The dynamics of honey bee queen microbiome and its mobilome under stress

Extensive research on honey bee workers’ microbiome has shown its significance for colony health. In contrast, the microbiome of the queen caste remains understudied despite its pivotal role as the single reproductive female. Here we explored the impact of honey bee workers and nutrition on the queen microbiome. Comparing metagenomes of queens from diverse locations we found the microbiome is predominantly shaped by the environment experienced early in life and comprises only four putative core bacterial species. Notably, our investigation revealed the presence of bacteriophages within the queen microbiome, and these phages bloomed in failed queens. To further understand how these mobile genetic elements shape the queen microbiome during stress, age-matched unmated queens were exposed to environmental conditions ranging from natural (with worker bees processing polyfloral pollen into royal jelly for queens) to unnatural (without workers and providing artificial diet to the queens). After 10 days, queen fitness, assessed through ovary weight, was reduced in queens without workers provisioning royal jelly. Interestingly, queens caged with workers processing artificial diet into royal jelly also exhibited reduced weight, suggesting that diet alone can alter queen fitness. Deep sequencing of worker and queen samples across the environmental stress gradient revealed changes in the bacterial community associated with diet and exposure to worker bees. We also discovered novel mobile genetic elements which differ in their abundance across the microbiome samples. Our results further underscore the significance of the mobilome in shaping the bacterial community of this important eusocial insect.