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Birds harbor complex gut bacterial communities that may sustain their ecologies and facilitate their biological roles, distribution, and diversity. Research on gut microbiomes in wild birds is surging and it is clear that they are diverse and important – but strongly influenced by a series of environmental factors. To continue expanding our understanding of how the internal ecosystems of birds work in their natural settings, we believe the most pressing needs involve studies on the functional and evolutionary aspects of these symbioses. Here we summarize the state of the field and provide a roadmap for future studies on aspects that are pivotal to understanding the biology of avian gut microbiomes, emphasizing prospects for integrating gut microbiome work in avian conservation and host health monitoring.