Post-transport recovery trajectory of the canine gut microbiome and metabolome

BACKGROUND: Transportation induces a multisystem stress response in companion animals, yet the integrated recovery dynamics across physiological, microbial, and metabolic domains remain poorly characterized. This study comprehensively tracked the 7-day recovery trajectory in dogs following road transport by analyzing clinical parameters, fecal microbiome and metabolome. RESULTS: Time-dependent changes were observed across domains, with differing temporal patterns. Fecal consistency improved rapidly, while behavioral scores exhibited a decrease followed by stabilization. Microbial alpha diversity initially decreased, with significant community restructuring persisting throughout recovery, culminating in a new stable state distinct from the arrival (D0) state. This shift was characterized by early enrichment of Fusobacterium and Clostridium sensu stricto 1, followed by late dominance of Erysipelatoclostridium, contrasting with the initial post-transport (D0) community dominated by Prevotella 9, Lactobacillus, Phascolarctobacterium, Anaerobiospirillum, Parabacteroides, and Prevotellaceae GA6A1 group. Metabolomic profiling confirmed a sustained metabolic shift, involving pathways in the biosynthesis of steroid and unsaturated fatty acids and the metabolism of butanoate and several amino acids. Strong cross-domain correlations linked specific microbial genera and metabolites with behavioral improvement, underscoring gut-brain axis involvement. CONCLUSION: By D7, several measures remained distinct from the arrival (D0) state, indicating persistent multi-system differences during the first week after transport. These findings elucidate the complex, coordinated adaptation to transport stress, highlighting ongoing clinical, microbial, and metabolic differences by D7 and providing a framework for interventions aimed at enhancing welfare and resilience in transported companion animals.