Geographical and seasonal analysis of the honey bee microbiome

We previously showed that colonies of thriving and non-thriving honey bees co-located in a single geographically isolated apiary harboured strikingly different microbiomes when sampled at a single time point in the honey season. Here we profiled the microbiome in returning forager bees from 10-12 hives in each of 6 apiaries across the southern half of Ireland, at early, middle and late time points in the 2019 season. Despite the wide range of geographical locations and forage available, apiary site was not the strongest determinant of the honey bee microbiome. However, there was clear clustering of the honey bee microbiome by time point across all apiaries, independent of which apiary was sampled. The clustering of microbiome by time was weaker although still significant in three of the apiaries, which may be connected to their geographic location and other external factors. The potential forage effect was strongest at the second timepoint (June-July) when the apiaries also displayed greatest difference in microbiome ecological diversity. We identified bacteria in the forager bee microbiome that correlated with hive health as measured by counts of larvae, bees, and honey production. These findings support the hypothesis that the global honey bee microbiome and its constituent species support thriving hives.