Utilizing a novel fecal sampling method to examine resistance of the honey bee (Apis mellifera) gut microbiome to a low dose of tetracycline

Disruption of host-associated microbial communities can have detrimental impacts on host health. However, the capacity of individual host-associated microbial communities to resist disturbance has not been well defined. Using a novel fecal sampling method for honey bees (Apis mellifera), we examined the resistance of the honey bee gut microbiome to disruption from a low dose of the antibiotic, tetracycline (4.5 μg). Prior to the experiment, bacterial communities from fecal samples were compared to communities from dissected whole guts of the same individuals to ensure fecal samples accurately represented the gut microbiome. Fecal samples were collected from lab-caged honey bees prior to, and five days after, tetracycline exposure to assess how antibiotic disturbance affected the communities of individuals. We used metrics of alpha and beta diversity calculated from 16S rRNA gene amplicon sequences to compare gut community structure. Low dose tetracycline exposure did not consistently change honey bee gut microbiome structure, but there was individual variation in response to exposure and specific taxa (one ASV assigned to Lactobacillus kunkeei and one ASV in the genus Bombella) were differentially abundant following tetracycline treatment. To assess whether individual variation could be influenced by the presence of tetracycline resistance genes, we quantified the abundance of tet(B) and tet(M) with qPCR. The abundance of tet(M) prior to tetracycline treatment was negatively correlated with change in community membership, assessed by difference in Jaccard dissimilarity over the five-day experiment. Our results suggest that the honey bee gut microbiome has some ability to resist or recover from antibiotic-induced change, specific taxa may vary in their susceptibility to tetracycline exposure, and antibiotic resistance genes may contribute to gut microbiome resistance.