All mammals host communities of commensal microbes in and on their bodies. Recent technological advances, combined with experimental studies in laboratory animals, are beginning to reveal the ubiquitous links between the gut microbiome and host disease, metabolism, immunity, and numerous other host functions. A new challenge of microbiome research is to understand how microbiomes function in natural ecosystems and within free-living hosts, in order to expand our understanding of the ecological principles underlying microbiome-host dynamics, and to facilitate applications that are relevant for population health.
Here I describe microbiome diversity and dynamics across multiple ecological scales in three wild herbivore populations. I elucidate mechanisms by which microbiome diversity is maintained in a population throughout temporal resource fluctuations, and identify relationships between diet, disease, and the microbiome in a population of African buffalo. At a larger spatial scale, I describe microbiome variation across a metapopulation of bighorn sheep, and identify correlations with geography, environment, and genetic structure. Finally, I demonstrate the potential utility of microbiome surveillance for wildlife conservation and management by elucidating the impacts of supplemental feeding on the gut microbiomes of elk in the Greater Yellowstone Ecosystem.
Taken together, this body of work contributes toward clarifying the ecological processes that shape the microbiomes of free-living hosts across multiple ecological scales. The patterns and processes identified in this dissertation lay the groundwork for understanding how host-associated microbiome communities may respond to changing environmental conditions, disease, and habitat alterations.