A new gut microbiome study of bears in eastern North Carolina expands our understanding of microbial ecosystems in omnivores and contributes to the broader idea that bear feces could help scientists monitor changes in the environment. The study also found that bears may play an unexpected role in dispersing antibiotic-resistant pathogens.

“American black bears (Ursus americanus) have a simple gut morphology and it doesn’t take long for food to pass through their system, which prevents regulation of the microbial ecosystem in the animal’s gut,” says Erin McKenney, corresponding author of a paper on the study and an assistant professor of applied ecology at North Carolina State University.

In other words, the bear’s immune system does not have time to respond to the introduction of new microbes; the bear’s gut can’t regulate which microbes make up its gut microbiome.

“Coupled with the fact that bears eat an exceptionally wide variety of foods, this means the gut microbiome of black bears can be highly variable,” says McKenney. “And, in theory, this also means that a bear’s gut microbiome would reflect its environment.

“We wanted to see if this is actually true and, if so, the extent to which we can use gut microbiome samples to get insights into both what is happening in the bear’s environment and what the bears are eating.”

For the study, researchers collected gut samples from 48 wild bears that had been harvested by hunters in eastern North Carolina. Specifically, the researchers obtained nine small-intestine samples and 39 large-intestine samples.

The researchers then used genetic sequencing techniques to identify the genus of microbes found in each gut microbiome, as well as the relative abundance of each type of microbe. In addition, the researchers conducted analyses to predict the functions that these microbe genera perform in the gut.

“Many of the findings were consistent with what we anticipated,” says Dorian Hayes, co-author of the study and a former NC State undergraduate who now works for the North Carolina Wildlife Commission. “The microbial communities we found in each gut microbiome were wildly variable across all of the samples, with each gut microbiome consisting of many different microbial taxa.

“We also found that, despite the highly variable taxa present in each microbiome, the predicted function of the microbial communities was very consistent from bear to bear,” Hayes says.

However, the study also produced some unexpected findings.

“It’s well-established that predators tend to have a lot of pathogens in their gut microbiomes, so we were prepared to find some pathogenic bacteria,” says McKenney. “But we were surprised to find that two of the most significant genera in the bear microbiomes are pathogens known to be resistant to antibiotics.

“Another surprise was that the most dominant genus across all of the samples was a microbe known to be associated with infection and obesity in humans,” McKenney says. “Many humans view obesity as bad, but contributing to obesity actually makes these microorganisms beneficial for bears, who want to pack on as much fat as possible to get through the winter.”

“Bears are fascinating, and the nature of their digestive system and feeding behavior means that they are essentially living biosensors of their environment,” says Diana Lafferty, co-author of the study and an associate professor of biology at Northern Michigan University. “The work we’ve done here helps us better understand the nuances of what is happening in their gut microbiome, and what that can tell us about not only bear health but environmental health. And while this work was done using gut samples, these findings can also help us interpret microbial samples collected from bear feces.

“Bears are expanding their range across much of the continental United States, and expanding our understanding of the microbial ecosystems in this species means that they could serve as a sentinel species for understanding changes in the environment,” says Lafferty.

The paper, “Gut site and sex-specific enrichment of bacterial taxa and predicted metabolic pathways in wild American black bear (Ursus americanus),” is published in the open access journal PLOS One. The paper was co-authored by former NC State undergraduates Erik De Jesus, Natalie Morais and Adrianna Staal; NC State M.S. graduates Taylor Hatfield, Christian Ivarsson and Kalle Simpson; NC State undergraduates Kaleb Holder and Hunter Payne; visiting undergraduate Holly Thompson; Colleen Olfenbuttel of the North Carolina Wildlife Resources Commission; and Rachael Hildreth of Northern Michigan University.

This work was done with support from the N.C. Wildlife Resources Commission and the NMU College of Arts and Sciences.