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

The gut microbiome of bees is vital for health of their hosts. Given the ecosystem functions done by bees, and declines faced by many species, it is of use to quantify natural variation in gut microbiome, the amount 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) was widely shared. ASVs of S. alvi and Lactobacillus were host specific, suggesting closer symbiotic relationships with their hosts. Honey bees exhibit different levels of alpha, beta and gamma diversities from bumble bees, likely driven by the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria that associate with Trypanosome and/or Nosema infections in bees.