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A gut feeling

Speed read
  • Bees, like all organisms, have a community of microbes living in their gut
  • Agricultural monoculture is negatively affecting these microorganisms
  • HPC machines can help us better understand the microbiomes within bees

Size is a matter of perspective. A skyscraper is enormous to a human, but microscopic on a galactic scale. Conversely, a bee is tiny compared to a person. But if you continue downward in size, eventually you’ll run into microbes.

These microscopic organisms present either as individual cells or a colony, but don’t let their size fool you. They actually play a big role in an animal’s gut health.

<strong>Scientists are scrambling</strong> to figure out why the honeybees that do the vital work of pollinating our crops are experiencing a rapid decline. Bioinformatician Eric Smith thinks at least part of the answer may lie in the bees’ microbiome. While both humans and bees coexist with the microbes in their bodies, each organism has different requirements of their tiny friends. Dr. Eric Smith, previously of the Newton Lab at Indiana University (IU) and now a bioinformatician at CoreBiome, attempted to dive into the specifics of bee microbiomes with the help of the Carbonate computer cluster.

Colony collapse disorder is hitting bees hard right now, and scientists are scrambling to figure out exactly why. Smith’s work could help us better understand what does—and doesn’t—help bees thrive.

Tiny creatures, big roles

As Smith explains, microbes are essential to a healthy gut because they help their host digest molecules they might not be able to break down otherwise. But that’s not all they do.

“The microbiome can provide pathogen protection and help with overall health,” says Smith. “If you have certain microbes present, and then you try to infect bees with a specific fungal pathogen, that fungal pathogen can’t take hold.”

<strong>More than half of US farmland</strong> is planted with just three crops: corn, wheat, and soybeans. This lack of variety may be contributing to the many problems plaguing honeybees. He continues, “We've also seen that insects that are raised without their microbiome end up being quite a bit smaller and more sickly than their counterparts that are raised with the microbiome.”

These effects may be especially important for honeybees. Specifically, honeybees are split into two factions – worker bees and the queen. While they start out as genetically identical eggs, the workers consume worker jelly while the queen is fed royal jelly, leading down two different developmental paths.

“The microbiomes of queens and workers differ quite a bit,” says Smith.  “Workers have anywhere between 8-10 different bacterial taxa which are the same among all workers, no matter which hives you sample from. You can sample a hive in Indiana and a hive in Europe, and they're going to have pretty much the same microbiome.”

“The queens have a very different microbiome,” Smith continues. “The queen's digestive tract is predominantly an acetic acid bacteria, which is actually one that provides fungal protection.”

This specialization of the queen bee’s microbial communities leads into one of the major problems facing bee populations: agricultural monoculture.

<strong>When honeybees forage,</strong> they carry microbes back to the hive along with nectar and pollen. But if they’re not getting enough diversity of plants, then microbe diversity also suffers. In 2017, more than 396 million acres of land in the US were devoted to crop farming. Of this, nearly 220 million acres were planted with corn, wheat, and soybeans. That’s around 55 percent of US cropland revolving around just three plants.

“Honeybees go out and forage, and they bring back pollen and nectar to the hive,” says Smith. “What comes back with them is microbes. You can imagine that microbes could be pretty specialized on the plants they happen to live on. And so, if they're not getting a big enough diversity of plants, they’re not getting big enough diversity of microbes coming back to the hive.”

Organism agnostic

Smith analyzed the DNA sequences of bees and their microbes using IU’s Carbonate computer cluster. Each genome he studied was about two megabases, and he examined more than several hundred genomes. This demanded machines capable of handling terabytes of data at a time.

Carbonate gave Smith access to the resources he needed, while also allowing him to easily collaborate with others. His work in this area attempts to better understand how microbes alter and improve the lives of their bee hosts.

Despite the obvious implications for bee health, Smith isn’t focused solely on our buzzing buddies.

“Bees are not necessarily something I was super interested in when I was younger,” says Smith. “I like to call myself organism agnostic. I like to use computational tools and comparative genomics to answer interesting or pressing questions.”

We may need more “organism agnostics.” Right now, most of the work studying microbiomes has to do with humans. That’s obviously important work, but we’ll need to broaden our gaze if we want to better comprehend what microbes are doing for all the organisms in our ecosystem.

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