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The Power of the Bee Gut Microbiome

Updated: Oct 5, 2023

A honeybee may seem too small to have one billion cells in its gut. But honeybees, like humans, have a uniquely specialized gut microbiome that has developed over millions of years of coevolution. It contains bacteria and fungi that take substances bees ingest and use them for good – to break down food into energy, release nutrients, dissolve toxins, and fight off infection. Likewise, there are viruses and parasites that take substances bees ingest for themselves, for example, Nosema parasites that leech iron from the bees.

A balanced gut microbiome helps optimize digestion and nutrition, and increases a bee’s ability to combat chalkbrood, fight off mites, support pesticide detoxification, and increase hive immunity. An unbalanced gut microbiome can lead to low weight, an intolerance for viruses, and vulnerability to pesticides.

The team at Strong Microbials sees the power of the bee gut microbiome firsthand. Throughout the year we care for bees in our rooftop apiary in Milwaukee, Wisconsin. And we collaborate with commercial, sideliner, and hobbyist beekeepers across the country to better understand bee health. Following are the ways the microbiome is the key to honeybee colony health and critical to bee survival.

1. One Billion Cells. According to a study released in 20152, the honeybee adult worker harbors a large bacterial community in the gut, with roughly 1 billion bacterial cells in mature workers. A study released in 20203 used metagenomic sequencing to find that there are also billions of viruses that attack the bacteria, and that 76% represent viruses that have never been seen before.

2. Extraction of Dietary Nutrients – Gut microbiomes of bees, like those of humans, digest food to separate and synthesize the vitamins and nutrients essential for life. Lactic acid bacteria (LAB) are abundant and important members of the honeybee gut microbiome. These bacteria provide multiple health benefits to honeybees: improved digestion, boost immunity and detoxifications systems.

3. Fending Off Pathogens - LAB stimulate the honeybee immune system which correlates to elevated levels of host defense antimicrobial peptides. Anti-microbial substances excreted by beneficial bacteria known as microbial metabolites, suppress disease pathogens such as Chalkbrood (caused by the fungus Ascophaera apis); European Foulbrood (EFB) pathogen (Melissococcus plutonius); American Foulbrood (AFB) (caused by spore forming Paenibacillus larvae ssp.); the microsporidian parasite Nosema ceranae and the widespread adult honeybee parasite Nosema apis.

A Natural Balance

One way to balance the bee gut microbiome naturally for optimized hive health and bee survival rates is through the use of probiotics. Honeybees accumulate their gut biome through direct social and environmental contact. Pesticides, monoculture farming, climate change, and a decline in natural habitat available to honeybees make it difficult for them to get the nutrients they need for a healthy microbiome on their own.

Take this 2019 field trial, for example. Previous research showed that feeding probiotic containing Lactobacilli stimulates honeybee immune response, and Bacilli prolong honeybee lifespan.

The field trial took place in Michigan and Wisconsin. It tested probiotic applications containing Bacilli and Lactobacilli direct-fed microbial (DFM) during spring and summer 2019. The trial was conducted by Strong Microbials, citizen science beekeepers, and small-scale beekeepers. The goal of the study was to evaluate the effect of probiotic on naturally occurring levels of Nosema infection.

  • Two apiaries were used.

  • 20 colonies per apiary were evaluated and randomly assigned to control group or DFM group in April.

  • New hygienic Carniolan queens were installed in May.

  • All colonies were managed equally and did not receive any treatments except for Varroa mites.

  • Every two weeks DFM group received 1 tablespoon = 10 grams dry, inside the hive application of SuperDFM-HoneyBee™.

  • The control group did not receive any treatment at the time.

Results of the field trial showed that the DFM treated colonies were stronger. This was based on how completely the bees covered the frames from end to end, how far down the bees go, and how crowded the bees looked. DFM colonies also had better brood patterns than the control group. With a range from 1-5, with 5 being the most solid or with the fewest open cells.

Probiotics also significantly improved the spring buildup, an important colony health factor, compared to negative control and lowered Nosema spore counts in the field faster. Naturally occurring Nosema spore counts in June were below 0.5 million spores/bee.

Strong Microbials is focused on developing natural microbial products that are friendly to the environment, bees, animals, and people. Contact us today to learn about our DFM products and how your colonies can benefit.

SuperDFM® Probiotics


1 W. K. Kwong et al., Dynamic microbiome evolution in social bees. Sci. Adv. 3, e1600513 (2017).

2 Powell JE, Martinson VG, Urban-Mead K, Moran NA. Routes of acquisition of the gut microbiota of Apis mellifera. Appl. Environ. Microbiol (2014).

3 G. Bonilla-Rosso, T. Steiner, F. Wichmann, E. Bexkens, P. Engel, Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota. Proc. Natl. Acad. Sci. U.S.A. 117, 7355–7362 (2020).

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