What if the very actions we take to save an endangered animal are quietly changing its fundamental biology? For the deep-snow mountain caribou of British Columbia, this isn’t just a thought experiment. A new study reveals that a common conservation method, called “maternity penning,” which protects pregnant caribou and their calves from predators, may be altering these animals’ unique digestive systems. This groundbreaking research raises a crucial question: are we helping these caribou survive in the short term, only to impact their long-term health and ability to thrive in the wild?
These aren’t just any caribou; they’re remarkable creatures that have adapted to life in high, snowy mountains. In winter, when other food is scarce, they rely almost entirely on specific “hair lichens” that hang from old-growth trees. Think of these lichens as their special superfood, completely different from the ground lichens eaten by other caribou. This unique diet, the study explains, supports an equally unique community of bacteria and other tiny organisms in their digestive tracts—what scientists call their “gut microbiome.” This microscopic world is incredibly important, helping the caribou break down tough plant material and get all the energy they need from their unusual diet.
The Caribou’s Digestive Secret: A Unique Gut Community
Researchers at the University of Alberta embarked on a scientific detective mission, analyzing the genetic clues left behind in caribou droppings. Their goal was to understand the eating habits and gut health of these elusive animals. They collected 67 fecal samples from different groups of caribou. These included wild, free-ranging deep-snow caribou, shallow-snow caribou from a different region, deep-snow caribou held in a maternity pen, and even semi-domesticated reindeer on a controlled diet.
By examining the DNA in these samples, the scientists could pinpoint exactly what the caribou had been eating (like lichens, algae, and plants) and identify the specific types of bacteria living in their guts. This detailed analysis showed that the wild deep-snow caribou truly have a specialized winter diet, relying heavily on hair lichens. This specialized diet, in turn, correlated with a distinctive gut microbiome—one that actually had fewer different types of bacteria compared to caribou eating other foods. This finding suggests a strong evolutionary link between their diet and their internal biology.
A particularly interesting discovery was the high presence of a bacterium called Paramuribaculum in the guts of free-ranging deep-snow caribou. This bacterium, along with others like Colidextribacter and Phocaeicola, plays a key role in breaking down complex carbohydrates. The researchers believe this specific microbial team is perfectly suited to digest the unique sugars found in the hair lichens these caribou consume.
How Maternity Penning Changes Caribou Diets
The most eye-opening part of the study concerned the caribou held in maternity pens. These animals, meant to be protected, showed significant changes in both their diet and their gut microbiome. While they still ate some hair lichens, a much larger portion of their food in the pens came from other types of lichens and, notably, more plants. For example, the presence of flax in their droppings clearly indicated they were consuming commercial feed, which contains flax.
This dietary shift had a direct impact on their gut microbes. Penned caribou had significantly less of the specialized Paramuribaculum bacteria. Instead, other related bacteria, like Muribaculum and Duncaniella, became more common. While these bacteria also help with digestion, the core takeaway is that a fundamental part of the caribou’s biology—their specialized gut ecosystem—was being reshaped by human intervention.
The Unseen Consequences for Caribou Conservation
This study highlights a complex challenge in saving endangered species: how do we protect them without unknowingly altering their natural adaptations? For the deep-snow mountain caribou, whose very survival depends on their ability to thrive on a specialized winter diet, maintaining a healthy and appropriate gut microbiome is absolutely vital.
The findings indicate that current maternity penning methods, while successful at keeping predators away, might need to be reevaluated. Conservation managers should consider the specific dietary needs of these caribou. This could involve ensuring that the food provided in pens—whether collected lichens or commercial feed—very closely matches what they would naturally eat.
Furthermore, the research supports the idea of regularly checking caribou droppings for changes in their diet and gut microbes, especially when they are in captivity or experiencing dietary shifts. This non-invasive monitoring could provide crucial information, allowing managers to adjust their strategies and potentially prevent unforeseen health problems. The ultimate goal is to safeguard not only these endangered creatures from immediate threats but also their long-term health and their innate ability to survive in the wild, a capability that, as this study powerfully demonstrates, begins with the invisible world inside their guts.
Paper Summary
Methodology
Researchers conducted a study using faecal DNA metabarcoding to analyze the diet and gut microbiome of 67 caribou samples. They collected samples from free-ranging deep-snow mountain caribou, shallow-snow caribou, deep-snow caribou in a maternity pen, and semi-domesticated reindeer. DNA was extracted, amplified for specific genetic markers (plants/fungi, bacteria/archaea), and then sequenced. Statistical analyses were performed to identify differences in diversity and composition between the groups.
Results
The study found that free-ranging deep-snow mountain caribou have a distinct winter diet of arboreal hair lichens, which is linked to a unique, less diverse gut microbiome. They had a high abundance of Paramuribaculum bacteria, associated with complex carbohydrate digestion. Caribou in maternity pens showed altered diets, consuming more other lichens and plants (including flax from commercial feed), leading to a significantly different gut microbiome with fewer Paramuribaculum and more Muribaculum and Duncaniella.
Limitations
Key limitations included seasonal sampling differences (winter vs. spring samples), inability to track microbiome changes post-release from pens, limited sample sizes for detailed within-group analysis, and the study of only one maternity pen. Inherent biases in DNA-based metabarcoding, such as varying DNA preservation and potential contamination, were also noted.
Funding and Disclosures
The study received funding from NSERC Discovery Grants (to T.S., L.S., C.C.S.C.) and a Canada Research Chair in Symbiosis (to T.S.), with additional support for S.S. from a Vanier Canada Graduate Scholarship. Funding agencies had no role in the study’s design, data, analysis, or publication decisions. The article is open access under a Creative Commons Attribution License.
Publication Information
The paper, titled “Endangered Deep-Snow Mountain Caribou Have a Distinct Winter Diet and Gut Microbiome That May Be Altered by Maternal Penning,” was published in Molecular Ecology in 2025. The publication reference is Molecular Ecology, 2025; 34:e17783, and it can be accessed at https://doi.org/10.1111/mec.17783. The authors include Scott Sugden, Robert Serrouya, Lalenia Neufeld, Helen Schwantjes, Colleen Cassady St. Clair, Lisa Stein, and Toby Spribille.