Linking fitness and the microbiota: exploring variation in microbial composition in the North American red squirrel (Tamiasciurus hudsonicus).

Abstract

The importance of microbial communities, or microbiota, to host physiology and fitness is readily becoming apparent in laboratory animals and humans. Yet, little is known about the association between microbiota composition and fitness in wild animals, including the relation to host health and temporal or spatial variation. In this thesis, the promiscuous North American red squirrel, Tamiasciurus hudsonicus, was used to investigate if oral, gut, and genital microbiota differed with correlates of host fitness, sex, or capture period. These objectives were met using various sequencing techniques, including 454-Roche and Illumina MiSeq sequencing. Microbiota composition varied in all three body regions investigated, suggesting the impact of body region is influential on microbial composition in red squirrels. Evidence of differences in composition between sexes was only significant in the oral microbiota, which also displayed significant variation in beta diversity analysis between recaptures. As such, future research should be cautious in interpreting results from a single temporal sampling period when quantifying characteristic microbiota composition in wild mammals, and should account for potential sex bias within study designs. Body condition, a rudimentary measure of host fitness, was not correlated with composition in the microbiota of any body region. However, there were significant correlations between immune status and the oral microbiota composition, suggesting that some measures of fitness may be related to microbiota composition in a wild mammal. Together these results provide, for the first time, a comprehensive view of inter- and intra- individual factors contributing to microbiota variation across body regions and provide evidence for a correlation between microbial composition and fitness in a wild mammal.