Linking fitness and the microbiome: exploring variation in microbial composition in the North American red squirrel (Tamiasciurus hudonsicus)

Supervised by Dr. Albrecht Schulte-Hostedde (website)

Master's project

The microbiome

The bacterial microbiome is, in brief, a bacterial community which inhabits a certain space. Recently much focus has been placed on the association between the gut microbiome and illness or behaviour in humans, yet little is known about the influence of the microbiome on health in wild mammals.

These results could have an important influence on the conservation of Species at Risk or the re-introduction of captively-bred individuals to the wild. These studies, however, must first define the 'normal' microbiome in order to evaluate the role of deviant microbiome communities on host fitness.

My project

My Master's thesis sought to close the gap between our knowledge of human and lab mammal microbiome/health interactions and our knowledge of how these interactions behave in the wild.

I chose to use the North American red squirrel as a model species for a few reasons. First, they are abundant, making larger sample sizes easier to obtain. Red squirrels are also territorial, making it possible to design a study that allowed for multiple captures of the same individuals, which ultimately allowed me to track changes in their microbiomes over time.

Initial results

The figure above depicts each individuals' buccal and faecal phylum abundances across two capture periods. Each individual has a unique identifier (M = male, F = female, No. = individual). To zoom in on the graph, click on the image.

Several pieces of information can be interpreted from this figure. For example:

The buccal and faecal microbiomes are distinct from each other in these individuals.
There are some intra-individual changes between captures, suggesting at least some amount of microbial variability within these individuals' microbiomes over time.

Complete results

My entire thesis and all results can be found here. The publications page on this website will also be updated periodically, as many of my results are either published, in press, or in preparation. Finally, you can view a sample of the Next Generation Sequencing pipeline (Illumina MiSeq) I constructed for this project on my GitHub page here.