This Review discusses the complex role of the gut microbe Akkermansia muciniphila in human health.

Gut microorganisms capable of producing ethanol cause alcohol intoxication, which can be corrected via faecal microbiota transplantation.

A short peptide derived from a commensal-fungal-secreted protein promotes repair in models of colon epithelial damage when delivered directly or via probiotic microbes.

Vaginal birth, exclusive breastfeeding and early contact with siblings promote colonization of the infant gut with bifidobacteria capable of producing aromatic lactates, a microbial and metabolite signal that is inversely related to the risk of allergen-specific sensitization and dermatitis later in life.

Whole-genome sequencing of polioviruses in Uganda following nOPV2 use showed high genetic stability and no sustained transmission, even though a rare double recombinant strain regained virulence, but did not spread due to high vaccination coverage.

A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

Experiments in mice and pigs revealed that l-theanine produced by Lactobacillus reuteri acts on host cells to increase the catabolism of branched-chain amino acids by stabilizing the expression of branched-chain amino acid transferases.

Vaginal birth, exclusive breastfeeding and early contact with siblings promote colonization of the infant gut with bifidobacteria capable of producing aromatic lactates, a microbial and metabolite signal that is inversely related to the risk of allergen-specific sensitization and dermatitis later in life.

Acanthamoeba polyphaga mimivirus generates a subcellular area in host cells that overcomes the mismatch between host and viral tRNA supply and demand.

A short peptide derived from a commensal-fungal-secreted protein promotes repair in models of colon epithelial damage when delivered directly or via probiotic microbes.

Jacob Smith interviews microbiologists from around the world for their insights about what’s next for the field. Despite numerous challenges, optimism and creativity are poised to usher in an exciting new era of microbiology.

Our January 2026 special issue commemorates the tenth anniversary of the journal and celebrates researchers, peer reviewers and readers from the microbiology community and beyond.

For the celebration of our tenth anniversary, Nature Microbiology asks the former editors to reflect on their time at the journal.

Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

A new community-led checklist provides reporting guidelines for microbiome research across environments.