Beehives are the honeypot for a city’s microbial secrets

What pathogens are lurking on city streets? Follow the honeybee's trail to find out.
Japanese beekeepers holding honeycomb up at the top of a Tokyo skyscraper

Beekeepers check honey levels at an urban apiary in Tokyo, Japan, in 2010. KAZUHIRO NOGI/AFP via Getty Images

The waste honeybees discard in their hives could hold valuable insight into the public health of our cities. In a study published this week in the journal Environmental Microbiome, scientists shared a new method for collecting microbial information from the environment using honeybee debris. Identifying germs in a city gives researchers a snapshot of the diversity of a city’s microbiome, which could lead to better health outcomes. The technique might also help in surveilling illness-causing bacteria and viruses among bees and humans. 

While we can’t see microorganisms, they play a critical behind-the-scenes role in shaping our survival. For example, microbes in the human gut support digestion, help keep our immune system healthy, and are the first line of defense from “bad” bacteria that cause food poisoning and other infections. Typically, the more diverse a person microbiome, the greater their health and well-being. One way to increase said variety is interacting with outside surroundings.

[Related: A link to depression might be in your gut bacteria]

“A lot of [microbes] are beneficial to human health,” says lead study author Elizabeth Hénaff, an assistant professor at the center for urban science and progress at New York University. “The goal of this study is understanding the whole breadth of diversity of microbiomes and the ones we’re interacting with in urban environments.” 

Hénaff and her colleagues knew they wanted to create microbial maps of different cities to get a better sense of  the diversity in each area. However, they weren’t sure what was the best way to move forward. One idea was swabbing noses, but it would be impractical to swab everyone in a broad and diverse area. The urban microbiomes might also differ from block to block, requiring extensive swabbing. Another option was wastewater surveillance, but the researchers wanted to look at everything urbanites came into contact with—not just what they digested. Then came the aha moment: they could study bee hives.

Because honeybees constantly interact with the environment when they forage for nectar, and they often carry back some bacteria, fungi, and other microorganisms from their travels  when they return to the hive. “As bees are foraging, they’re traversing all of these microbial clouds related to other aspects of the built environment,” explains Hénaff. “They’ve traversed the microbial cloud of a pond, a body of water, and groups of human beings if they happen to be in the same park where they’re going.”

The scientists used a technique called metagenomic sequencing to study all the genes found in a single environmental sample. This allowed them to match genes to different microbial species related to hive health and, in turn, learn the health status of the bees. But first they had to figure out what sample should be collected from the hive.  

In a pilot project in Brooklyn, New York, the scientists worked with local beekeepers. They took swab samples of honey, propolis (a resin-like material used to cover the inside of hives), debris, and bee carcasses—anything that could provide the most information on microorganisms.

Subsequently, they discovered that the microbes found in honey and propolis were similar across hives. “Bees are really good at controlling the microbial environment of their own beehives,” adds Hénaff. The only material that differed from hive to hive was the debris left at the bottom of the hive, and this became the source they collected in the next set of experiments.

To profile urban microbiomes, the team took samples of debris from 17 tended hives from four cities across the world: Sydney and Melbourne in Australia, Tokyo, and Venice. The DNA extracted from the bee debris contained material from different sources, including plants, mammals, insects, bacteria, and fungi in the area. 

Honeybee hive debris in test tubes at a Cooper Union lab
Collected honeybee-hive debris in preparation for DNA extraction at The Cooper Union in New York City. Devora Najjar

Each city carried a unique microbial profile that gave a snapshot of how life is like there. The single Venice hive used in the study was filled with wood-rotting fungi. Hénaff says the findings makes sense since most buildings are built on submerged wood pilings. In Australia, the two Melbourne hives had large amounts of eucalyptus DNA, while Sydney’s revealed high levels of a bacterium called Gordonia polyisoprenivorans, that breaks down rubber. Tokyo’s dozen hives displayed genetic hints of lotus and wild soybean—a common plant found in Eastern Asia. There were also high levels of a soy sauce fermenting yeast called Zygosaccharomyces rouxii

“Most interesting to me was that [the results] didn’t feel like a disjoint metric from all the other things we know about these cities and their culture, but it actually felt like a puzzle piece we didn’t know existed that fit into our general understanding of these cities,” says Hénaff.

The debris were also helpful in identifying microbes involved in bee health. The team found three honeybee crop microbial species—Lactobacillus kunkeii, Saccharibacter sp. AM169, and Frishella perrara—along with five species related to the insects’ gut health. Three honeybee pathogens were also identified across cities. 

Next, the study identified the human pathogens bees could pick up when venturing outside. The researchers focused on the hive information collected in Tokyo because it had more hives than the other cities, and so had more data for DNA sequencing. They detected two bacteria: one that could cause bacillary dysentery and another involved in cat scratch fever. They then took the pathogen behind cat scratch fever, Rickettsia felis, and reconstructed the genome. Doing so allowed them to not only confirm the species was in the city, but that it had the bacteria-associated molecules to allow it to spread disease. 

[Related: 5 ways to keep bees buzzing that don’t require a hive]

Profiling the microbiome of different cities may be an additional tool for detecting potentially harmful pathogens in humans, says Hénaff. It could also open up new ways of surveying airborne pathogens—a growing interest since the recent arrival of SARS-CoV-2.

Jay Evans, a research entomologist at the US Department of Agriculture who was not involved in the study, says the new approach is “fine” and can help in identifying at least the microorganisms found in urban floral environments. However, he expressed reservations about overvaluing some results. Evans notes that one of the species genome-mapping algorithms used in the study is known to be “a bit greedy,” matching the best microorganism available at the moment. This suggests some genetic matchups to bacteria may not actually be the right fit, and that further tests would be needed to confirm their presence. Because bees can pick up non-living hitchhikers like pesticides, Evans also says it would be nice for the researchers to contrast these biological results with pesticide-specific studies and how that affects hive microbiomes.