General microbiome

[REVIEW] Host–microbiota interactions in immune-mediated diseases – Ruff, Greiling and Kriegel – Nature Reviews Microbiology

[REVIEW] Diversity within species: interpreting strains in microbiomes – van Rossum et al. – Nature Reviews Microbiology

Animal microbiome

Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species – Ellegaard et al. – Current Biology

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study – Matejkova et al. – Scientific Reports

Characterization of Cutaneous Bacterial Microbiota from Superficial Pyoderma Forms in Atopic Dogs – Older et al. – Pathogens

Water and extremophile microbiome

Cryptic fungal diversity revealed in deep- sea sediments associated with whale-fall chemosynthetic ecosystems – Nagano et al. – Mycology

Bioinformatics

[PREPRINT] Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization – Goren et al. – bioarxiv

A Distance-Based Framework for the Characterization of Metabolic Heterogeneity in Large Sets of Genome-Scale Metabolic Models – Cabbia et al. – Patterns

FORENSIC: an Online Platform for Fecal Source Identification – Roguet et al. – mSystems

Techniques

Bacterial mock communities as standards for reproducible cytometric microbiome analysis – Cichocki et al. – Nature Protocols