Microbial dysbiosis in familial Crohn’s Disease, probiotic treatment of captive Colorado Toads, microbiome forecasting in the ocean, a new r package for phylogenetic trees, and MacArthur winner Dianne Newman.
General microbiome
Classic Spotlight: 16S rRNA Redefines Microbiology – Igor B. Zhulin – Journal of Bacteriology
Human vaginal microbiome
Microbiome Composition and Function Drives Wound-Healing Impairment in the Female Genital Tract – Alexander S. Zevin – PLOS Pathogens
Human respiratory microbiome
Clinical implications of microbial biofilms in chronic rhinosinusitis and orbital cellulitis – Niranjan Nayak – BMC Ophthalmology
Human gut microbiome
Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio
Prebiotic Effects of Xylooligosaccharides on the Improvement of Microbiota Balance in Human Subjects – Shyh-Hsiang Lin – Gastroenterology Research and Practice
Metformin and the Gut Microbiome in Diabetes – Sridevi Devaraj – Clinical Chemistry
Classic Spotlight: Bacteroides thetaiotaomicron, Starch Utilization, and the Birth of the Microbiome Era – George A. O’Toole – Journal of Bacteriology
Review: The human microbiome and juvenile idiopathic arthritis – Anouk Verwoerd – Pediatric Rheumatology
Animal experiments
A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens – Kavita J. Rangan – Science
Animal microbiome
Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity – Jordan G. Kueneman – Proceedings of the Royal Society B
Press: Probiotic treatment protects endangered Colorado toads from lethal fungal infection – University of Colorado Boulder
Plant, root, and soil microbiome
Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy – Keiji Watanabe – Springer Plus
Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico – Silvia Pajares – PeerJ
Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities – Haishui Yang – Journal of Ecology
Water microbiome
Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone – Stilianos Louca – PNAS
New model could point way to microbiome forecasting in the ocean – Science Daily
Built environment microbiome
Buzz Off! An Evaluation of Ultrasonic Acoustic Vibration for the Disruption of Marine Microorganisms on Sensor Housing Materials – Jonathan S. McQuillan – Letters in Applied Microbiology
Bioinformatics and metagenomics
MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples – Moreno Zolfo – Nucleic Acids Resarch
ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data – Guangchuang Yu – Methods in Ecology and Evolution
Techniques
This article is not about primer barcodes, but compares 16S rRNA V6 PCR/454 sequencing to V4 PCR/Illumina sequencing:
Choice of molecular barcode will affect species prevalence but not bacterial community composition – Karen Lebret – Marine Genomics
Webinar | Combating the “garbage-in-garbage-out” paradigm: The importance of library prep in next-gen sequencing workflows – Maura Costello – Science
Microbes in the news
Bacteria have sculpted the world we live in, and that’s why MacArthur winner Dianne Newman studies them – Deborah Netburn – LA Times
Book Review: “Let Them Eat Dirt: Saving Your Child from an Oversanitized World” provides suggestions for a microbially rich and healthy childhood – Anne Estes – Mostly Microbes
Professionally printed version of Gut Check:The Microbiome Game available for a limited time from MOBIO. See below for a chance to win a free copy! – Anne Estes – Mostly Microbes
New Research Collaboration Explores Microbiome of the Space Station – Astrobiology Magazine
Swarms of magnetic bacteria could be used to deliver drugs to tumors – Science Daily
How do antibiotic-resistant bacteria get into the environment? – Suzanne Young and Valerie Harwood – The Conversation
Using bacteria to clean up oil – Anmar Frangoul – CNBC
Penn: Plant-made Antimicrobial Peptide Targets Dental Plaque and Gum Tissues – Penn News
Bacteria Hysteria
Note: little science here other than a 1997 paper, but lots of promotion for a certain manufacturer of stainless steel coffee mugs. Proceed with caution:
You should be washing your coffee mug way more than you think – Melia Robinson – Business Insider
And this one quotes a study from 1994, which looked at plant-based, not plastic sponges that were deliberately inoculated with pathogens. Proceed with caution:
Loofahs Have More Bacteria Than You Think — In Fact, You Should Probably Throw Yours Out – Lily Feinn – Bustle
Science, publishing, and career
Mark Zuckerberg and Priscilla Chan announce $3 billion effort aimed at curing disease – Shayla Love – STAT News
With some of my tweets!
A future without women – no female Future Prize nominees – Carla Bleiker – Deutsche Welle
Microbiome Digest - Bik's Picks 