Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!
General microbiome
A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports
Multi-site human microbiome
REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research
REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.
Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand
Human oral microbiome
Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports
Human skin microbiome
Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica
Human gut microbiome and virome
Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv
The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One
The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders
The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients
Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter
Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter
Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter
Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter
Metabolomics
REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology
Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Estaki et al. – bioRxiv
Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition
Animal microbiome (for animals in the wild)
No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports
Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal
Plant, root, and soil microbiome
The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Zolti et al. – Microbiology
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc
Built environment (subways, indoor surfaces)
Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation
Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology
Food microbiology
Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients
Bioinformatics/Resources
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research
Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications
Hi Microbiome Digest team, first a shout out to continuing this wonderful resource for us microbiome enthusiasts. I arrived to this particular page from an AltMetric link when I was looking at my recent pre-print only to find that the first author listing of the pre-print seems to credit the 2nd author instead of the first. Morck et al. – bioRxiv <- should be Estaki et. al. This is regarding the May 27 listing titled " Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice". I'm not sure if this is an automation derived error on your processing end or just an oversight but would be grateful for its correction. Thanks!
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Hi,
sorry, this was my mistake. I corrected it.
Best,
Axel
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Much appreciated!
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Hi Mehrbod,
It seems the post was already changed to reflect this. Thank you for bringing this to our attention!
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