Nature Microbiology

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02401-8 Evolved phage cocktails outsmart biofilm defences

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02408-1 Deep learning reveals that prion-related proteins contain hidden ‘prionin’ peptides with antibacterial activity, including two candidates that reduced infections in mice.

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02405-4 Prophage FRφ rewires the flagellar apparatus of its Enterobacter sp. host through RNA-guided repression of native flagellin, favouring its own phage-encoded isoform. This enhances host motility and reduces immune recognition, boosting bacterial fitness in mice.

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02402-7 Dietary lipids disturb colonic microbiota–mucus interactions and microbial transformation of host-derived bile acids. This altered bile acid pool triggers increased lipid absorption in the small intestine, revealing an unexpected link between the colonic mucus niche and small intestinal lipid metabolism.

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02382-8 A ubiquitous skin fungus, frequently associated with skin pathology, is important for maintenance of the skin barrier function through tryptophan derivatives that act as aryl hydrocarbon receptor agonists.

Nature Microbiology, Published online: 16 June 2026; doi:10.1038/s41564-026-02394-4 In mouse models, small intestine microbiota of children suffering from environmental enteric dysfunction is transmitted maternally and recapitulates growth defects by modulation of inflammatory pathways

Nature Microbiology, Published online: 16 June 2026; doi:10.1038/s41564-026-02417-0 Author Correction: A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice

Nature Microbiology, Published online: 15 June 2026; doi:10.1038/s41564-026-02389-1 Purine bias is critical for gene expression in bacteria, preventing premature transcription in species that exhibit runaway transcription.

Nature Microbiology, Published online: 12 June 2026; doi:10.1038/s41564-026-02373-9 Phage–bacteria coevolution is associated with field-specific anti-phage defence and locally adapted phage populations, resulting in phage-resistant but weakly virulent pathogens.

Nature Microbiology, Published online: 12 June 2026; doi:10.1038/s41564-026-02388-2 In a cerebral organoid model, Ebola virus persists by infecting neurons, astrocytes and microglia, driving local inflammation, cell-specific responses, viral adaptation and cell-to-cell spread.

Nature Microbiology, Published online: 12 June 2026; doi:10.1038/s41564-026-02384-6 The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of host cells through effector-triggered immunity.

Nature Microbiology, Published online: 12 June 2026; doi:10.1038/s41564-026-02380-w Metabolic modelling and experimental validation reveal that current probiotics lack the functional diversity of native microbes, identifying vaginal species that inhibit Gardnerella vaginalis through the dual mechanisms of resource competition and d-lactic acid production.

Nature Microbiology, Published online: 10 June 2026; doi:10.1038/s41564-026-02381-9 Higher lipid intake in mice causes damage to goblet cells with depletion of Akkermansia muciniphila and increase in Clostridium scindens abundance, which produces secondary bile acids that activate pathways driving increased intestinal fat absorption.

Nature Microbiology, Published online: 10 June 2026; doi:10.1038/s41564-026-02392-6 The poxvirus A16/G9 entry protein is shown to be a potent cross-protective antigen for incorporation into recombinant vaccines, but its immunogenicity in current live vaccines is restricted by the viral A56/K2 fusion suppressor complex.

Nature Microbiology, Published online: 09 June 2026; doi:10.1038/s41564-026-02400-9 In Bacillus subtilis, wall teichoic acids sustain rod shape by filling nanoscale pores in the cell wall. The presence of wall teichoic acids limits the activity of PBP1, a cell wall synthase that promotes isotropic (omnidirectional) growth, thereby maintaining the balance between circumferentially directed and iso…

Nature Microbiology, Published online: 04 June 2026; doi:10.1038/s41564-026-02396-2 Effective science communication can help scientists shape impactful research questions, and crucially it can foster curiosity, showcase the importance of research and encourage support and engagement from non-scientists.

Nature Microbiology, Published online: 03 June 2026; doi:10.1038/s41564-026-02375-7 Single-cell studies uncovered specialization of epithelial cells in intestinal defence. The epithelial cell-targeting cytokine IL-22 protected mice from cholera by promoting the genesis of mucus-secreting cells.

Nature Microbiology, Published online: 02 June 2026; doi:10.1038/s41564-026-02352-0 A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.

Nature Microbiology, Published online: 02 June 2026; doi:10.1038/s41564-026-02362-y Seawater contains a complex tapestry of metabolites, but for most, the microorganisms and pathways that process them remain unknown. A metabolomics analysis links a particular marine metabolite, homarine, to its bacterial degraders, genes and metabolic products, providing a roadmap for linking metabolites to micro…

Nature Microbiology, Published online: 01 June 2026; doi:10.1038/s41564-026-02378-4 Engineered Bacteroides thetaiotaomicron, Btbots, use a genetic AND circuit to sense nitric oxide and deoxycholic acid as inflammatory signal in the gut to release therapeutic molecules, TFF3 and IL-35, that alleviate colitis in mice.