D3087: Evaluating genotypic and phenotypic strain variation among honey bee gut bacterial isolates

Western honey bees (Apis mellifera) are important pollinators, yet are threatened by a combination of factors such as poor nutrition, pesticide use, pathogens, and parasites. Similar to most organisms, the gut microbiome of the honey bee is important for host health, but it is not well known how environmental factors like pesticides impact these microbes. It is typically considered that the honey bee has low taxonomic complexity in the gut microbiota containing ~8 core bacterial genera, including Bifidobacterium, Lactobacillus, Snodgrassella, Bartonella, Apibacter, Frischella, Gilliamella, and Acetobacter. However, this culture-dependent study challenged the simplicity of the honey bee gut microbiome by examining strain variation of over 500 bacterial isolates acquired from the guts of six Western honey bees that occupied three different hives in the same environment. We evaluated genotypic strain variation by culturing on four media types and sequencing the 16S rRNA gene of the isolates, and compared that to phenotypic variation in their response to a common neonicotinoid pesticide, imidacloprid, by exposing a subset of isolates to various concentrations in 96-well plate assays and measuring growth. We obtained cultured representatives from nearly all of the core bacteria, and the majority of isolates exhibited reduced growth with imidacloprid compared to controls, while other isolates were robust to altered growth in the presence of the pesticide. Furthermore, isolates with identical 16S rRNA sequences had significantly different growth responses to pesticides, suggesting greater phenotypic variation and complexity within the honey bee gut microbiome.