Antibiotics play a critical role in managing bacterial and parasitic infections that may threaten colony health. They are an important tool that beekeepers use to manage disease, but their effects can extend beyond harming pathogens. These treatments may also disrupt the beneficial microbes that bees rely on for digestion, immunity and survival.

Bee-ware: Antibiotics and Gut Health

To treat Nosema disease in honey bees, the only approved antimicrobial in North America is Fumagillin-B ®. This compound, derived from the fungus Aspergillus fumigatus, has been shown to reduce the prevalence and intensity of Nosema spp. infections ¹. Fumagillin is typically administered in the fall or spring, depending on colony needs and label recommendation ¹. Fumagillin-B works by targeting a protein in the parasite called methionine aminopeptidase type 2 (MetAp-2) ² . This protein is essential for Nosema spp. spore development, and by inhibiting it, Fumagillin disrupts the parasite’s life cycle ². 

Figure 1: Picture of Nosema spp. spores viewed under a microscope (400x). As an example, the arrow indicates a single spore (ATTTA©, 2025)

Another antibiotic that is used in beekeeping is oxytetracycline hydrochloride (OTC). It has been used to manage European Foulbrood (EFB) and American Foulbrood (AFB) ³. Oxytetracycline works as a bacteriostatic antibiotic, meaning it restricts the bacteria from growing and interferes with protein synthesis ³. However, it has also been found to reduce core gut bacteria like Bifidobacteria , which supports digestion and immune signaling ⁴. Bifidobacteria is an important bacterium that plays a role in the digestion and metabolism of a variety of plant-produced carbohydrates ⁸.

This disruption of the gut microbiome, known as dysbiosis, can have serious consequences. For example, a study showed that honey bees treated with an antibiotics, penicillin-streptomycin, showed reduced expression of genes responsible for producing antimicrobial peptides (AMPs), compared to bees who were infected with Nosema ceranae ⁵. This can lead to a weakened immune system, as AMPs play a critical role in immune defense ⁵. Another study found that bees infected with Nosema spp. and treated with antibiotics had higher spore loads and more severely disrupted gut bacteria ⁶. Long-term use of antibiotics like oxytetracycline has also been linked to a reduction in genetic diversity among core bacteria, such as Gilliamella ⁷. This bacterium is important for producing pyruvate, which is essential for the break down of glucose ¹¹.

The effects of dysbiosis go beyond just gut health. A disrupted microbiome, whether caused by disease or antibiotics, may lead to greater susceptibility to pathogens, disrupted expression of developmental genes, and compromised immune function ⁸. Disruption of the gut microbiome has also been associated with increased loads of other parasites, such as Lotmaria passim, in adult honey bees ⁹. These effects can weaken the entire colony, especially if antibiotics are used without a plan.

Another concern with frequent antibiotic use is the development of antibiotic resistance. In both North America and Argentina, where oxytetracycline is commonly used, resistance has been reported in Paenibacillus larvae, the bacteria which causes American Foulbrood ⁹. Following antibiotic use, resistance genes in the gut microbiome have been shown to increase ¹⁰. These genes may spread between colonies through cross-contamination, and residues of antibiotics have been detected in the environment ⁹. When antibiotics are overused, pathogens can evolve resistance, making it significantly more difficult to treat infections effectively.

That is why it is so important to only treat when necessary and to support bees afterwards. A healthy gut microbiome is one of the best defenses bees have against diseases. Unnecessary antibiotic use can compromise colony health by disrupting the balance in the bee’s gut microbiome. Maintaining a healthy gut year-round helps reduce the pressure of pathogens and the need for antibiotics. There are other ways to ensure gut health is being supported in bees, which will be discussed in a future blog.  

Written by Kaitlyn Newton, ATTTA Seasonal Apiculturist 

Connecting with ATTTA Specialists

If you’d like to connect with ATTTA specialists or learn more about our program, you can:

visit our website at https://www.perennia.ca/portfolio-items/honey-bees/

Email attta@perennia.ca

References:

1.      Prouty, C., Jack, C., Sagili, R. and Ellis, J.D., 2023. Evaluating the efficacy of common treatments used for Vairimorpha (Nosema) spp. control. Applied Sciences, 13(3), p.1303.

