All organisms in nature are targets for parasite attack. Symbiotic microbial species living within hosts can provide a strong barrier against infection, beyond the host’s own immune response. We now know that ‘protective microbes’ are key components of plant, animal, and human microbiota, determining host health in the face of parasite infection. The realisation that these microbes can evolve challenges our understanding of how hosts may resist infections diseases across evolutionary time. Thus far in the project, we have shown that the microbiota can facilitate infection and indeed worsen disease severity, advancing our thinking on microbiota-pathogen relationships. We have also discovered new ways in which microbes can evolve along the mutualist-parasite continuum to protect their host. We are currently using experimental evolution, followed by detailed genomic analysis, to understand the evolutionary and ecological dynamics of symbiotic interactions. We also evaluating the outputs with a view to pushing the conceptual boundaries for thinking about 'protective microbes' in environmental and clinical settings.