CONCLUSION
The ability to study the same individuals and populations throughout the annual cycle greatly enhances our understanding of the consequences of changing environments and seasonal physiological stressors on gut microbiota. We demonstrate that a significant compositional shift occurs in the community structure of gut bacteria as Kirtland’s Warblers migrate from The Bahamas to Michigan. Additionally, we describe a species-specific core microbiome and the proportion of bacterial lineages retained across three periods of the annual cycle within individuals. Though Kirtland’s Warblers were recently removed from the endangered species list, continued management and research is needed for this species to survive. Healthy gut microbiota should be included in the maintenance of threatened and endangered species (Allan et al. 2018; Roth et al. 2019; DeCandia et al. 2020) and this study provides model data as to how species with small population sizes and extreme habitat specialization react to changing environments.