiology Reviews
Partial least squares regression can aid in detecting differential abundance of multiple features in sets of metagenomic samples – Ondrej Libiger – Frontiers in Genetics
Techniques
A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys – Rebecca C Mueller – FEMS Microbiology Ecology
Biofilms
Classic Spotlight: Before They Were Biofilms – George A. O’Toole – Journal of Bacteriology
Microbes in the news
How Bacteria and Brown Fat Can Spur Weight Loss – Mandy Oaklander – Time
A cultural revolution in the study of the gut microbiome – Medical Xpress
Italian olive trees are withering from this deadly bacteria – PBS Newshour
Behind the scenes: Microbial biogeography of a university campus – Ashley Ross – MicroBEnet
Irish company makes biggest breakthrough for microbiology testing in dairy industry in 100 years – Independent Ireland
Bacteria, Archaea – Some Methane In Hydraulic Fracturing Is Even More Natural Than Assumed – Science 2.0
Sweet and sticky: Bacteria use sugars to bind to human cells – Phys.org
Science, publishing, and career
The Unwritten Code of Conduct: Each day this week, my supervisor has walked into my office and made verbal demands that I remove content from my beloved blog – The Research Whisperer
A lesson on misleading graphs from the National Review – Lenny Teytelman – The Spectroscope
Women in STEM research: Better Data and Information Sharing Could Improve Oversight of Federal Grant-making and Title IX Compliance – US Government Accountability Office
Why do scientists like anonymity? Lenny Teytelman – Protocols
[hr]
Microbiome Digest - Bik's Picks 