Environmental Perturbations during the Rehabilitation of Wild Migratory Birds Induce Gut Microbiome Alteration and Antibiotic Resistance Acquisition

Wild migratory birds are essential for sustaining healthy ecosystems, but the effects of a rehabilitation period on their gut microbiomes are still unclear. Here, we performed longitudinal sampling, 16S rRNA sequencing, and antibiotic resistance monitoring of the gut microbiome of six species of wild migratory birds protected as natural monuments in South Korea that are subject to short- or long-term rehabilitation periods. Overall, gut microbiome diversity was significantly decreased in the early stages of rehabilitation, and it did not recover to a level comparable to that of wild birds. Moreover, while the abundance of short-chain fatty acid-producing bacteria decreased, that of zoonotic pathogens increased, indicating rehabilitation-induced dysbiosis. The metabolic pathways involved in the degradation of aromatic pollutants were significantly downregulated, suggesting the depletion of pollutant-degrading microorganisms. Antibiotic resistance of Escherichia coli significantly increased during rehabilitation, particularly ciprofloxacin and tetracycline resistance, and seven of the rehabilitated wild birds acquired multidrug resistance. The diet and habitat changes experienced by wild migratory birds during rehabilitation may have induced the observed gut microbiome dysbiosis and acquisition of antibiotic resistance. These rehabilitation-induced alterations might affect the adaptability of wild birds to their natural environments and contribute to the spread of antibiotic resistance after their release. IMPORTANCE Wild migratory birds are key for ecosystem health but highly sensitive to anthropogenic activities. Therefore, wild migratory birds often undergo rehabilitation to prevent species extinction or biodiversity monitoring. However, the impact of rehabilitation on the gut microbiome of wild migratory birds, which is closely associated with host fitness, remains unclear. For the migratory bird species considered natural monuments in South Korea evaluated here, such impacts could include rehabilitation-induced gut microbiome dysbiosis and acquisition of antibiotic resistance, with possible repercussions on the adaptability of wild birds and spread of antibiotic resistance in the environment after their release. Therefore, the dynamics of the gut microbiome and antibiotic resistance should be considered for implementing sustainable rehabilitation strategies.