Honey bees are associated with gut microorganisms essential for their nutrition and health. The composition of the microbial community can be used as a biological health indicator and is characterized using biomarker fatty acids. Commonly, gut microorganisms are exposed to pathogens and to an array of chemical and biological pest control methods. RESULTS: We found a strong negative effect on microbial gut community composition when exposed to the bee pest control chemicals oxytetracycline, oxalic acid and imidacloprid, and when inoculated with the bee pest Nosema spp.