ABSTRACT Animal microbiomes are shaped by a complex interplay of host genetics, environment, and lifestyle. Transitions of animals from wild to managed or domesticated conditions can impact the structure and function of their microbiomes. Among insects, the Western honey bee ( Apis mellifera ) is a promising model for studying these dynamics, given its long history of domestication and importance in agriculture. Despite extensive research on managed honey bee microbiomes, direct comparisons with wild populations remain scarce. Here, we compared the gut microbiomes of wild honey bee colonies from the Welder Wildlife Refuge in South Texas, which have remained unmanaged for over 30 years, with those from the closest managed apiary, located approximately 40 miles away. Using quantitative PCR and 16S ribosomal RNA gene sequencing, we found that managed bees harbored significantly higher bacterial loads but lower microbial diversity than wild bees. Although both groups shared a conserved microbiome dominated by core bacterial genera, distinct amplicon sequence variants and predicted metabolic pathway profiles differentiated them. Managed bee microbiomes were enriched in amino acid interconversion and antibiotic resistance-associated pathways, whereas wild bee microbiomes exhibited broader metabolic versatility, including amino acid biosynthesis and aromatic compound degradation. PCR screening further revealed a higher prevalence of tetracycline resistance markers in managed bees. Together, these findings indicate that long-term absence of human management and distinct ecological pressures shape honey bee gut microbiomes, influencing community composition and potentially functional capacity, underscoring the importance of natural environments to maintain microbial diversity and resilience. IMPORTANCE Understanding how human management shapes the microbiomes of domesticated species is essential for predicting their resilience to environmental stressors. Honey bees ( Apis mellifera ) are critical pollinators whose health and productivity are closely tied to their gut microbiota, but nearly all microbiome studies have focused on managed colonies. This study leverages the Welder Wildlife Refuge in South Texas, one of the few documented and well-studied sites in the United States where honey bee colonies have persisted unmanaged for decades, to directly compare managed and wild populations. We show that managed bees harbor higher bacterial loads but reduced microbial diversity and greater antibiotic resistance potential. These findings demonstrate that long-term absence of human intervention can preserve microbial diversity, offering insights into how domestication, antibiotic exposure, and environmental simplification influence the evolution and ecology of host-associated microbiomes.
Motta et al. (Thu,) studied this question.