The avian gut microbiota: community, physiology and function in wild birds

Gastrointestinal microbiota play a vital role in maintaining organismal health, through facilitating nutrient uptake, detoxification and interactions with the immune system. The gastrointestinal microbiota of birds has been poorly studied, especially in wild species under natural conditions. Studies of avian gut microbiota are outnumbered ten to one by studies of mammals, and are dominated by research on domestic poultry. Unlike domestic poultry, wild birds vary widely in environmental preferences, physiology, and life‐history traits, such as migratory behavior and mating systems. Species characteristics result in a vast diversity in gut microbiota and its composition and function. Avian life‐history characteristics pose selection pressures on the gut microbiota, and ultimately affect host health. Here, we review current knowledge of the gut microbiota of wild birds, including: partitioning of digestive function and microbiota among different gastrointestinal compartments, microbial diversity and function in the context of host diet, energetics and behavior, and the intrinsic and extrinsic factors impacting gut microbiota in free‐living birds. The shared core microbiota of wild bird species is dominated by members of four major phyla: Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. However, microbial communities varies inter‐ and intra‐specifically, and among gastrointestinal tract sections. To conclude, we identify three key research areas that warrant further investigation: 1) expanding the range of avian host taxa investigated, 2) identifying the function of avian gut microbiota in physiology and immunology, and 3) transitioning from observational studies to experimental manipulations to identify key determinants of wild bird gut microbiota composition.