Supplementary Tables

Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by the presence of a core gut microbiota composed of a few bacterial taxa. However, bumble bee gut microbiota taxonomic composition and community structure can vary with species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial <i>Bombus impatiens</i> suppliers, wild <i>B. impatiens</i>, and three other wild bumble bee species sampled from a portion of their native eastern North American range. We found that gut microbiota taxonomic community structure varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that <i>Apibacter </i>is consistently present in some wild bumble bee species—suggesting it may be a previously unrecognized core phylotype of bumble bees—and that commercial <i>B. impatiens </i>colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, high-level gut microbiota metabolic potential was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated. Overall, these results provide new insight into bumble bee gut microbiota community structure and function, and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species.