Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.