February 8, 2020

Have a nice Saturday, everyone! Today, in this Digest: several reviews, including some of them about the microbiome and Irritable Bowel Syndrome, Autism, Chemotherapy, C. difficile infection and more. Additionally, there is a very interesting study (Obata et al., Nature), showing new evidence about the relationship between the microbiota, the gut, and the nervous system. 


Human and General Microbiome

Neuronal programming by microbiota regulates intestinal physiology – Yuuki Obata – Nature

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults – Samuel T. Westreich – The Journal of Nutritional Biochemistry

Review: Microbiome and Its Role in Irritable Bowel Syndrome – Mark Pimentel – Digestive Diseases and Sciences 

Review: Gut microbiota changes in children with autism spectrum disorder: a systematic review – Lucius Kang Hua Ho – Gut Pathogens

Review: Relationship Between the Gut Microbiome and Systemic Chemotherapy – Samantha M. Ervin – Digestive Diseases and Sciences 

Review: The infant gut microbiome as a microbial organ influencing host well-being – Francesca Turroni – Italian Journal of Pediatrics

Review: Increasing incidence of inflammatory bowel disease in children and adolescents: the significance of the environmental factors – Sowon Park – CEP

Review: Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection – Melina Kachrimanidou – Microorganisms (MDPI)

Review: Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review – Qi Yang – Nutrients

Opinion: Food, microbes, sex and old age: on the plasticity of gastrointestinal innervation – Tomotsune Ameku – Current Opinion in Neurobiology

The effects of proton pump inhibitors on the microbiome in young children – EI Levy – Acta Paedriatica

Targeted Approaches for In Situ Gut Microbiome Manipulation – Gail A. M. Cresci – JPEN

Dysbiosis of the Oral Ecosystem in Severe Congenital Neutropenia Patients – Egija Zaura – Proteomics Clinical Applications

Comparing Analytical Methods for the Gut Microbiome and Aging: Gut Microbial Communities and Body Weight in the Osteoporotic Fractures in Men (MrOS) Study – Michelle Shardell – The Journals of Gerontology: Series A

Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy – Medini K. Annavajhala – mSphere

Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients – J. Casper Swarte – Journal of Clinical Medicine

Comparison of serum microbiome composition in bipolar and major depressive disorders – Sang Jin Rhee – Journal of Psychiatric Research


Animal Microbiome / Animal Experiments

Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host – C. J. Newbold – Animal

Review: Comparative methane production in mammalian herbivores – M. Clauss – Animal

Review: Regulation of gastrointestinal and renal transport of calcium and phosphorus in ruminants – M. R. Wilkens – Animal

Degeneration of the intestinal microbial community in PI3Kγ-knockout mice – Yi Li – Microbial Pathogenesis

Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats – Juan Dai – Toxicology

Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections – Madeline A. Fujishiro – PLoS ONE

Time of Feeding Alters Obesity-Associated Parameters and Gut Bacterial Communities, but Not Fungal Populations, in C57BL/6 Male Mice – Marie van der Merwe – CDN

Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients – Fengping Liu – PeerJ


Beneficial Microbes and Compounds

Review: Surface components and metabolites of probiotics for regulation of intestinal epithelial barrier – Qing Liu – Microbial Cell Factories 

Polysaccharides from Polygonatum kingianum improve glucose and lipid metabolism in rats fed a high fat diet – Wen Gu – Biomedicine & Pharmacotherapy

Structural modulation of gut microbiota during alleviation of non-alcoholic fatty liver disease with Gynostemma pentaphyllum in rats – Shu-Hua Shen – BMC Complementary Medicine and Therapies


Plant Microbiome

Metagenomics methods for the study of plant-associated microbial communities: A review – Ayomide Emmanuel Fadiji – Journal of Microbiological Methods

Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome – Kenneth Acosta – PLoS ONE



Computational Modeling of the Human Microbiome – Shomeek Chowdhury – Microorganisms (MDPI)

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling – Valery V. Panyukov – International Journal of Molecular Sciences

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