Outlook | Published:

Microbiome: The puzzle in a bee's gut

Nature volume 521, page S56 (21 May 2015) | Download Citation

By analysing bacteria that live in the digestive tracts of bees, researchers hope to learn about the role of microbes in insect health.

Cross-section of a honeybee hindgut with staining showing the symbiotic bacterium Snodgrassella alvi (yellow), other bacteria (green), insect-cell nuclei (blue) and insect tissue (red). Image: M. Steele/Univ. Texas, Austin

Sometimes, serendipity arrives on the wings of disease. It was colony collapse disorder (CCD), a mysterious condition that hit honeybee hives in autumn 2006, that brought bees to the laboratory of evolutionary biologist Nancy Moran. Moran, working at the time at Yale University in New Haven, Connecticut, had been studying microbes that live inside aphids and leafhoppers since the early 1990s. Owing to her knowledge of insect-associated bacteria, she was brought in by a team of genome sleuths to analyse RNA samples from sick honeybees. The quest1 yielded no culprit for CCD, but Moran was surprised to find that whether the bees were healthy or ill, their hindgut (equivalent to the mammalian intestine and rectum) carried a characteristic handful of species that make up 99% of the gut microbial population. “Every single bee had the same bacteria,” says Moran, who is now at the University of Texas at Austin.

Around the same time, research on the role of microbes in mammalian health was just dawning — helped by a new wave of genomic tools. With her first comprehensive look at the bee microbiome, Moran was hooked. Understanding how these different players help or harm the bee can shed light on bee health, she realized. The small and consistent set of bacteria — unlike the variable species found in the fruit fly Drosophila, a common model organism — made studying the microbiome simpler in bees than in mammals. And, because honeybees are social animals that share microbial species, they might provide a good model for studying gut bacteria in mammals too, she says.

Community effort

Since Moran's first foray into the honeybee microbiome, a handful of other labs have confirmed her basic finding that all honeybees' guts contain the same core species of bacteria. Bumblebees, although less well studied, also have a characteristic hindgut microbiota, including some of the same species that inhabit honeybees. Honeybees emerge from the pupal stage with a clean hindgut and, over their first three days, acquire the right microbes through interactions within the hive. But researchers have not yet unravelled the mystery of why bee microbiomes are the same across colonies. “There's something special that we still haven't pinpointed in bumblebees and honeybees that allows them to have this very specific microbiota,” says Quinn McFrederick, an entomologist at the University of California, Riverside.

Scientists are starting to figure out how gut bacteria can affect honeybees, with several microbial roles emerging. The earliest hint of function came from work published in 2011 by Swiss researchers: by raising bumblebees without gut microbiota, they discovered2 that the core population of microbes confers protection against trypanosome parasites, which are highly virulent in bumblebees and also present in honeybees. In 2014, Moran's group reported3 that some strains of Gilliamella bacteria in honeybees' guts can degrade pectin, a sugar found in pollen walls. And more recently, researchers in the lab of microbiologist Irene Newton of Indiana University, Bloomington, analysed4 RNA from the entire honeybee microbiota to learn more about the microbes' roles. Their key finding was that many species probably help to metabolize carbohydrates — the major constituent of nectar and pollen.

Another lab, led by Jay Evans of the Agricultural Research Service in Beltsville, Maryland, has been exploring the effect of one particular honeybee gut microbe — Snodgrassella alvi — on viral infections. At the 2014 meeting of the International Union for the Study of Social Insects, Evans presented research, conducted with Moran's group, showing that the presence of S. alvi can cut the number of viruses in a hive by as much as half, apparently by triggering a systemic immune response. Promoting populations of this species, for example by probiotic supplementation, might improve hive health, Evans says.

Despite the progress in determining function, “there are some very basic things that we don't have answers for”, Newton says — starting with a clearer picture of which organisms are present. Moran's group has shown that there are six to eight core species in the honeybee hindgut. But other species present in fewer numbers could also be playing an important part. Furthermore, 'species' is a much more approximate concept in the microbial world than in multicellular organisms (including humans), and genetic diversity among strains within species might be important. To further complicate the picture, Newton's group reported5 this year that the queen bee's microbiome is completely different from that of the worker honeybees that have been the focus of most research. This distinction suggests that the queens acquire their microbiota in a different manner from workers.

The gut microbiome is not the only microbial community that is important to bees, says Kirk Anderson, a microbial ecologist at the Carl Hayden Bee Research Center in Tucson, Arizona. Anderson studies bacteria living on the inside walls of the hive, an environment he likens to skin. “These bacteria have evolved to make a living in one of the most extreme antibiotic environments on the planet,” he says — referring to honey and other bee foodstuffs, which are full of antimicrobial chemicals. His work suggests that this external microbiome may have protective effects. “People are looking at gut bacteria,” he says, “but there are all these other populations.”

And beyond even these unknowns, there are many other types of bees to explore. “We've probably looked at some 20 species of bees out of a total of more than 20,000,” says McFrederick. “There's still a lot to be learned.”


  1. 1.

    et al. Science 318, 283–287 (2007).

  2. 2.

    & Proc. Natl Acad. Sci. USA 108, 19288–19292 (2011).

  3. 3.

    , & Proc. Natl Acad. Sci. USA 109, 11002–11007 (2012).

  4. 4.

    , , , & Environ. Microbiol. (2014).

  5. 5.

    , & Appl. Environ. Microbiol. (2015).

Download references

Author information


  1. Alla Katsnelson is a freelance science writer in Northampton, Massachusetts.

    • Alla Katsnelson


  1. Search for Alla Katsnelson in:

About this article

Publication history




Further reading

  • Characterisation of the British honey bee metagenome

    • Tim Regan
    • , Mark W. Barnett
    • , Dominik R. Laetsch
    • , Stephen J. Bush
    • , David Wragg
    • , Giles E. Budge
    • , Fiona Highet
    • , Benjamin Dainat
    • , Joachim R. de Miranda
    • , Mick Watson
    • , Mark Blaxter
    •  & Tom C. Freeman

    Nature Communications (2018)


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Newsletter Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing