In the wait of Christmas weekend and holidays, some quick reading for updates in microbiome field. Today’s digest include articles on improving metagenomic data analysis and integrating different -omics datasets; review article on potential of microbiome to address antimicrobial resistance and meta-analysis on benefits of probiotic supplements in kidney disease.

General microbiome

Microbiome as a tool and a target in the effort to address antimicrobial resistance – David A. Relman – PNAS

Gut microbiota and health: connecting actors across the metabolic system – F. Fava – Proceedings of the Nutrition Society

Dietary sugar silences a colonization factor in a mammalian gut symbiont – Guy E. Townsend II – PNAS

Human gut microbiome

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life – Tommi Vatanen – Nature Microbiology

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota – Bálint Kintses – Nature Microbiology

Fecal Microbiota Transplantation for the Critically Ill Patient – Berkeley N. Limketkai – Nutrition in Clinical Practice

Effects of probiotic supplements on the progression of chronic kidney disease: a meta‐analysis – Sibei Tao – Nephrology

Signatures within the esophageal microbiome are associated with host genetics, age, and disease – Nandan P. Deshpande – Microbiome

Human oral microbiome

Oral microbiomes in children with asthma and dental caries – Sergey V. Cherkasov – Oral Diseases

Animal experiments

Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity – Tulika Arora – Americal Journal of Physiology Endocrinology and Metabolism

Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome – Xiaoyun Wang – Cell Research

Antidepressant treatment modulates the gut microbiome and metabolome during pregnancy and lactation in rats with a depressive-like phenotype – Anouschka S. Ramsteijn – BioRxiv

Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer’s Disease using 16S rRNA gene and metagenomic sequencing analysis – Weijun Peng – Aging

Prebiotics and synbiotics – in ovo delivery for improved lifespan condition in chicken – M. Siwek – BMC Veterinary Research

The response of colonic mucosa-associated microbiota composition, mucosal immune homeostasis, and barrier function to early-life galactooligosaccharides intervention in suckling piglets – Jue Wang – Journal of Agricultural and Food Chemistry

Techniques

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis – Michael H. Schwartz – Nature Communications

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data – Nicole M. Davis – Microbiome

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy – Mohammad Sajjad Ghaemi – Bioinformatics

Introducing THOR, a model microbiome for genetic dissection of community behavior – Gabriel L. Lozano – BioRxiv

Microbes in the news

Prebiotics Benefit the Gut Microbiome of Both Children and Adults – Market watch

Non-microbiology picks

Technologies to address antimicrobial resistance – Stephen J. Baker – PNAS