Space, time, and captivity: quantifying factors influencing the microbiome of an alpine ungulate

The community of microorganisms in the microbiome is affected by host species, diet, and environment and is linked to normal functioning metabolism, immune system, and development. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. We assayed the gut microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified microbiome diversity and composition between groups in the wild and captivity, across space, and over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across the summer. Pairwise dissimilarity estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.