Host and microbial factors influence bacterial colonization of the honey bee gut

The guts of many animals are colonized by host-specific microbes, yet the extent to which host filtering shapes microbial colonization and host specificity remains poorly understood. Here, we use gnotobiotic honey bees (Apis mellifera) as a model system to systematically assess the colonization potential of a phylogenetically and ecologically diverse panel of 56 bacterial strains. This panel included native symbionts, opportunistic bee-associated taxa, gut microbes from other bee species, and non-bee environmental isolates. Bacterial load was highest for native strains and declined with increasing phylogenetic distance from native core symbionts. Competition with other bacteria reduced load across all groups, but native strains were least affected. Completeness of shared KEGG metabolic pathways correlated with load in some taxa, but metabolic capacity alone did not fully explain patterns of host filtering. A key finding was that AMP sensitivity varied widely among strains and was highest in closely related bee-associated bacteria. Notably, even highly successful colonizers such as Gilliamella and Snodgrassella were AMP-sensitive. AMP sensitivity showed a negative correlation with bacterial load, but not with the frequency of host colonization. These findings suggest that AMPs modulate symbiont abundance rather than acting as strict barriers to colonization. Overall, our results reveal that host filtering in the bee gut is multifaceted, integrating immune-mediated barriers, microbial traits, and competitive interactions.