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Members of the gut microbiota genus  Bifidobacterium  are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of  Bifidobacterium  isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of  Bifidobacterium castoris ,  Bifidobacterium animalis  and  Bifodobacterium pseudolongum  were detected in wild mice ( Apodemus sylvaticus ,  Apodemus agrarius  and  Apodemus flavicollis ), but not voles or shrews.  B. castoris  constituted the most commonly recovered  Bifidobacterium  (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated  B. castoris  clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including  in vitro  growth assays, suggested that mouse-derived  B. castoris  strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that  Bifidobacterium  has a labile relationship with its host over evolutionary time scales.

Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential