Honey bee microbiome associated with different hive and sample types over a honey production season

Western honey bees (Apis mellifera) are important pollinators in natural and agricultural ecosystems, and yet are in significant decline due to several factors including parasites, pathogens, pesticides, and habitat loss. A new beehive construction called the FlowTM hive was developed in 2015 to allow honey to be harvested directly from the hive without opening it, resulting in an apparent decrease in stress to the bees. Here, we compared the Flow and traditional Langstroth hive constructions to determine if there were any significant differences in the bee microbiome. The bee-associated bacterial communities did not differ between hive constructions and varied only slightly over the course of a honey production season. Samples were dominated by taxa belonging to the Lactobacillus, Bifidobacterium, Bartonella, Snodgrassella, Gilliamella, and Frischella genera, as observed in previous studies. The top ten most abundant taxa made up the majority of the sequence data; however, many low abundance organisms were persistent across the majority of samples regardless of sampling time or hive type. We additionally compared different preparations of whole bee and dissected bee samples to elaborate on previous bee microbiome research. We found that bacterial sequences were overwhelming derived from the bee guts, and microbes on the bee surfaces (including pollen) contributed little to the overall microbiome of whole bees. Overall, the results indicate that different hive constructions and associated disturbance levels do not influence the bee gut microbiome, which has broader implications for supporting hive health.