Antibiotic treatment of honey bee colonies alters early gut microbiome assembly and induces persistent dysbiosis in newly emerged workers

Authors: Allen, Nathan; Copeland, Duan; Mott, Brendon; Erickson, Robert; Anderson, Kirk

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2025
Publication Date: 8/8/2025
Citation: Allen, N.O., Copeland, D.C., Mott, B.M., Erickson, R.J., Anderson, K.E. 2025. Antibiotic treatment of honey bee colonies alters early gut microbiome assembly and induces persistent dysbiosis in newly emerged workers. Scientific Reports. 15: Article 29031. https://doi.org/10.1038/s41598-025-12823-9.
DOI: https://doi.org/10.1038/s41598-025-12823-9

Interpretive Summary: The honey bee worker gut microbiome is an important factor in the health and behavior of the host. Dysbiosis in the gut has detrimental effects on worker bees, making workers and colonies less robust against further stressors. The gut microbiome is assembled during the first days of adult life, developing to a mature state within the first week in healthy bees. Species composition, spatial distribution in the gut, and temporal species succession patterns all follow predictable and consistent patterns, creating a recognizable healthy worker gut microbiome. Though these quantities change with the age, task, and diet of the host, the mature microbiome is robust to minor disturbances. Mechanisms driving healthy microbiome assembly remain unclear, but abiotic, host-microbe, and microbe-microbe interactions are likely important to this development. Worker microbiomes may be altered to a dysbiotic state through stresses such as nutritional insufficiencies, pathogen exposures, and antibiotics. Antibiotic use for control of bacterial diseases of larvae has been common beekeeping practice for decades, however unintended negative effects on the gut microbiota has been shown to decrease survivorship of affected workers and alter task-related behavioral patterns. Here, we examine succession of the worker gut microbiome across the first three weeks of adulthood in bees treated with the common beekeeper antibiotic tylosin. We found that both microbiome size and structure were significantly altered by tylosin treatment, and these did not recover to match control microbiomes by the time of typical foraging onset. Certain Bifidobacterium and Bombilactobacillus species were strongly depleted by treatment, creating persistent dysbiotic states. These results illustrate early microbiome assembly in the worker gut and the negative effects of Tylosin treatment on dynamic microbiome maturation.

Technical Abstract: The honey bee worker gut microbiome is an important factor in the health and behavior of the host. Dysbiosis in the gut has detrimental effects on worker bees, making workers and colonies less robust against further stressors. The gut microbiome is assembled during the first days of adult life, developing to a mature state within the first week in healthy bees. Species composition, spatial distribution in the gut, and temporal species succession patterns all follow predictable and consistent patterns, creating a recognizable healthy worker gut microbiome. Though these quantities change with the age, task, and diet of the host, the mature microbiome is robust to minor disturbances. Mechanisms driving healthy microbiome assembly remain unclear, but abiotic, host-microbe, and microbe-microbe interactions are likely important to this development. Worker microbiomes may be altered to a dysbiotic state through stresses such as nutritional insufficiencies, pathogen exposures, and antibiotics. Antibiotic use for control of bacterial diseases of larvae has been common beekeeping practice for decades, however unintended negative effects on the gut microbiota has been shown to decrease survivorship of affected workers and alter task-related behavioral patterns. Here, we examine succession of the worker gut microbiome across the first three weeks of adulthood in bees treated with the common beekeeper antibiotic tylosin. We found that both microbiome size and structure were significantly altered by tylosin treatment, and these did not recover to match control microbiomes by the time of typical foraging onset. Certain Bifidobacterium and Bombilactobacillus species were strongly depleted by treatment, creating persistent dysbiotic states. These results illustrate early microbiome assembly in the worker gut and the negative effects of Tylosin treatment on dynamic microbiome maturation.