MICROBIOME: Microbiomes in birds: a review of links to health and reproduction

Abstract

Microbiomes have emerged as a key component essential for maintaining the health of an organism. Additionally, the roles of microbiomes are multifaceted, some unique to specific body areas and organs while others, particularly the gut microbiome, having broader effects on the entire organism. Comparative literature is emerging that compares microbiomes across mammals and birds. Domestic poultry have been the most extensively studied relative to their role in production agriculture. These data have provided a great deal of information about the effects of diet and nutritional requirements relative to the gut microbiome, productivity, and resilience to diseases. Conversely, limited research has been conducted on wild birds, despite them inhabiting a broad array of ecological niches and environments, providing a rich diversity in their adaptations to different habitats. Migratory birds and raptors are of particular interest. Migratory birds encounter a range of ecosystems and provide a link between allopatric populations. Raptors occupy high positions in the food chain, with potential exposure to biomagnification of environmental contaminants and pathogens. This review overviews our current understanding of the structure and function of avian microbiomes as related to avian health and reproduction in domestic and wild birds, highlighting knowledge gaps in need of further investigation for more effective conservation of rapidly declining avian populations. Lay summary Birds are among the most endangered organisms on the planet, vulnerable to many environmental challenges, including disease, loss of habitat, shortage of food resources, and climate-related change. They need to adapt to these challenges to survive and flourish. While the links between the gut microbiome, diet, resistance to infection, and behavior have been well studied in humans, laboratory animals, and domestic or captive birds, comparatively little is known about these associations in wildlife, where diet is expected to be more varied and seasonal. This is especially true for wild bird species. We review the information that is available on the microbiomes of both domestic and wild birds, highlighting knowledge gaps in our understanding of the health and reproduction of wild birds, toward furthering their conservation.