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Your Honey’s Secrets
By: Jay Evans, USDA Beltsville Bee Lab
Last month, I discussed DNA fingerprints left behind by bees and their associates as they crawl over hive surfaces. There are now many cases where scientists have accurately identified even brief visitors to the hive. These same techniques are also being used to screen honey stored in beehives or found on store shelves. There is a longstanding need to identify the plant origins of particular honeys, since labels are important to discerning customers. Confirming plant sources can also help resolve local from imported honeys and pure honeys from honeys rich in supplemental syrups. As we develop genetic signatures for life on earth (see the Earth Biogenome Project, which aspires to do just that for all major life forms, https://www.earthbiogenome.org/), identifying plant honey sources and spotting frauds is getting pretty accurate. In addition, thanks to the stickiness of honey for all things in the environment, we can now learn far more about bees from their honey than simply plant stories. Honey has identifiable markers for the bee races that did the work, bee pathogens and parasites that tried to interfere with that work, and even the bony creatures that harvested the honey or sought respite in quiet parts of the hive.
Combined with chemical analysis for pesticides and unwanted honey additives, combing honey for DNA fingerprints is becoming a robust science. At the 2026 American Beekeeping Federation annual meeting, German beekeeper and detective Bernhard Heuvel gave a remarkable presentation on work alongside European scientists to crack cases of honey fraud. His YouT ube presentations (https://www.youtube.com/@BernhardHeuvel) show a gutsy attempt to bring violations to light while also hinting at more that could be done to use signals in honey to investigate interesting hive questions.
Here, I will jump to genetic tests for honey traits, discounting the longstanding use of chemistry by honey integrity sleuths. Chemical cues for bona fide and fraudulent honey have been immensely helpful for decades. Unfortunately, the bad guys have chemists too, leading to an arms race whereby one side cracks the case and then the other side comes back with even more elusive fake honey. This arms race is so politely mature that Mr. Heuvel presented many cases where wholesale dealers in funny honey were openly advertising the various chemical diagnostics their product could fool. I will also give too little attention to the use of color and microscopic traits for identifying honey sources, a robust field for decades but one that I feel falls short of DNA testing in exploring the wealth of available information.
DNA has the potential to be a hypersonic weapon on the side of scientists and regulators seeking to use botanical cues to win the honey fraud arms race. While you won’t taste it, true honey carries pollen from the plants whose nectar was collected to make that honey. Genetic ‘barcodes’ unique to pollen from specific plants have, for many of us, taken the place of painstaking microscopic assays. Pollen barcodes from true honey can be screened in two ways. The more common way is to target individual genes and compare their sequences (variable strings of the four nucleotides that make up DNA). A second way is to generate so-called ‘shotgun’ sequences of all DNA found in a honey source and then sort those DNA sequences into bins. The former technique remains the simplest and has been used in dozens of studies aimed at knowing everything from local flowering patterns to industry honey blends. This technique works pretty well at capturing most of the plant diversity in a particular honey and can be a nice tool to keep honest packers honest. As one example of that, Sophie Dodd and colleagues were able to ferret out adulterated honey in the UK by simply noting the presence of DNA from suspected additives (Dodd, Sophie, Zoltan Kevei, Zahra Karimi, et al. (2025) Detection of sugar syrup adulteration in UK honey using DNA barcoding. Food Control 167: 110772. https://doi.org/10.1016/j.foodcont.2024.110772.) Using primers tuned to corn and rice, they were able to accurately identify both at levels of 1%. Corn pollen could appear accidently in UK honey at low levels thanks to blown or collected pollen, but rice is never grown there. Consequently, signs of rice DNA would suggest adulteration by feeding colonies or (more likely) blending foreign rice syrups into extracted honey.
While single-gene tests targeting specific plant genes are the common choice, DNA sequencing of honey for ‘all’ signs of life has tremendous advantages. First, single-gene barcodes rely on near-perfect matches for an idealized sequence. Nature loves to produce genetic variations, some of which will make a particular plant species invisible to barcode screening. There is an art to designing barcodes that accurately capture entire plant communities, but a recent computational review suggests it is naïve to expect barcode studies to give a completely unbiased report (Ranieri, L., Lorusso, L., Mottola, A., Intermite, C., Piredda, R., & Di Pinto, A. (2025). Authentication of the Botanical Origin of Honey: In Silico Assessment of Primers for DNA Metabarcoding. Journal of Agricultural and Food Chemistry, 73(24), 15429–15442. https://doi.org/10.1021/acs.jafc.5c02276).
Many of these biases can be overcome through DNA sequencing. Samuele Bovo and colleagues in Italy gave this field a large boost early on (Bovo S, Ribani A, Utzeri VJ, Schiavo G, Bertolini F, Fontanesi L (2018) Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature. PLoS ONE 13(10): e0205575. https://doi.org/10.1371/journal.pone.0205575). They confirmed the labeled plant sources of two honeys and produced an enticing treasure of tagged bee pathogens and hitchhikers, from viruses to waxmoths. In fact, a huge advantage of DNA sequencing comes from the insights gathered about other living organisms in the hive, starting with the bees that did all the work to make that honey. A 2025 review shows the current state of the art for honey forensics using DNA sequencing. Priit Paluoja and colleagues sampled nearly 400 honeys (a large leap from the two honeys in the Bove sample) and used updated computational methods to identify the sequences they generated (Paluoja, P., Vaher, M., Teder, H. et al. (2025) Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens. npj Sci Food 9:91. https://doi.org/10.1038/s41538-025-00464-1). This study, focused on honeys from Estonia, shows the value of sequencing for honey plant sourcing. Given the diversity of plants found for each sample, and the fact that many plant species reside on only a single continent, it seems trivial to use these methods to identify when honeys or fractions of honeys come from a particular country, with or without attribution. On the pests and pathogens front, the study found the agent causing American foulbrood in many honeys (a long-known fact even for colonies that are not showing symptoms) but especially high levels of this pathogen in two colonies with diagnosed disease. The method also accurately showed an absence of small hive beetle in Estonian honeys but did find traces of this pest in honeys from the US and other foreign sources. This suggests that the method will work well to monitor for invasive mites and insects, from Tropilaelaps to hornets. Bulk DNA sequencing is getting more accessible as costs decrease and computational methods to process piles of data get better. Given these advances, honey fraudsters are on alert and scientists can better explore honey bee diversity and the honey footprints of hive associates past and present.