2.      Peirson, M. and Pernal, S.F., 2024. A systematic review of fumagillin field trials for the treatment of Nosema disease in honeybee colonies. Insects, 15(1), p.29.

3.      Masood, F., Thebeau, J.M., Cloet, A., Kozii, I.V., Zabrodski, M.W., Biganski, S., Liang, J., Marta Guarna, M., Simko, E., Ruzzini, A. and Wood, S.C., 2022. Evaluating approved and alternative treatments against an oxytetracycline-resistant bacterium responsible for European foulbrood disease in honey bees. Scientific Reports, 12(1), p.5906.

4.      Baffoni, L., Alberoni, D., Gaggìa, F., Braglia, C., Stanton, C., Ross, P.R. and Di Gioia, D., 2021. Honeybee exposure to veterinary drugs: how is the gut microbiota affected?. Microbiology Spectrum, 9(1), pp.10-1128.

5.      Romero, S., Nastasa, A., Chapman, A., Kwong, W.K. and Foster, L.J., 2019. The honey bee gut microbiota: strategies for study and characterization. Insect molecular biology, 28(4), pp.455-472.

6.      Li, J.H., Evans, J.D., Li, W.F., Zhao, Y.Z., DeGrandi-Hoffman, G., Huang, S.K., Li, Z.G., Hamilton, M. and Chen, Y.P., 2017. New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection. PloS one, 12(11), p.e0187505.

7.      Luo, S., Zhang, X. and Zhou, X., 2024. Temporospatial dynamics and host specificity of honeybee gut bacteria. Cell Reports, 43(7).

8.      Raymann, K. and Moran, N.A., 2018. The role of the gut microbiome in health and disease of adult honey bee workers. Current opinion in insect science, 26, pp.97-104.

9.      Mosca, M., Gyorffy, A., Milito, M., Di Ruggiero, C., De Carolis, A., Pietropaoli, M., Giannetti, L., Necci, F., Marini, F., Smedile, D. and Iurescia, M., 2025. Antibiotic Use in Beekeeping: Implications for Health and Environment from a One-Health Perspective. Antibiotics, 14(4), p.359.

10. Baffoni, L., Alberoni, D., Gaggìa, F., Braglia, C., Stanton, C., Ross, P.R. and Di Gioia, D., 2021. Honeybee exposure to veterinary drugs: how is the gut microbiota affected?. Microbiology Spectrum, 9(1), pp.10-1128.

11. Kešnerová, L., Mars, R.A., Ellegaard, K.M., Troilo, M., Sauer, U. and Engel, P., 2017. Disentangling metabolic functions of bacteria in the honey bee gut. PLoS biology, 15(12), p.e2003467.

Honey bees rely on more than just pollen and nectar to stay healthy. Inside their digestive system lives a complex community of microbes that play a vital role in their survival. This blog explores the honey bee gut microbiome, how it changes with the seasons and why nutrition and microbial balance are essential for colony health.

Bee Healthy: Inside the Gut!

The gut microbiome includes all the organisms that live in the digestive tract. Examples of these organisms include bacteria and fungi. Bacteria that live in the honey bee gut microbiome can be core bacteria, which form a consistent community of cells, or non-core bacteria like Bartonella, Commensalibacter and Frischella ¹. Common fungi in adult Honey bees are Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, and the fungus Saccharomyces, which is common in young bees ¹.  The microbiome aids in the digestion of food and absorption of nutrients, helping bees get the most out of their diet. Proper nutrients support a strong immune system, which protects against harmful pathogens. Beyond digestion, the microbiome also influences other important systems in the bee’s body, including endocrine signaling, olfactory processing and memory pathways ¹. Disturbances to the gut microbiome, caused by stress or poor nutrition, can interfere with bee development and influence gene expression related to their immunity, metabolism, and behaviour¹.

Inside the bee’s gut, there are five core beneficial bacteria. These belong to the genera Bifidobacterium, Bombilactobacillus, Gilliamella, Lactobacillus, and Snodgrassella, and are present in healthy honey bees¹. These bacteria are passed between the bees through social contact and help maintain gut stability. To support these microbes, bees rely on a diet rich in macronutrients and micronutrients. Macronutrients like pollen and nectar are needed in large amounts. Pollen provides honey bees with proteins, lipids, vitamins, and essential sterols, while nectar is their main source of carbohydrates ².  Micronutrients, though required in trace amounts, are equally vital. These include vitamins, minerals, phytochemicals and phytosterols, all of which support bee health ³.

