General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

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

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols