Abstract
Free-living animals encounter a wide range of stressors that can shape behavior, physiology, and health across their lifetime. Increasing evidence suggests that the gut microbiome may play an important role in mediating these responses, yet we still know relatively little about how host-associated microbial communities respond to ecological stressors in wild animals. This gap is especially important for wild animal welfare, where microbial communities may provide insight into host condition, stress physiology, and the capacity of animals to maintain homeostasis under changing environmental conditions. Thus, in this dissertation, I evaluated the broader potential of the microbiome as a tool for assessing welfare in free-living animals, and then investigated how a prevalent ecological stressor, predation risk, influences the gut microbiome of wild white-footed mice (Peromyscus leucopus). In Chapter 2, I reviewed the promise and limitations of using the gut microbiome as a biomarker of wild animal welfare, arguing that microbiome-based approaches are most powerful when integrated with behavioral, physiological, and ecological measures. In Chapter 3, I showed that chronic auditory predation risk reorganized gut microbial communities in captive wild-caught mice, with the strongest effects emerging at the community level rather than through broad shifts in alpha diversity. In Chapter 4, I examined these relationships in free-living mice and found that predation risk altered microbial community structure in a natural population, while associations among the microbiome, glucocorticoids, and behavior were subtle and context-dependent. Overall, this work provides novel insight into how ecological stressors shape host-associated microbial communities in wild mammals. These findings highlight the importance of studying the microbiome in ecologically realistic contexts and suggest that microbial responses may reveal dimensions of wild animal welfare that are not fully captured by conventional behavioral or endocrine measures.