Figure 1: Honey bee eating honey  (ATTTA ©, 2018)

Nutritional supplements also play an important role in helping bees rebuild their gut microbiome and immune system, especially in early spring when natural forage is limited. There are many types of supplements available, including pollen patties for protein and lipid support, probiotics that introduce beneficial bacteria, and prebiotics that help existing gut microorganisms survive. When used appropriately, these supplements could support immune function and reduce pathogen loads. However, they should be given to boost the digestive system of bees and not be used as a replacement for natural forage. Some research is required to fully understand the benefits of nutritional supplements to overall bee health.

The structure of the bee’s digestive system also influences where microbes live. The crop temporarily stores nectar inside the bee ⁴. The midgut is where enzymes are secreted to aid digestion and nutrient absorption ⁴. The crop and midgut do not have stable bacteria because they are exposed to external microbes that enter the digestive tract ⁵. The hindgut, which includes the ileum and rectum, is where most of the core beneficial bacteria reside. It provides a more stable environment for the helpful microbes ⁵. This is also where water and mineral reabsorption occur, and processing of metabolic waste ⁴. Honey bees also have Malpighian tubules, which act like kidneys, excreting waste products into the hindgut to be removed from the body ⁴. 

Figure 2: Digestive Anatomy of a Honey bee (ATTTA ©, 2025)

Honey bee gut microbiome does not just vary between individual bees but also changes with the seasons. While the total number of bacteria in the gut remains relatively stable year-round, the diversity and composition of those bacteria shift depending on the environmental conditions ⁶.  In spring, microbial diversity is highest, likely from the new foraging activity and exposure to a wide range of pollen and nectar sources ⁶. In summer and winter, diversity tends to decrease, with Gilliamella and Snodgrassella becoming the dominant bacteria ⁶. These seasonal shifts are influenced by temperature, precipitation and forage availability, all shape the microbial community in the bees’ gut. A diverse and balanced microbiome in spring helps bees recover from the winter stress and prepare for the active seasons ahead.
 
Maintaining a healthy gut microbiome is essential for honey bee health, especially in spring, when colonies are rebuilding after winter. Understanding what goes on inside the bees’ gut and ensuring they receive proper nutrients and microbial support can help beekeepers promote stronger colonies.

Written by Kaitlyn Newton, ATTTA Seasonal Apiculturist 

Connecting with ATTTA Specialists

If you’d like to connect with ATTTA specialists or learn more about our program, you can:

visit our website at https://www.perennia.ca/portfolio-items/honey-bees/

Email attta@perennia.ca

References:

1.    Motta, E.V. and Moran, N.A., 2024. The honeybee microbiota and its impact on health and disease. Nature Reviews Microbiology, 22(3), pp.122-137.

2.    Khan, K.A., Ghramh, H.A., Ahmad, Z., El-Niweiri, M.A. and Mohammed, M.E.A., 2021. Honey bee (Apis mellifera) preference towards micronutrients and their impact on bee colonies. Saudi Journal of Biological Sciences, 28(6), pp.3362-3366

3.    Tsuruda, J.M., Chakrabarti, P. and Sagili, R.R., 2021. Honey bee nutrition. Veterinary Clinics of North America: Food Animal Practice, 37(3), pp.505-519

4.    De Paula, J.C., Doello, K., Mesas, C., Kapravelou, G., Cornet-Gómez, A., Orantes, F.J., Martínez, R., Linares, F., Prados, J.C., Porres, J.M. and Osuna, A., 2022. Exploring honeybee abdominal anatomy through micro-CT and novel multi-staining approaches. Insects, 13(6), p.556.

5.    Romero, S., Nastasa, A., Chapman, A., Kwong, W.K. and Foster, L.J., 2019. The honey bee gut microbiota: strategies for study and characterization. Insect molecular biology, 28(4), pp.455-472.

6.   Castelli, L., Branchiccela, B., Romero, H., Zunino, P. and Antúnez, K., 2022. Seasonal dynamics of the honey bee gut microbiota in colonies under subtropical climate: Seasonal dynamics of honey bee gut microbiota. Microbial ecology, 83(2), pp.492-500.