A non-invasive method for profiling the gut microbiome and virome of honey bee queens

High honey bee colony mortality worldwide has underscored the critical role of queen bee health in colony survival, with poor queen quality frequently linked to colony losses. The gut microbiome plays fundamental roles in immunity, nutrition, and reproduction, making its characterization essential for understanding stressors that impact queen health, longevity, and fecundity, yet its role in mediating stress responses remains poorly understood. Here, we present a novel, non-invasive method for collecting feces from queen honey bees and demonstrate its potential as a powerful tool for profiling the gut microbiome, detecting stressor exposure, and screening for viral infections. We outline five key objectives: 1) determine the minimum number of fecal deposits required for successful 16S rRNA amplicon sequencing, 2) evaluate whether queen feces provide a reliable proxy for gut microbiome characterization; 3) explore the potential for fecal analyses to indicate exposure to temperature stress, 4) refine collection methods to improve DNA quality, and 5) assess the feasibility of using queen feces for virus screening. This approach provides a groundbreaking opportunity to repeatedly monitor the gut microbiome and virome of individual queens throughout their adult lifespan, assess their response to environmental stressors, and evaluate their health prior to importation and colony installation.