May 16, 2018

Today we have a interesting set of reviews. In addtion: research about virome in infants, microbiome changes in Alzheimer’s disease and changes in neonate and maternal microbiome under gestational diabetes. We have also the report of the Oral Microbiome Bank of China and some papers about invertebrate microbiome.  


Human/General Microbiome

Review: Microbiome-Immune Interactions and Liver Disease – James H. Tabibian –  Clinical Liver Disease

Review: Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications – Anne Hall – Journal of Pediatric Gastroenterology and Nutrition

Review: Starch Tolerance and the Short Bowel – Jan de Laffolie – Journal of Pediatric Gastroenterology and Nutrition

Review: Microbial Fermentation of Starch: Its Impact on the Range of Acceptable Carbohydrate Intake – Satish C. Kalhan – Journal of Pediatric Gastroenterology and Nutrition

Review: Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories – K. L. Stanhope – Obesity Reviews

Review: On the potential role of intestinal microbial community in hepatocarcinogenesis in chronic hepatitis B – Ashraf Mohamadkhani – Cancer Medicine

Review: The gut microbiota and the brain-gut-kidney axis in hypertension and chronic kidney disease – Tao Yang – Nature Reviews Nephrology

Review: Epithelial Barrier Dysfunctions in Atopic Dermatitis: A Skin-Gut-Lung Model Linking Microbiome Alteration and Immune Dysregulation – T.H. Zhu – British Journal of Dermatology

Review: Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions – Sheng Zhang – Journal of Cancer

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann​ – PeerJ

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus – Jinfeng Wang – Gut

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease – Sumathi Sankaran Walters – SOJ Microbiology & Infectious Diseases

Gut Microbiome is Altered in Patients with Alzheimer’s Disease – Zhuang, Zhen-Qian – Journal of Alzheimer’s Disease

The Oral Microbiome Bank of China – Peng Xian – International Journal of Oral Science


Animal Microbiome

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice – Maria Carolina S Mendes – World Journal of Gastroenterology

A cytokine network involving IL-36γ, IL-23, and IL-22 promotes antimicrobial defense and recovery from intestinal barrier damage – Vu L. Ngo – PNAS

Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome – Anja Malawi Brandon – Environmental Science and Technology

Supplementation with organic acids showing different effects on growth performance, gut morphology and microbiota of weaned pigs fed with highly or less digestible diets – S. Li – Journal of Animal Science

Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3”Me) – Xin Zhang – Molecular Nutrition and Food Research

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – Francisca Zepeda-Paulo​ – PeerJ

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts – Anne Duplouy – PeerJ

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution


Food Microbiome

The changes of dominant lactic acid bacteria and their metabolites during corn stover ensiling – Zhenshang Xu – Journal of Applied Microbiology

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing – Ziqiang Pan – Journal of Food Protection

Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers – Shan Duan – World Journal of Microbiology and Biotechnology



Preprint: Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysisPatricia Vera-Wolf (and featuring our Microbiome Digest founder, Elisabeth Bik)BioRxiv

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments – Alexandre Almeida – GigaScience

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – Molecular Ecology


Beneficial Microbes and Compounds

Review: Vitamin D in inflammatory bowel disease: more than just a supplement – John Gubatan – Current Opinion in Gastroenterology

Review: Bleach for Atopic Dermatitis – Melody Maarouf – Dermatitis

Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27 – Se-Eun Jang – Scientific Reports



Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen – Tim Rollenske – Nature Immunology


Environmental Microbiome (including Built environments)

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K.Nuy – Science of The Total Environment

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing – Lauren O’Connell​​ – PeerJ


Antimicrobial Resistance

Emerging Infectious Diseases, Antimicrobial Resistance and Millennium Development Goals: Resolving the Challenges through One Health – G. V. Asokan – Central Asian Journal of Global Health



Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins – Nitzan Koppel – eLife

The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase – Kemin Tan – Protein Science


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