Exploring gut microbiomes when the snow comes

Have you ever put your ear on a hive during winter? You would hear how bees inside actively buzz to keep warm while slowly eating their food supplies. These bees don’t sleep, nor their particular gut microbiomes.
Published in Microbiology
Exploring gut microbiomes when the snow comes

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Honeybees carry out various ‘professions’ within the hive to keep the colony functional and alive. These tasks are divided among sterile female worker bees that are as crucial as the queen or drones. Some workers clean the hive, others feed larvae and take care of the brood, or are foraging nectar and pollen to feed the colony. A regular worker bee experiences most of these jobs, and its diligence leads to its short life during the foraging season. But when winter comes, the main task is to survive cold months until spring kicks in.  Thus the lifespan of winter bees lasts several months, unlike the hard-working bees born between spring and early autumn that live only a few weeks. Naturally, being stuck within the hive during cold months means surviving on stored honey and pollen that might differ from the diet available along the flowering season. The age of the bee, season, as well as diet, might influence the bee’s gut microbiota composition and density.

In our group, we were often questioning the importance of season and other factors in shaping the bee gut microbiome. Thus, to better understand possible shifts in its structure, we started a monthly sampling of bees. Aiming to get a complete picture, including the size of the microbiome and loads of its respective bacterial members, we combined quantitative and sequencing approaches. We also wanted to get a glimpse of the variability between individuals, which led us to dissect and analyse more than 600 bee guts. The ‘Monthly sampling’ project was carried on one of our hives for two years, and then we added more hives during the third year. Sampling mostly meant sitting in kneeling in front of the hive and waiting for incoming foragers. This strategy changed in winter when we had to quickly open hives and get some bees from top of the frames while trying to disturb the bees as little as possible. Interestingly, winter bees are very good at getting under the layers of clothes, and their stings were to me the most painful ones. But it was worth it. These moments spent either by sampling for this quite demanding side project or by taking care of our colonies were the best part of our PhDs, together with Olivier Emery. Even more during bright sunny days with a stunning view on the majestic French Alps across Lake Geneva, on the shore of which our campus is located.

Mountain view from the University of Lausanne on a sunny winter day (photo: L. Kešnerová).

So what did we learn? Different bee tasks require specific behaviours that are usually linked to a particular diet. We could observe this when dissecting guts: rectums of foragers contained floral nectar, while those of winter bees were stuffed with pollen beebread coming from winter food stocks. Pollen is a very rich diet. This fact, combined with the tendency of in-hive bees to retain their feces, defines the diet as a major factor causing an increase in the number of microbes in winter bee guts. We supported this finding by including in our study also experimental bees kept on different diets, and pollen-eating nurses, that are the younger bees taking care of the in-hive tasks before they become foragers. Altogether, this brought a new quantitative dimension to our knowledge of the honeybee gut microbiota during its life and over seasons.

Olivier Emery with his hives right after sampling the last batch of winter bees in January 2018 (photo: O. Emery).

This was not all… While the foragers, which are more exposed to the environment, possessed many minor species in their guts, these almost disappeared from winter bees. However, winter bees appeared to have characteristic shifts in their gut community structureThe most striking difference was that the winter microbiota was remarkably dominated by Bartonella, a genus including also blood-borne pathogens of mammals [1]. This opens new questions because we do not yet know why is this bacterium so predominant during winter - is it due to the age of bees, diet, or lower temperature? Moreover, how the physiology of overwintering bees could be affected by Bartonella, and whether it is beneficial or pathogenic still remains to be resolved. Although future studies should address these questions specifically, several unpublished observations from colleagues from other parts of the world with temperate climate suggest that this trend is not linked only to our region.

Bees are considered a keystone species that maintain stable ecosystems of Earth. Sadly, due to human activity, more and more colonies die during winter [2, 3]. This points to the critical importance of winter bees for colony survival. We should, therefore, try to better understand factors influencing their health and resilience - including the gut microbiota and its functions.


We hope that our study will inspire new investigations and reinforce the efforts to save the bees that are not only important but also a very interesting study subject thanks to their complex social organisation.


Original article: Kešnerová L, Emery O, Troilo M, Liberti J, Erkosar B, Engel P. Gut microbiota structure differs between honeybees in winter and summer. The ISME Journal 2019; 1–14.

Cover image: ID 65234424 © Savin Sorin Matei Contescu | Dreamstime.com


1.         Segers FH, Kešnerová L, Kosoy M, Engel P. Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. ISME J 2017.

2.         Guzmán-Novoa E, Eccles L, Calvete Y, Mcgowan J, Kelly PG, Correa-Benítez A. Varroa destructor is the main culprit for the death and reduced populations of overwintered honey bee (Apis mellifera) colonies in Ontario, Canada. Apidologie 2010; 41: 443–450.

3.         Genersch E, Ohe W von der, Kaatz H, Schroeder A, Otten C, Büchler R, et al. The German bee monitoring project: a long term study to understand periodically high winter losses of honey bee colonies. Apidologie 2010; 41: 332–352.



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