Gut metagenome raw sequence reads from Apis mellifera and Bombus spp.. Gut metagenome

The gut microbiome of bees is vital for the health of their hosts. Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections. We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey and bumble bee species in a suburban-rural landscape. We identified simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus. At the strain level, one G. apicola amplicon sequence variant (ASV 1) was widely shared across honey bees and bumble bees. However, we detected one G. apicola strain that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees. On the other hand, ASVs of S. alvi and Lactobacillus were more host specific, suggesting closer symbiotic relationships with their hosts. Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities from those of bumble bees, a likely a result of the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria that associate with Trypanosome and/or Vairimorpha infections in bees.