Divergent microbiome signatures in managed and wild honey bee populations in South Texas

Animal microbiomes are shaped by a complex interplay of host genetics, environment, and lifestyle, and transitions from wild to managed or domesticated conditions can impact microbial community structure and function. Among insects, the western honey bee (Apis mellifera) is a promising model for studying these dynamics, given its long history of domestication and critical role in agriculture worldwide. Despite extensive research on managed honey bee microbiomes, direct comparisons with wild populations remain scarce. In this study, we compared the gut microbiomes of wild honey bee colonies from the Welder Wildlife Refuge in South Texas, which have been unmanaged for over 30 years, with those from the closest managed apiary found approximately 40 miles away. Using quantitative PCR and 16S rRNA amplicon sequencing, we found that managed bees harbored significantly higher bacterial loads but lower microbial diversity compared to wild bees. Although both groups shared a conserved core microbiome dominated by key bacterial genera, distinct differences emerged at the amplicon sequence variant (ASV) level, with some ASVs uniquely associated with either managed or wild bees. Predicted metabolic pathway profiles further revealed divergent functional potentials, with wild bees exhibiting broader metabolic versatility including amino acid biosynthesis and aromatic compound degradation pathways. Our findings suggest that long-term absence of human management and differing ecological pressures may shape honey bee gut microbiomes, impacting both community composition and functional capacity. These results highlight the importance of natural environments in maintaining microbial diversity and resilience in honey bees, with implications for apiculture and conservation.