Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.
Events
2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA
Pregnancy and birth
Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports
Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology
Human skin microbiome
Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio
Human urinary tract microbiome
Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology
Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology
Human respiratory microbiome
Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases
Human gut microbiome
Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports
Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection
Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology
Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne
Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics
Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology
Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine
Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology
Models of microbiome research
Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS
Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio
Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology
Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports
More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports
Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition
Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract
Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology
Animal microbiome
Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology
Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports
Plant, root, and soil microbiome
Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology
Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma
Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports
Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology
Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography
Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology
Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science
Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science
Water and pollution microbiome
Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences
Built environment microbiome
Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology
Viruses and phages
Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology
Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters
Sequencing techniques
A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ
Bioinformatics and metagenomics
Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ
Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ
Metabolomics
Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics
More microbiology
Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE
Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports
Microbes in the news
Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News
Gut environment could reduce severity of malaria – EurekAlert
Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist
The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News
Plants trick bacteria into attacking too soon – Chris Samoray – Science News
Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine
Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire
Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert
Science, publishing, and career
Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews
I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science
Change the system to halt harassment – Joan Schmelz – Nature
Bik’s Picks
The peptidergic control circuit for sighing – Peng Li – Nature
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My apologies if this is documented somewhere, but what is the significance of the green links versus the blue links?
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Not documented anywhere, but the green links are articles that I featured in the first lines of each digest. Just to help the reader find those featured articles faster.
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Ah, never made the connection. Maybe highlight the summary in green as well to make a visual connection between the two? Or perhaps I’m the only one who didn’t figure it out. 🙂
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