It is possible to gauge the health of honeybees through they honey they produce, researchers in Greece have revealed. The researchers have optimised a method to characterise DNA traces in honey, revealing the species that honeybees interact with. The method allows for monitoring of the variability of bee diets across the year, revealing bee microbiota in a non-invasive way, as well as identifying pathogenic species they are confronted by. Organism's ecological niche is a delicate balance of interactions and adjustments to other species coexisting within the same habitat. By pollinating trees and flowers, honeybees exploit a large number of flowering plant species for their own food resources and growth. On the other hand, honeybee colonies are also weakened when environmental conditions favour the propagation of pathogenic species, such as Varroa mites. The species dynamics of the honeybee ecological niche are therefore inextricably linked with the type of habitat the bees live in and its seasonal changes. Faced with the increasing restructuring of agricultural areas and the effects of climate change, bee ecological niches are becoming more vulnerable. A better understanding of the dynamics of interactions between bees and surrounding species will help to identify risk periods and zones for bees. Honeybees make honey by regurgitating the nectar and pollen from the flowers they forage and then placing it in the cells of their hive until enough water evaporates. Through this process, honey comes into contact with a variety of organisms and, therefore, contains DNA from multiple species, collectively called environmental DNA (eDNA); this originates from foraged plants, the gut bacteria of bees, and potential hive pathogens. The now published, optimised method called ‘direct-shotgun metagenomics’, involves sequencing and comprehensive identification of the eDNA fragments found in honey. In this study, researchers analysed several samples of honey from an apiary located in a typical Mediterranean landscape. They identified more than 40 species of plants that reflect all the botanical diversity surrounding the hives. Contrary to what one might think, the ecological niche of bees extends well beyond plants. In the analysed honey samples, the researchers revealed an even greater number of bacterial eDNA species, the vast majority of which emanates from microorganisms considered to be harmless and which comprise the core species of the bee microbiome. Researchers also looked for the presence of eDNA from putative pathogens. They found that traces of Varroa mite eDNA in honey directly matched with observed hive contamination. It is a promising sign that this research could eventually be used to monitor and anticipate disease and pathogens in large scale studies.