The Canadian Bee Gut Project, led by Allen-Vercoe, is creating the nation’s first comprehensive database of honeybee gut microbes (the beneficial, harmful, and unknown microscopic organisms living in bee digestive systems). This pioneering research explores how these microbes affect bee health, behavior, and winter survival rates across Canada, with the goal of developing new strategies to protect these essential pollinators.
Honeybee populations are declining due to human-related factors such as habitat loss, pesticide exposure, and infectious diseases—threatening both the Canadian beekeeping economy and food security by reducing the availability of crops that depend on bee pollination. A promising solution lies in managing the honeybee gut microbiome, a vital system of microbes that influences digestion, detoxification, immune response, and overall colony health. When this microbiome becomes imbalanced—due to environmental stressors or antibiotic use—honeybees become more vulnerable to disease and exhibit overall diminished survival rates. Despite its importance, current best management practices in beekeeping lack standardized tools for assessing microbiome health or implementing corrective actions. Understanding the honey bee gut microbiome through genomic approaches and next-generation sequencing is essential for advancing our knowledge of microbial impacts on bee health as well as informing sustainable beekeeping practices that promote healthier, more resilient populations.
Dr. Emma Allen-Vercoe’s research team addressed the urgent issue of honeybee colony loss by focusing on a largely overlooked but critical factor: the gut microbiome. Through the Canadian Bee Gut Project, modeled after the Human Microbiome Project, Allen-Vercoe’s team is building the first nationwide database of honeybee gut microbiomes and genetic profiles across Canada. This ambitious initiative combines DNA sequencing, genomics, advanced data analysis, and samples collected from commercial beekeepers to establish baseline data on the microbes that support honeybee health. Recognizing that antibiotic use and pesticide exposures have disrupted these beneficial microbial communities, the project aims to restore microbial balance and resilience within colonies. By analyzing both genetic material and metabolic products alongside beekeeper observations, the research identifies connections between microbial populations and colony outcomes, such as disease resistance and stress tolerance.ecies name recognition.
The Canadian Bee Gut Project has made substantial strides in understanding the honeybee gut microbiome through sampling of ~30,000 individual bee samples from >700 colonies across 100+ sites over eight provinces. Comprehensive molecular analysis has identified over 4,000 unique bacterial strains associated with honey bees in Canada, with nearly 30% representing unclassified microbial ‘dark matter’ – species that remain uncultured and that have no formal name to reference them by, yet may play critical roles in honey bee health. Addressing this knowledge gap, the research team has already characterized a novel bacterial genus and species, Apirhabdus apintestini, found in honeybee digestive tracts, with additional novel strains currently under investigation. Moreover, a new software tool named “isolateR” was developed by Dr. Brendan Daisley (lead postdoctoral fellow in the project) for expediting discovery of novel microbial isolates with broad ranging potential for application across diverse scientific disciplines.
Current extensions of this research are also beginning to unravel the complex mechanisms by which symbiotic gut bacteria help honeybees resist disease, including the inhibition of Melissococcus plutonius, which is a highly prevalent pathogen in Canada and the causative agent of European foulbrood in bees. Ultimately, the data generated from this project will be made available through an open-access, interactive microbiome database, serving as a lasting resource for beekeepers, scientists, and policymakers to explore microbial diversity, track emerging pathogens, and develop targeted management strategies to support honey bee health and resilience.
evolutionary information to accurately fill in gaps.
The Canadian Bee Gut Project is transforming our understanding of honeybee health through microbiome research, promoting biodiversity at both microscopic and ecosystem levels. By establishing standardized baselines of honeybee microbial ecology across Canada, the project will guide agricultural policies and practices. The project’s collaborative approach, involving beekeepers and researchers nationwide, has created a comprehensive dataset that enhances our ability to address insect population decline. This work not only advances scientific knowledge but also offers practical strategies to enhance honeybee resilience despite environmental challenges.
Reid, G., Allen-Vercoe E., Al, K., Burton, J.P., Daisley, B.A., Dixon, B., Mousavi, H. Solberg, S.O., Peixoto, R.S., Silverman, S., Skokovic-Sunjic, D. (2025). Beneficial microbes for One Health in Canada: a review of evidence and a policy proposal. FACETS 10, 1-32. https://doi.org/10.1139/facets-2024-0182
Daisley, B.A., Vancuren, S.J., Brettingham, D.J.L, Wilde, J., Renwick, S., Macpherson, C.V., Good, D.A., Botschner A.J., Yen, S., Hill, J.E., Sorbara, M.T., Allen-Vercoe E. (2024). isolateR: an R package for generating microbial libraries from Sanger sequencing data. Bioinformatics 40, btae448. https://doi.org/10.1093/bioinformatics/btae448
Mallory, E., Freeze, G., Daisley, B.A., Allen-Vercoe, E. (2024). Revisiting the role of pathogen diversity and microbial interactions in honeybee susceptibility and treatment of Melissococcus plutonius infection. Frontiers in Veterinary Science 11, 1495010. https://doi.org/10.3389/fvets.2024.1495010
Killam S.M., Daisley B.A., Kleiber M.L., Lacika, J.F., Thompson G.J. (2024). A case for microbial therapeutics to bolster colony health and performance of honey bees. Frontiers in Bee Science 2, 1422265. https://doi.org/10.3389/frbee.2024.1422265
Daisley, B.A., Pitek, A.P., Mallory, E., Chernyshova, A.M., Allen-Vercoe, E., Reid, G., Thompson, G.J. (2023). Disentangling the microbial ecological factors impacting honey bee susceptibility to Paenibacillus larvae infection. Trends in Microbiology 31, 521-534. https://doi.org/10.1016/j.tim.2022.11.012
Daisley, B.A., Chernyshova, A.M., Thompson, G.J., Allen-Vercoe, E. (2022). Deteriorating microbiomes in agriculture-the unintended effects of pesticides on microbial life. Microbiome Research Reports 1, 6. https://doi.org/10.20517/mrr.2021.08
Macpherson, C., Daisley, B., Mallory, E., & Allen-Vercoe, E. (2024). The untapped potential of cell culture in disentangling insect-microbial relationships. Microbiome Research Reports, 3(20). http://dx.doi.org/10.20517/mrr.2023.66
Quinn, M., Daisley, B., Vancuren, S., Bouchema, A., Niño, E., Reid, G., Thompson, G., & Allen-Vercoe, E. (2024). Apirhabdus apintestini gen. nov., sp. nov., a member of a novel genus of the family Enterobacteriaceae, isolated from the gut of the western honey bee Apis mellifera. International Journal of Systematic and Evolutionary Microbiology, 74, 006346. https://doi.org/10.1099/ijsem.0.006346
Dr. Brendan Daisley, Dr. Graham Thompson
Amira Bouchema, Matthew Quinn, Elizabeth Mallory, Julia Lacika, Anna Chernyshova, Maria Rodriguez, Christine Macpherson, Ailish Moore, Dylan Brettingham, Jordan Meers, Kalyna Kit, Dr. Brendan Daisley
Western University
