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The paper, titled "A network-based meta-analysis of the honeybee gut microbiome: geographic, seasonal, and pesticide-associated shifts," was authored by Nelli Vardazaryan, Lusine Adunts, Inga Bazukyan, Magdalina Zakharyan, Honglian Liu, Chrats Melkonian, and Lilit Nersisyan.
A honeybee carries only a handful of bacterial species in its gut, and much the same handful whether it lives in Armenia, Denmark, or New Zealand. That small community digests pollen the bee cannot digest alone, trains its immune system, and shapes how it develops.
Pesticides are one suspected cause of honeybee losses. What they do to this community has been unclear, because studies have kept disagreeing with each other.
The team analyzed over 500 gut samples from worker bees, combining eight published datasets with new Armenian samples generated with Yerevan State University. Running everything through the same pipeline made the studies directly comparable.
They also asked a different question of the data. Instead of tracking one species at a time, they looked for groups of bacteria that move together, using a new open-source tool called tsantsR.
The core community held. Season and city life shifted the balance between residents, but the same few were present everywhere.
The chemicals, though, left different marks.
Oxalic acid and neonicotinoid insecticides came with a rise in opportunists, bacteria such as Klebsiella and Serratia that sit quietly in a healthy gut and can turn harmful when conditions change.
Glyphosate did something stranger. The weedkiller pushed out Snodgrassella alvi, one of the core residents, and made room for Pseudomonas carrying genes that appear able to break glyphosate down. Rather than simply losing bacteria, the gut may be gaining ones that can feed on the chemical.
"What surprised us is that the community does not just degrade under glyphosate. Some bacteria could move in and metabolize it. That is a very different story from simple harm, and it is one worth testing experimentally," said Lilit Nersisyan of ABI.
The study was conducted in collaboration with the Institute of Molecular Biology NAS RA, the Institute of Biology at Yerevan State University, Karolinska Institutet, Utrecht University, and Wageningen University & Research.
The article is available open access: https://doi.org/10.1038/s41598-026-62172-4
