October 10, 2020

Good morning everyone! 

Highlights of today’s microbiome digest include: 

  • A genome-wide association study showed an association between host genetic variants and the gut microbiome in the Chinese population.
  • Association of sugar intake with the gut microbiome composition in the Malmö Offspring Study.
  • Gut microbial changes in Holstein cows from birth to adulthood.
  •  Fecal microbiome and antimicrobial resistance profiles in healthy Australian foals.
  • A new method for the detection of functional potential from metagenomic sequences.

Enjoy reading!

General microbiome

Review: Interactions among microbes, the immune system, and the circadian clock – John F. Brooks – Seminars in Immunopathology

https://link.springer.com/article/10.1007%2Fs00281-020-00820-1

Comment: Know Your Model: Microbiota & phenotypes – Michelle N. Perry – Lab Animal

https://www.nature.com/articles/s41684-020-00660-4

The wasted chewing gum bacteriome – Leila Satari – Scientific Reports

https://www.nature.com/articles/s41598-020-73913-4

A realism-based approach to an ontological representation of symbiotic interactions – Matthew Diller – BMC Medical Informatics and Decision Making

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-020-01273-0

Review: Multi-omics tools for studying microbial biofilms: current perspectives and future directions – Chaminda J. Seneviratne – Critical Reviews in Microbiology

https://www.tandfonline.com/doi/abs/10.1080/1040841X.2020.1828817?journalCode=imby20

Review: Challenges & opportunities for phage-based in situ microbiome engineering in the gut – Peter J Voorhees

https://www.sciencedirect.com/science/article/abs/pii/S0168365920303503?via%3Dihub

Human gut microbiome

Review: Modulation of the Microbiome in Parkinson’s Disease: Diet, Drug, Stool Transplant, and Beyond – Ethan G. Brown – Neurotherapeutics

https://link.springer.com/article/10.1007%2Fs13311-020-00942-2

Review: Gut microbiome and anorexia nervosa: The relationship between microbiome and gut-brain interaction in the context of anorexia nervosa – J. Seitz – Nervenarzt

https://link.springer.com/article/10.1007%2Fs00115-020-01003-x

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases – Fengzhe Xu – Microbiome

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00923-9

Gut microbiota composition in relation to intake of added sugar, sugar-sweetened beverages and artificially sweetened beverages in the Malmö Offspring Study – Stina Ramne – European Journal of Nutrition

https://link.springer.com/article/10.1007%2Fs00394-020-02392-0

Gut microbiome mediated epigenetic regulation of brain disorder and application of machine learning for multi-omics data analysis – Harpreet Kaur – Genome

https://cdnsciencepub.com/doi/10.1139/gen-2020-0136

Review: The Gut Microbiome and Bone Strength – Macy Castaneda – Current Osteoporosis Reports

https://link.springer.com/article/10.1007%2Fs11914-020-00627-x

Review: Effects of Antibiotic Treatment on Gut Microbiota and How to Overcome Its Negative Impacts on Human Health – Camila Fontoura Acosta Ribeiro

https://pubs.acs.org/doi/10.1021/acsinfecdis.0c00036

Mechanisms linking the human gut microbiome to prophylactic and treatment strategies for COVID-19 – Gemma E Walton- British Journal of Nutrition

https://www.cambridge.org/core/journals/british-journal-of-nutrition/article/mechanisms-linking-the-human-gut-microbiome-to-prophylactic-and-treatment-strategies-for-covid19/A3E1ADF2053768F34BCA72BF620AC86F

Oral and respiratory microbiome

Toll like Receptor signalling by Prevotella histicola activates alternative NF-κB signalling in Cystic Fibrosis bronchial epithelial cells compared to P. aeruginosa – Anne Bertelsen – PloS One

https://pubmed.ncbi.nlm.nih.gov/33031374/

Vaginal microbiome

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D Gerson – American Journal of Perinatology

https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0040-1717098

Animal microbiome / Animal experiments

Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin – Yan Xu – Current Microbiology

https://link.springer.com/article/10.1007%2Fs00284-020-02218-6

High-Fat Proteins Drive Dynamic Changes in Gut Microbiota, Hepatic Metabolome, and Endotoxemia-TLR-4-NFκB-Mediated Inflammation in Mice – Muhammad Ijaz Ahmad – J. Agric. Food Chem

https://pubs.acs.org/doi/10.1021/acs.jafc.0c02570

Dynamic change of the gastrointestinal bacterial ecology in cows from birth to adulthood – Chun Y. Guo – Microbiology Open

https://onlinelibrary.wiley.com/doi/10.1002/mbo3.1119

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

https://www.nature.com/articles/s41598-020-73827-1

Effects of inulin and isomalto-oligosaccharide on diphenoxylate-induced constipation, gastrointestinal motility-related hormones, short-chain fatty acids, and the intestinal flora in rats – Junhong Lan – Food & Function

https://pubs.rsc.org/en/content/articlelanding/2020/FO/D0FO00865F

Probiotic-fermented blueberry juice prevents obesity and hyperglycemia in high fat diet-fed mice in association with modulating the gut microbiota – Hao Zhong – Food & Function

https://pubs.rsc.org/en/content/articlelanding/2020/FO/D0FO00334D

Faecal microbiota and antimicrobial resistance gene profiles of healthy foals – Yuhong Liu – Equine Veterinary Journal

https://beva.onlinelibrary.wiley.com/doi/10.1111/evj.13366

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Lariviere-Gauthier – Letters in Applied Microbiology

https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/lam.13406

Probiotics / prebiotics

Review: Current status of probiotics for prevention and management of gastrointestinal cancers – Abdul Arif Khan – Expert Opinion on Biological Therapy

https://www.tandfonline.com/doi/abs/10.1080/14712598.2021.1828858?journalCode=iebt20

Plant, root, and soil microbiome

Characterization of the Leaf Microbiome from Whole-Genome Sequencing Data of the 3000 Rice Genomes Project – Veronica Roman-Reyna – Rice

https://thericejournal.springeropen.com/articles/10.1186/s12284-020-00432-1

Air, water and extremophile microbiome

Review: Urbanisation reduces the abundance and diversity of airborne microbes – but what does that mean for our health? A systematic review – Emily J. Flies – Science of The Total Environment

https://www.sciencedirect.com/science/article/abs/pii/S0048969720338596

Impact of a synthetic fungicide (fosetyl-Al and propamocarb-hydrochloride) and a biopesticide (Clonostachys rosea) on soil bacterial, fungal, and protist communities – BertrandFournier – Science of The Total Environment

https://www.sciencedirect.com/science/article/abs/pii/S0048969720331557

Methods

RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing – Zhikai Xing – Microorganisms

https://www.mdpi.com/2076-2607/8/10/1563

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