The microbiome is adding a new dimension to the understanding of evolutionary theory. According to the holobiont theory of evolution, selection acts on the genes of the host and on the microorganisms that he carries. In this perspective, multicellularity can arise both from the cooperation of genetically identical cells and genetically heterogeneous cells. Since several of the commensals we carry have a life cycle outside the host, this consideration requires to rethink commensalism in a much wider sense, expanding the limits of the host. Insects provide several examples of the degree at which the host coevolves with the microbiome. Recently there is increasing evidence indicating that fungal ecology includes the insect gut. During their evolution, invertebrates developed defence mechanisms against parasites and pathogens, improving their immune system. Although they lack an acquired immune component, as occurs in vertebrates thus relying only on an innate component, insects have expanded it upon traits of plasticity and adaptation against pathogens in the form of immune priming. The interaction between insects and fungi thus provides a useful example on how microorganisms can invade the host and pass from a passenger state to a commensal state, establishing a network of mutualistic interactions. In the attempt to address the mutual advantages of these dynamic interactions we will discuss how Saccharomyces cerevisiae strains can protect against bacterial infections both invertebrates and mammals by eliciting trained immunity. We will thus show how the presence of fungi can shape the bacterial insect microbiome, thus underlining the ecological relevance of this interaction. In this perspective, we will rethink how multicellular communities of genetically very different cells can be modelled and seen as a network of competitive and cooperative interactions, where the whole is made of interchangeable and disposable parts that can be acquired or lost, through the interaction with the environment.