A curious tale of microbes and crop fermentation

In a recently published study, we asked if bees without access to the natural world or flowers accumulate alcohol in their digestive system because of microbial activity. Let’s walk through what we found and why it might matter.

Honeybees, similarly to humans, have a gut microbiota: a community of bacteria that helps them digest food, fight off pathogens, and maintain overall health. The crop, a kind of "nectar stomach," also has its own, more specialized set of microbes. In natural conditions, bees constantly exchange these microbes through contact with nest mates and flowers. But in laboratory cages, just like humans on a sterile diet in a hospital room, bees lose some of their environmental microbes. We asked if these shifts in the crop microbiota allow other, more opportunistic microbes to take over and start fermenting sugars. To answer, we compared two groups of bees: hive bees, allowed to grow up and forage naturally, and caged bees, kept in the lab and cut off from environmental microbes. We then analyzed the bees' crop content for ethanol levels, to see if any fermentation was taking place, and microbial communities, to see what kinds of bacteria were living there. We found low ethanol levels in both groups, but caged bees had ethanol in their crops more often than hive bees. Also, caged bees had different microbes in their crops. They had fewer of the usual nectar-associated bacteria (like Apilactobacillus) and more of the types that can produce ethanol (like Gilliamella and Bifidobacterium).

A plot that visualizes the microbiota in bees as well as food and water samples, with hive and caged bees broadly overlapping. Plot from the article by Antoł et al. (2025).

Is it possible that the microbial communities that live in a honeybee crop might be producing ethanol, like a tiny internal brewery? If so, and changes in diet and environment can tilt the microbial balance toward fermentation, what else might these microbes be doing? In humans, we now know gut microbes can influence everything from immune health to mood. Could similar dynamics play out in bees? In our study, caged bees didn’t just lose microbial diversity. They gained potentially “fermentative” microbes. This microbial shift could be harmless, or it could subtly change how bees process food, handle stress, or respond to infection. To understand these effects, we’ll need to look beyond the mere presence of microbes and start asking what they’re doing. Future studies may use metabolomics, RNA sequencing, or experimental manipulation of bee microbiomes to dig deeper.

Find out more in our open access Microbial Ecology article, here.