Gut microbiome shifts during frog development parallel host-association patterns across vertebrate lineages

The developmental habitat transitions between aquatic and terrestrial environments in frogs offer a compelling model to investigate how environmental shifts shape gut microbiota. However, our understanding of how these transitions influence gut microbial communities across frog development remains limited. Here, we investigated how habitat changes during frog development affect gut microbiota composition and compared these patterns with host-microbiome interactions across vertebrates. Frog gut microbiota composition changed across developmental stages, and the proportion attributable to the surrounding environmental communities was highest at the egg stage and declined thereafter. Functional analysis of gut microbiota revealed that oxygen-related microbial phenotypes shifted from aerobic to anaerobic during development. Habitat preference analysis further demonstrated that mammals have higher proportions of animal-associated microbes in their guts than non-mammals (Actinopterygii, Amphibia, Aves, and Reptilia). These findings indicate that the aquatic-to-terrestrial transition is accompanied by a reduction in the environmental contribution to the gut community rather than by an increase in host selection, providing an ecological framework for interpreting host-association patterns across vertebrate lineages.