Microbes gone wild

By: Alicia Halhed, University of Guelph

Would you believe me if I told you that most of the species on Earth were organisms you couldn’t see with your bare eyes? What about if I said that much of that diversity lived inside your body? Well, that’s your microbiome - a community of microorganisms that may include bacteria, fungi, and eukaryotes. Your microbiome is dynamic and changes over time. Different species will also have very different microbiomes, for example in birds and squirrels.

I am a master’s student in the bioinformatics graduate program at the University of Guelph, which means I use statistics and computer science to solve problems in biology.

The problem I am trying to solve is how microbiomes assemble themselves in wild animals. Knowing about the microbiome is essential to understanding the health of the organisms they live in.

Trying to understand microbiome assembly is like if you were trying to improve your health. You couldn’t just understand one thing, make changes there, and then say you’re perfectly healthy. There’s a lot more moving parts that you need to change depending on your current lifestyle.

The two ecological systems I currently study are North American red squirrels living near Kluane National Park (Yukon, Canada) and Canada jays living in the south end of Algonquin Provincial Park (Ontario, Canada). Both species have been the subjects of long-term ecological monitoring projects trying to understand how they survive the harsh winters in Canada.

Just like our muscles at different locations in our body plays a specific role in our bodies’ function, microbiomes have specific roles to play in their environment. Like the different types of muscles found throughout the body, the type of microbes present change depending on their location.

In squirrel part of my research, I analysed the squirrels’ fecal microbiome (yes, poop!). Fecal microbiomes are important because they allow us to understand what microorganisms live in the digestive system. While some bacteria living in the digestive system can make the squirrel sick, most can help the squirrel digest the food it consumes.

In medicine, some circumstances even warrant fecal microbiome transplants, where fecal matter (poop) from a healthy individual is introduced in the digestive system of a sick individual. I know fecal microbiome transplants may seem gross but introducing healthy microbes this way has had much success in treating digestive conditions such as ulcerative colitis.

While my research is not about treating specific health conditions in squirrels, my findings inform how microbes spread themselves through the population. This is a process known as local homogenization, where microbiomes near to one another (i.e., in neighbouring squirrels) become more similar. So, if a squirrel is host to a pathogen, they are most likely to pass that illness-causing pathogen to their immediate neighbours.

For the Canada jays, I chose to study their oral microbiome instead of their fecal microbiome. These birds store perishable food in trees to consume in the winter when no fresh food is available. Since the foods are coated in saliva before they get stored, the microbiome in the jay’s oral cavity gets transferred to the food item via the saliva. Any microbes on the food have the potential to break it down – we know they help with digestion!

Warm climates encourage microbial growth, which poses a threat to the quality of foods that Canada jays have to consume in the winter if the temperatures are warmer than expected. Understanding how the Canada jay’s oral microbiome might contribute to food preservation and winter survival is essential to ensuring the species’ can continue living in their current habitat.

My analysis on the Canada jays’ oral microbiomes identified strong seasonal differences in which microorganisms were present in the microbiome and what the microorganisms were doing. For example, microorganisms in the fall were seen to produce extra Vitamin B12. Having enough B12 is known for preventing weight loss – which is important if you’re a small bird trying to survive the harsh Canadian winters!

While we cannot see our microbiomes with our eyes, I hope you now understand how they contribute to animal health. Continuing to study microbiomes, especially in wild animals, is vital for predicting how animal health may be affected in response to climate change.

Edited by B.G. Borowiec and A.E. McDonald. Header photo adapted by B.G. Borowiec. Stock photos from Unsplash and Wikimedia Commons.