General microbiome

A 16th century Escherichia coli draft genome associated with an opportunistic bile infection – Long et al. – Communications Biology

Pregnancy and early life

[PREPRINT]Strong pathogen competition in neonatal gut colonisation – Mäklin et al. – bioRxiv

Human skin microbiome

Dysbiosis of Skin Microbiota with Increased Fungal Diversity is Associated with Severity of Disease in Atopic Dermatitis – Schmid et al. – JEADV

Human gut microbiome

Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China – Sun et al. – mSystems

A comprehensive analysis of the microbiota composition and host driver gene mutations in colorectal cancer – Yuan et al. – Investigational New Drugs

[REVIEW]Vegetarianism, Microbiota and Cardiovascular health: Looking back, and forward – Kumar et al. – European Journal of Preventive Cardiology

[REVIEW]Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis – So, Loughman & Staudacher – The American Journal of Clinical Nutrition

Profiling gut microbiota and bile acid metabolism in critically ill children – Kean et al. – Scientific Reports

Super-taxon in human microbiome are identified to be associated with colorectal cancer – Dai et al. – BMC Bioinformatics

The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease – Xu et al. – Gut Pathogenes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Immune checkpoint inhibitors unleash pathogenic immune responses against the microbiota – Hu et al. – PNAS

Deletion of both Dectin-1 and Dectin-2 affects the bacterial but not fungal gut microbiota and susceptibility to colitis in mice – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

Fecal microbiome of horses transitioning between warm-season and cool-season grass pasture within integrated rotational grazing systems – Weinert-Nelson, Biddle & Williams – Animal Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Full-Length 16S rRNA Gene Sequences from Raw Sewage Samples Spanning Geographic and Seasonal Gradients in Conveyance Systems across the United States – LaMartina, Schmoldt & Newton – Microbiology Resource Announcements

Techniques

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level – Ge et al. – PNAS