Abstract
Chronic wasting disease is a fatal, contagious, neurodegenerative prion disease that affects both captive and free-ranging Cervid populations in North America, Scandinavia, and South Korea. Previous studies have shown links between chronic wasting disease status and the microbiome, as well as links between other prion diseases and microbiome shifts. However, there is a gap in knowledge for how the microbiome is affected during different stages of chronic wasting disease progression. Here, we expand this research by analysing the microbiome of white-tailed deer at different pathological stages of the disease: negative, lymph node positive, and brain and lymph node positive. We used a previously published 16S rRNA dataset to determine diversity metrics, core microbiome, indicator taxa, and differential abundance. Our results showed no significant difference in either sex for alpha and beta diversity. In contrast to this, we found a significant shift in core microbiome composition for male deer across pathology states, as well as a significant change in differential abundance for both sexes across pathology states. We found shifts in differential abundance in bacterial phyla associated with carbohydrate fermentation, short-chain fatty acid production, and energy metabolism. Our findings suggest that the microbiome shifts as disease progresses in terms of its composition and abundance, but not in terms of diversity metrics, and that these shifts are sex-dependent. Our differential abundance findings suggest that chronic wasting disease pathology states cause shifts related to core metabolic guilds rather than individual taxa.