The Genome Exposome Microbiome–Phenome (GEM–P): a conceptual framework for social bees

The gut microbiome of social bees is a small, specific set of symbionts that contributes to nutrition, detoxification, immune function and behaviour, with effects on colony performance and resilience. In recent years, the field has expanded, but studies still analyse host genetics and environmental exposures separately and often rely on cor relations between microbes and health traits. This makes it difficult to distinguish when microbiome differences primarily reflect host or environmental factors from when they may contribute mechanistically to bee health. A key challenge is context dependence: similar microbiome shifts may be associated with different trait outcomes depending on life stage and task, exposure history, and colony transmission structure. We present the Genome Exposome Microbiome–Phenome (GEM–P) framework as an integrative organisational framework for social bees. GEM–P treats genome, lifetime exposures (exposome), and the gut microbiome as interacting components shaping phenotypes at both individual and colony scales. Phenotypes can, in turn, modify subsequent exposures and microbiome states. We use GEM–P to map evidence on genetic filtering, exposomal drivers, microbiome assembly and function, and phenotypic outcomes, and to highlight study designs that help distinguish among alternative biological pathways without requiring comprehensive multi-omics approaches. GEM–P provides a practical way to generate pathway-specific hypotheses and interpret microbiome–phenotype associations across contexts.