Dominant factors shaping the gut microbiota of wild birds

ABSTRACT The role of the gut microbiota in regulating host physiology and health is well established, with effects on host development, behaviour, nutrition, immunity, and reproductive strategy. While mammalian and insect microbiomes have attracted considerable research attention, avian microbiome research is deservedly growing, given the key roles that birds play in ecosystem services and functioning. Here we review recent literature (2008–2021) on the gut microbiome of wild birds, focusing on the role of key drivers that shape gut bacterial communities: diet, environment, and the phylogeny of host species. While most studies on avian gut microbiomes are confined to domestic poultry research, studies of wild birds have been increasing, particularly for the orders Passeriformes, Charadriformes, and Anseriformes. Four bacterial phyla dominate the gut microbiota of wild birds: Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes with varying abundances and compositions across taxa. Diet was reported to be the most influential factor shaping avian gut microbiomes, followed by phylogeny, habitat, the nest environment and seasonal variation. However, the current scarcity and large variation in reported patterns limits a clear understanding about how the ecology and evolution of birds are affected by the gut microbiome. Increased research effort is needed that links microbial diversity to function and avian health, with an expansion of sampling across host phylogenetic lineages, environmental conditions, dietary niches, and life stages. A shift towards field-based experimental approaches will further contribute towards more conclusive findings, which will serve to advance threatened species management in both captivity and in the wild.