Geographically widespread honeybee‐gut symbiont subgroups show locally distinct antibiotic‐resistant patterns

How long‐term antibiotic treatment affects host bacterial associations is still largely unknown. The honeybee‐gut microbiota has a simple composition, so we used this gut community to investigate how long‐term antibiotic treatment affects host‐associated microbiota. We investigated the phylogenetic relatedness, genomic content ( GC percentage, genome size, number of genes and CRISPR ) and antibiotic‐resistant genes (ARG) for strains from two abundant members of the honeybee core gut microbiota ( Gilliamella apicola and Snodgrassella alvi ). Domesticated honeybees are subjected to geographically different management policies, so we used two research apiaries, representing different antibiotic treatment regimens in their apiculture: low antibiotic usage (Norway) and high antibiotic usage (Arizona, USA ). We applied whole‐genome shotgun sequencing on 48  G. apicola and 22 S. alvi . We identified three predominating subgroups of G. apicola in honeybees from both Norway and Arizona. For G. apicola , genetic content substantially varied between subgroups and distance similarity calculations showed similarity discrepancy between subgroups. Functional differences between subgroups, such as pectin‐degrading enzymes ( G. apicola ), were also identified. In addition, we identified horizontal gene transfer ( HGT ) of transposon (Tn10)‐associated tetracycline resistance (Tet B) across the G. apicola subgroups in the Arizonan honeybees, using interspace polymorphisms in the Tet B determinant. Our results support that honeybee‐gut symbiont subgroups can resist long‐term antibiotic treatment and maintain functionality through acquisition of geographically distinct antibiotic‐resistant genes by HGT .