Environment Supersedes Host Lineage in Shaping the Gut Microbiome of Squirrels in the Pacific Northwest

Shiling Zhao
Undergraduate (Animal Sciences – Nutrition)
Dr. Andreas Chavez
Animal Sciences

Both host genetics and environmental factors have been shown to influence the establishment and composition of the gut microbiome, but it remains unclear whether host genetics or environment has a stronger effect in shaping the gut microbiome. The present study exploits a natural reciprocal transplant system of island and mainland Tamiasciurus hudsonicus (red squirrels) and T. douglasii (Douglas squirrels) in the Pacific Northwest to investigate the relative strength of genetic and environmental factors in influencing gut microbiome composition. Phylogeographic analysis of Tamiasciurus squirrels have shown a closer genetic relatedness between Vancouver Island (VI) red squirrels and interior mainland red squirrels despite the closer geographic proximity between VI red squirrels and coastal mainland Douglas squirrels. We extracted DNA from cecal samples of 35 red squirrels (13 VI and 22 mainland) and 34 Douglas squirrels specimens collected between 2008 and 2010 and amplified the V4 region of the bacterial 16s rRNA gene. The data were grouped by collection site, species identity, and geographic region, which we established based on the World Wildlife Fund's terrestrial ecoregion classifications that consider flora and fauna communities and environmental conditions. Surprisingly, our principal coordinate analysis (PCoA) plots for Bray-Curtis dissimilarity and weighted Uni-Frac distance showed VI red squirrels clustered with coastal mainland Douglas squirrels instead of with interior mainland red squirrels. Similarly, permutational analysis of variance (PERMANOVA) tests for Bray-Curtis and weighted Uni-Frac showed a large distance between the VI and interior mainland red squirrels. Altogether, these results suggest that the environment is a stronger driver of the gut microbiome in Tamiasciurus in the Pacific Northwest than host lineage is. Our findings from this natural reciprocal transplant system provide additional support to a growing number of studies indicating that the environment overshadows phylogenetic effects of the host species in shaping the gut microbiome.