Good morning everyone! In today’s microbiome digest we have several reviews and research articles focused on the human microbiome, some animal studies, few interesting methods such as Kraken2 for 16S rRNA analysis, and Convolutional Neural Network for prediction of host phenotypes from microbial samples. Enjoy reading!!
General microbiome
Review: CRISPR screens in the era of microbiomes – François Rousset – Current Opinion in Microbiology
Chapter: Genetic Transformation of Fusobacterium nucleatum – Akihiro Yoshida – Methods in Molecular Biology
Perspective: Gut microbiota: a potential therapeutic target for Parkinson’s disease – José Fidel Baizabal-Carvallo – Neural Regeneration Research
Processing has differential effects on microbiota accessible carbohydrates in whole grains during in vitro fermentation – Caroline Smith – Applied Environmental Microbiology
Human gut microbiome
Gut microbiota and oral contraceptive use in overweight and obese patients with polycystic ovary syndrome – Nesrin Damla Eyupoglu – The Journal of Clinical Endocrinology and Metabolism
Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population – Siqi Ye – The Journal of Dermatology
Faecal microbiota transplantation for the treatment of diarrhoea induced by tyrosine-kinase inhibitors in patients with metastatic renal cell carcinoma – Gianluca Ianiro – Nature Communications
Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism – Amira Metwaly – Nature Communications
Review: The potential role of the gut microbiota in shaping host energetics and metabolic rate – Elle C Lindsay – Journal of Animal Ecology
Oral and respiratory microbiome
Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment– Marlos Barbosa-Ribeiro – Clinical Oral Investigation
2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals – Judith Neukamm – BMC Biology
Comparing the nasal bacterial microbiome diversity of allergic rhinitis, chronic rhinosinusitis and control subjects – Weigang Gan – European Archives of Oto-Rhino-Laryngology
Maternal Oral Health Influences Infant Salivary Microbiome – K. Ramadugu – Journal of Dental Research
Animal microbiome / Animal experiments
Dietary supplementation of sodium sulfate improves rumen fermentation, fiber digestibility and plasma metabolome through modulating rumen bacterial communities in steers – Yuchao Zhao – Applied Environmental Microbiology
Salmonella enterica serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses to Overcome Colonization Resistance in Swine – Danisa M Bescucci – Applied Environmental Microbiology
Germ-Free Conditions Modulate Host Purine Metabolism, Exacerbating Adenine-Induced Kidney Damage – Eikan Mishima – Toxins
Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression – Jichun Chen – International Journal of Molecular Sciences
Plant, root, and soil microbiome
Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied Environmental Microbiology
Water and extremophile microbiome
Dissolved microcystin release coincident with lysis of a Microcystis-dominated bloom in western Lake Erie attributed to a novel cyanophage – McKindles et al – Applied Environmental Microbiology
Methods
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome
Chapter: Predicting Host Phenotype Based on Gut Microbiome Using a Convolutional Neural Network Approach – Derek Reiman – Artificial Neural Networks
Techniques
Review: Application of Next Generation Sequencing in Laboratory Medicine – Yiming Zhong – Annals of laboratory medicine