December 24, 2018

Good morning everyone, Today’s digest mainly focusing on the methods such as SigClust a novel clustering algorithm, mm-tSNE a method for visualizing high-dimensional data and aMiAD – a novel microbial diversity association test. Additionally, several review articles and research using human as well as animal experiments showing the relationship of the gut microbiome in Alzheimer’s, Parkinson, atopic dermatitis, antidepressant and anti-inflammatory, heart failure, NAFLD, irritable bowel syndrome and colorectal cancer and their role in the protection against the acute arsenic toxicity. Enjoy Reading.

General microbiome

Review: The microbiome of the nose – Matthew Rawls – Annals of Allergy, Asthma, and Immunology

The Gut Microbiome in Food Allergy – William Zhao – Annals of Allergy, Asthma, and Immunology

Prenatal stress enhances postnatal plasticity: The role of microbiota – Sarah Hartman – Developmental Psychobiology

Review: The gut microbiome and heart failure – Adilah F. Ahmad – Current Opinion in Cardiology

Synthetic consortia of nanobody‐coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis‐associated diseases and co‐morbidities – Kenneth Timmis – Microbial Biotechnology

Gut microbiome

The gut microbiota-derived metabolite trimethylamine N-oxide is elevated in Alzheimer’s disease – Nicholas M. Vogt – Alzheimer’s Research & Therapy

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study – Martin Steen Mortensen – BMC Microbiology

Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis – Mahboobeh Mahdavinia – The Journal of Allergy and Clinical Immunology

Editorial: Emerging evidence linking the gut microbiome to neurologic disorders – Jessica A. Griffiths – Genome Medicine

Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa – Mun Fai Loke – Plos One

Review: Impact of maternal HIV exposure, feeding status, and microbiome on infant cellular immunity – Sonwabile Dzanibe – Journal of Leukocyte Biology

Review: Inherited nongenetic influences on the gut microbiome and immune system – Kathryn A. Knoop – Birth Defects Research

New insights into porcine milk N-glycome and the potential relation with offspring gut microbiome – Chunlong Mu – Journal of Proteome Research

Unraveling gut microbiota in Parkinson’s disease and atypical parkinsonism – Michela Barichella – Movement Disorders

Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease – Monika Rau – United European Gastroenterology Journal

Skin microbiome

A tryptophan metabolite of the skin microbiota attenuates inflammation in atopic dermatitis via the aryl hydrocarbon receptor – Jinlei Yu – The Journal of Allergy and Clinical Immunology

Nasal microbiome

Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota – Reed M. Stubbendieck – Applied and Environmental Microbiology

Plant Microbiome

Metabolic niches in the rhizosphere microbiome: New tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange – Richard P Jacoby – Journal of Experimental Botany

Animal experiments

Chronic stress-induced gut dysfunction exacerbates Parkinson’s disease phenotype and pathology in a rotenone-induced mouse model of Parkinson’s disease – Hemraj B.Dodiya – Neurobiology of Disease

Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties – Bruk Getachew – BMC Microbiology

Dietary l-Tryptophan Supplementation Enhances the Intestinal Mucosal Barrier Function in Weaned Piglets: Implication of Tryptophan-Metabolizing Microbiota – Haiwei Liang – International Journal of Molecular Science

In Vivo Effects of Einkorn Wheat (Triticum monococcum) Bread on the Intestinal Microbiota, Metabolome, and on the Glycemic and Insulinemic Response in the Pig Model – Francesca Barone – Nutrients

Diet-Independent Correlations between Bacteria and Dysfunction of Gut, Adipose Tissue, and Liver: A Comprehensive Microbiota Analysis in Feces and Mucosa of the Ileum and Colon in Obese Mice with NAFLD – Eveline Gart – International Journal of Molecular Science

Abnormality in Maternal Dietary Calcium Intake During Pregnancy and Lactation Promotes Body WEIGHT gain by Affecting the Gut Microbiota in Mouse Offspring – Ping Li – Molecular Nutrition Food Research

Bilberry anthocyanin extract promotes intestinal barrier function and inhibits digestive enzyme activity by regulating the gut microbiota in aging rats – Jing Li – Food and Function

The gut microbiome is required for full protection against acute arsenic toxicity in mouse models – Michael Coryell – Nature Communications

Gut microbiota was modulated by moxibustion stimulation in rats with irritable bowel syndrome – Xiaomei Wang – Chinese Medicine


Rapid analysis of metagenomic data using signature-based clustering – Timothy Chappell – BMC Bioinformatics

Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data – Xianchao Zhu – BMC Bioinformatics

Coupled dynamics of intestinal microbiome and immune system—A mathematical study – Akane Hara – Journal of Theoretical Biology

An adaptive microbiome α-diversity-based association analysis method – Hyunwook Koh – Scientific Reports

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