Priority effects determine community composition at the strain level in the honeybee gut microbiota

Gut microbial communities often differ at the strain level among individual hosts, but the mechanisms driving this variation remain poorly understood. One potential factor is priority effects, a process in which differences in the timing and order of microbial colonization influence subsequent community assembly (“first come, first served” dynamics). We hypothesize that such priority effects operate at the strain level within species, where closely related bacteria exhibit niche overlap, and that these dynamics can lead to community divergence even under similar environmental conditions. We tested these predictions, using the gut microbiota of honeybees, which harbor conserved microbial communities that differ in strain composition among individual bees. We sequentially colonized microbiota-depleted honeybees with two distinct microbial communities composed of the same twelve core microbiota species but different strains, ensuring that individuals shared species-level composition but differed at the strain level. We found that firstcomer strains consistently dominated the resulting communities, suggesting strong priority effects. Dropout experiments in which the firstcomer strain of a species was removed led to only partial increases in the colonization success of the conspecific latecomer, suggesting that both intra- and inter-species interactions contribute to priority effects. Our findings highlight the significant role of priority effects in strain-level community assembly and reveal their influence in shaping the specialized gut microbiota of honeybees, with important implications for the development of probiotic strategies in beekeeping.