Bees aren’t the only pollinators, but 87% of flowering plants rely on animals for pollination—with bees doing a large share. Their role in global crop production, worth $200 billion annually, makes them a major research focus. In recent years, scientists have turned their attention to bee microbiomes—communities of microbes living in and on bees, including bacteria, fungi, viruses, and archaea—to understand how they support pollination and health in a changing climate.
There are over 20,000 bee species, with 77.4% being solitary, such as mason or mining bees. However, honey and bumble bees, which are social, dominate research—54% of it—even though honey bees aren’t native to the U.S. Despite this, they’re essential to modern agriculture and are more abundant than ever. While native bees were often overlooked due to their lesser economic value, research on these species is growing.
Like humans, bees rely on gut microbiomes for health. A microbiome is a community of microorganisms that live on and inside a larger organism. These microorganisms, or microbes– bacteria, fungi, viruses, etc.– acquired mainly through flowers, aid in digesting tough pollen grains and help bees build fat reserves. Healthy microbiomes also offer protection against pathogens, with bacteria like Lactobacillus acidifying the gut to ward off parasites.

Flowers serve as transmission hubs for both helpful and harmful microbes. For bumble bees, some flower-produced yeasts increase visitation, though possibly at a cost to seed production. Plant pathogens may exploit bees by overwintering in their nests, demonstrating that even mutualisms can have downsides.
Microbiomes vary by geography, bee species, life stage, and social role. For example, queen bees—fed royal jelly—host different microbes like Bombella apis, which survives in that unique diet. During metamorphosis, bees reset their microbiomes and rebuild them through interaction with the colony and environment.

Human activity significantly affects bee health. In apple orchards, fungicides—though deemed safe for adult bees—disrupt brood cell microbiomes. Glyphosate, a widely used herbicide, alters bacterial diversity and reduces bees’ immunity. Contaminants from wastewater, like heavy metals and antibiotics, further disrupt microbial balance. American bees, often treated preventively with antibiotics, show more antibiotic resistance than their European counterparts, raising concerns for long-term health.
Not all findings are bleak. Probiotic and prebiotic supplements—like acacia gum—show promise in strengthening bee immunity and digestion. Probiotics are microorganisms that benefit their host, in this instance, bees, while prebiotics are food for the microorganisms. These additions enhance foraging, pathogen resistance, and overall colony resilience by supporting beneficial gut microbes.
Studying bee microbiomes helps us better protect pollinators. It also reminds us to reduce pesticide use and care for even the smallest organisms. Healthy microbes are crucial—not just for bees, but for entire ecosystems, including our own.
Resources
Bees just wanna have fungi: a review of bee associations with nonpathogenic fungi by Danielle Rutkowski, Makena Wetson and Rachel L. Vannete
Want to Save the Bees? Focus on Habitat, Not Honey Bees by Rich Hatfield and Matthew Sheperd
Microbiome by Julie Segre
Honey Bee Nutrition by Zachary Huang
In Defense of Plants: Plants, Bees and the Microbes They Share with Quinn McFrederick
Matters Microbial #6: What’s the buzz on honey bee microbes? with Irene Newton
Glyphosate and a glyphosate-based herbicide affect on bumblebee gut microbiota by Marjo Helander et. al
Glyphosate induces immune dysregulation in honey bees by Erick VS Motta, J Elijah Powell and Nancy A Moran
Uptake of the Plant Agriculture-Used Antibiotics Oxytetracycline and Streptomycin by Cherry Radish-Effect on Plant Microbiome and the Potential Health Risk by Lichun Yin et. al
Probiotics positively influence honeybee health, Western research finds by Western University
Effects of Prebiotics and Probiotics on Honey Bees (Apis mellifera) Infected with the Microsporidian Parasite Nosema ceranae by Daniel Borges, Ernesto Guzman-Novoa and Paul H Goodwin
By Lexie Leeser, Agent Associate and Master Gardener Coordinator, Baltimore County, University of Maryland Extension.






















