Nature Microbiology

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.

Nature Microbiology, Published online: 01 June 2026; doi:10.1038/s41564-026-02366-8 The scientific information ecosystem is dysbiotic, but the conditions for ecological succession towards a more diverse, inclusive and resilient ‘infobiome’ are present. Scientists, institutions and platform builders should act together.

Nature Microbiology, Published online: 28 May 2026; doi:10.1038/s41564-026-02370-y Deoxycholic acid 3-sulfate, a sulfated bile acid primarily produced by a gut commensal bacterium, Enterococcus raffinosus, strengthens the intestinal barrier, dampens inflammation and protects against paediatric sepsis in mice models.

Nature Microbiology, Published online: 27 May 2026; doi:10.1038/s41564-026-02355-x The prophage of a clinical Enterobacter isolate uses an RNA-guided transcription factor to alter flagellar composition, leading to enhanced bacterial motility and improved gut colonization in a mouse model.

Nature Microbiology, Published online: 27 May 2026; doi:10.1038/s41564-026-02372-w As population-scale microbiome studies become increasingly common, the need for strategies to actively involve and communicate results to participants effectively are needed to ensure future involvement, and to better inform and distribute the outcomes of research equitably.

Nature Microbiology, Published online: 27 May 2026; doi:10.1038/s41564-026-02377-5 By integrating DMS profiles, evolutionary trajectories and epidemiological data, a deep-learning framework enables the spatiotemporal prediction of emerging dominant SARS-CoV-2 variants.

Nature Microbiology, Published online: 27 May 2026; doi:10.1038/s41564-026-02363-x Structural analysis reveals that the type VI secretion system effector cargo is enclosed within hexameric Hcp3 rings that form sequentially to enable effector loading and delivery by the Pseudomonas aeruginosa H3-type VI secretion system.

Nature Microbiology, Published online: 26 May 2026; doi:10.1038/s41564-026-02348-w Public trust and policy impact depend on communication in local languages. Nonetheless, one language, English, dominates scientific publishing. Multilingual science communication is not outreach — it is part of research responsibility.

Nature Microbiology, Published online: 26 May 2026; doi:10.1038/s41564-026-02368-6 Wall teichoic acids confer rod shape in the Gram-positive model organism Bacillus subtilis by occluding pores in the cell wall, thereby preventing runaway isotropic (non-oriented) peptidoglycan synthesis.