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Abstract The aim of this study is to compare the bacterial load in the guts of honey bees supported and unsupplemented with probiotic supplements. To investigate the effects of a commercial bee probiotic containing different Lactobacillus species and different spice extracts on the composition of the gut microbiota of honey bees, QPCR counts of Lactobacillus spp. and Firmicutes phylum gene copies in gut mixtures from 12 different bee groups with and without probiotic supplementation were performed. There was a significant difference between the levels of Lactobacillus spp. in the guts of both groups. When Lactobacillus spp. levels in the guts of honey bees not given probiotics were compared to the Lactobacillus spp. levels in the guts of honey bees given probiotics, it was determined that there was an approximately 5.5-fold difference. However, it was observed that there was no significant difference in the Firmicutes load in the bee guts of both groups. These findings show that the applied probiotic formulation significantly affects the intestinal microbiome of healthy individuals and provides a proportional change in microbial abundance, especially in terms of Lactobacillus spp.