Today we will honor #PenguinAwarenessDay with an older paper, but all others links are brand new. There is the cave microbiome, bacteria in fermented yak milk, and a warning about comparing data obtained in mouse models. Here we go:
Perspective: Where Next for Microbiome Research? – Matthew K. Waldor – PLOS Biology
Review: The Microbiome and Graft Versus Host Disease – Nathan Mathewson, Pavan Reddy – Current Stem Cell Reports
Review: The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill? – Lajos Rózsa – Biology Direct
Review: Prevention of Microbial Communities: Novel Approaches Based Natural Products – George D. Mogosanu – Current Pharmaceutical Biotechnology
Human respiratory microbiome
Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome – Arvind Venkataraman – mBio
Review (behind paywall, even at Stanford): Immunology, genetics and microbiota in the COPD pathophysiology: potential scope for patient stratification – Rajneesh Malhotra, and Henric Olsson – Expert Review of Respiratory Medicine
Human gut microbiome
Helicobacter pylori infection as a protective factor against multiple sclerosis risk in females – Marzena J Fabis Pedrini – J Neurol Neurosurg Psychiatry
Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers – A Lavelle – Gut
Review: The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases? – Gerardo Nardone, Debora Compare – United European Gastroenterology Journal
Pregnancy and birth
Review: Human Milk: Mother Nature’s Prototypical Probiotic Food? – Michelle K McGuire, and Mark A McGuire – Advances in Nutrition
Animal models of microbiome research
Perspective: How informative is the mouse for human gut microbiota research? – Thi Loan Anh Nguyen – Disease Models & Mechanisms
Attenuated portal hypertension in germ-free mice: Function of bacterial flora on the development of mesenteric lymphatic and blood vessels – Sheida Moghadamrad – Hepatology
High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy – Young Suk Kim – Anaerobe
Antibiotic perturbation: An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile – Matthew Miezeiewski – ISME J
Animal microbiome
This is a 2013 article, but I included it to honor today’s #PenguinAwarenessDay:
Interspecific variations in the gastrointestinal microbiota in penguins – Meagan L. Dewar – MicrobiologyOpen
Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata using functional metagenomics – María Alcaide – Applied and Environmental Microbiology
Plant microbiome
Structure, variation, and assembly of the root-associated microbiomes of rice – Joseph Edwards – PNAS USA
Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri – E. Marie Muehe – Applied and Environmental Microbiology
Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics – Martin Grube – ISME J
Soil microbiome
Profiling microbial communities in manganese remediation systems treating coal mine drainage – Dominique L. Chaput – Applied and Environmental Microbiology
Bacterial succession in paddy soils derived from different parent materials – Rong Sheng – Journal of Soils and Sediments
Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization – R. Zornoza – Geoderma
Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA# – Swathi A. Turlapati – Frontiers in Microbiology
Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust – Alberto Robador – Frontiers in Microbiology
Water microbiome
Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean – Mary Thaler and Connie Lovejoy – Applied and Environmental Microbiology
The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly – Chuck Pepe-Ranney, Ed Hall – BioRxiv
Catchment-scale biogeography of riverine bacterioplankton – Daniel S Read – ISME J
Microbiome of the built environment
Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas – I. Gandolfi – Applied Microbiology and Biotechnology
The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes – Yantian Ma – Nature Scientific Reports
A long-term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus – B.A. Potter – Letters in Applied Microbiology
Bioreactor microbiology
Groundwater Chemistry Determines the Prokaryotic Community Structure of Waterworks Sand Filters – Christian N. Albers – Environmental Science & Technology
Impact of Organic Load Shock on the Dynamic Transition of Microbial Communities During the Anaerobic Start-up Process – Jie Li – Energy Procedia
Food microbiology
High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk – Wenjun Liu – Annals of Microbiology
Viruses and phages
Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome – Bonnie L Hurwitz – ISME J
BSc thesis: Metagenomic study of the human gut virome during the first year of life – David Mayo Muñoz – Universitat Politecnica de Valencia
Metagenomics
Strong spurious transcription likely a cause of DNA insert bias in typical metagenomic clone libraries – Kathy N Lam, Trevor C Charles – BioRXiv
Commentary: Capturing bacterial chromosome conformation – Andrea Du Toit – Nature Reviews Microbiology
Metabolomics
Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology
Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology
Review: The Role of Colonic Bacteria in the Metabolism of the Natural Isoflavone Daidzin to Equol – Fatemeh Rafii – Metabolites
Microbes in the news
Can the Microbiome Mutiny? – Carl Zimmer – National Geographic
Fast-Paced Microbiome (about Rob Knight) – Genome Web
Researchers urge caution in studies of mice and microbes – Sarah DeWeerdt – SFARI
Gut microbes trigger autoimmune disease later in life in mice – Science Codex
Ulcer Bacteria Tied to Lower Multiple Sclerosis Risk in Women – HealthDay
Breweries partner with bacteria-detecting Philadelphia start-up – Diane Mastrull – Philly.com
New Species Discovered Beneath Ocean Crust – Robert Perkins – Pressroom USC
Ancient Viruses Gain New Functions in the Brain – Andrea Alfano – Scientific American
Science, publishing, and career
Is it Ph.D. or PhD? And are PhDs who act like MDs a special kind of douchebag? Twitter debates – Chris Seper – MedCityNews
Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? – Julie K. Pfeiffer – mBio
Don’t be that dude: Handy tips for the male academic – Tenure She Wrote
Science and art
Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu – Jonathan Eisen – The Tree of Life
Bik’s Picks
Exercise at depth alters bradycardia and incidence of cardiac anomalies in deep-diving marine mammals – Terrie M. Williams – Nature Communications
What’s Up With That: Birds Bob Their Heads When They Walk – Nick Stockton – Wired
Over 80 percent of Americans support “mandatory labels on foods containing DNA” – Ilya Somin – Washington Post
The Discoloration of the Taj Mahal due to Particulate Carbon and Dust Deposition – M. H. Bergin – Environmental Science & Technology
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Microbiome Digest - Bik's Picks 