Characterizing the bacteriophage of bumble bee gut symbionts

Bumblebees are essential pollinators. Gut bacteria are hypothesized to contribute to bumblebee health. Bacteriophage (phage) are viruses which infect bacteria. Phage influence the bacterial communities they infect via predator-prey dynamics and by transferring genes amongst their hosts. While recent studies have examined phage communities present in bee guts, these studies have been restricted to honeybees. As a result, the diversity of phage in the gut of bumblebees and how phage influence bee gut bacterial communities remain unexamined. Here we apply shotgun-metagenomic sequencing to characterize the diversity and function of phage present in the gut of both bumble and honeybees. Additionally, because applying viromic sampling to populations of wild insects is limited by the large input mass required for targeted viromes, we also test if total metagenomes recovered from individual bees can estimate the communities inferred from targeted viromes. To accomplish these objectives, we prepared targeted viromes and paired total metagenomes from 3 Bombus impatiens and 3 Apis melifera hives. To characterize the similarity of bumble and honeybee phage communities, we construct phage genome networks. To compare phage recovery between sampling methods, we compare the number and type of phage identified from both methods and visualize the similarity of virome and total metagenome inferred communities using beta-diversity ordinations. To the best of our knowledge, this is the first work to examine the phage communities associated with bumblebees and to test sampling methods for phage detection in bees. These outcomes will significantly advance our understanding of bee-phage communities.