Despite major variations in diet, host phylogeny is a major determinant of microbiome composition in mammals, but whether this trend exists in all vertebrates was unknown. Song, Sanders et al. analysed the gut microbiomes of ~900 vertebrate species, including 315 mammals and 491 birds, and assessed the contributions of diet, the relatedness of hosts and physiology to the taxonomic composition of the microbiomes. The authors found strong correlations between microbial community similarity, diet and host phylogenetic distance in nonflying mammals. By contrast, gut microbiome composition weakly correlated with diet and host phylogeny in birds, with little evidence of host specificity. Remarkably, bat gut microbiomes follow the same trend as birds, with little correlation with either diet or phylogeny. These findings suggest that host–gut microbiome phylosymbioses depend on host factors that were lost during adaptation to flight.