Tracking Microbiome Composition and Stability Across Indian Social Honeybees Foraging in a Homogeneous Mustard Crop Landscape.

Microbial communities are essential for host health and ecosystem stability. However, whether host identity or shared foraging resources shapes microbiome structure among co-occurring species remains poorly understood. We studied bacterial and fungal communities of four Indian honeybee species in a mustard monoculture resource condition, integrating behavioural observation-based pollinator data with microbial co-occurrence networks derived from metabarcoding. Microbiome composition was more strongly associated with host identity rather than with foraging behaviour, bee abundance, or landscape use. This has strong implications for how microbial sharing among co-occurring social honeybee species can be limited, thereby preventing them from influencing each other's microbiomes through shared foraging and driving variable pollinator health within a shared ecosystem. While core bacterial taxa were shared, relationships among bacterial cobionts, unlike those among fungal genera, remained species-specific. Microbial diversity, along with community structure and function, influenced network stability, with a highly modular microbial network of Apis cerana exhibiting more predicted network robustness to simulated perturbations. In summary, host-specific filtering shaped the microbiome more than resource homogenisation, with closely related species facing unique risks of disruption of microbial co-occurrence, with broader implications for vulnerability to microbiome imbalance, environmental stress, and emerging infections.