Comparative Analysis of Nasal and Cloacal Bacterial Communities in Three Sea Turtle Species under Rescue Center Conditions

The mucosal microbiome plays a critical role in host health, yet the structural dynamics of the sea turtle nasal microbiome remain largely unexplored, and the ecological driving mechanisms of the cloacal microbiome under specific rescue contexts remain poorly understood. This study employed 16 S rRNA gene amplicon high-throughput sequencing to analyze bacterial community diversity in the nasal cavity and cloaca of green turtles (Chelonia mydas), hawksbill turtles (Eretmochelys imbricata), and olive ridley turtles (Lepidochelys olivacea) rehabilitated at the Naozhou Island Rescue Station. Results showed that the nasal microbiota exhibited high environmental plasticity. Holding conditions significantly explained > 50% of the variation in the green turtle nasal microbiota: unlike the low dominance and high evenness characteristics of the indoor group, specific outdoor environmental pressures drove the targeted enrichment of Sedimenticolaceae; whereas short-term indoor individuals displayed individual signatures associated with facial physical injury and stress. Beyond environmental effects, distinct species-specific patterns were also observed in the nasal cavity: the stable, high-abundance colonization of Deinococcota in hawksbill and olive ridley turtles constituted a distinct feature distinguishing them from green turtles. Regarding the cloacal microbiome, host species identity exerted the most significant effect, showing strong phylogenetic conservatism. The green turtle cloacal microbiota demonstrated significant environmental resistance, maintaining a core composition of Proteobacteria, Bacteroidota, and Campilobacterota. Hawksbill and olive ridley turtles reflected specific differentiation and functional convergence of the cloacal microbiota driven by dietary guilds: both exhibited a uniform high abundance of Cardiobacteriaceae, while Brumimicrobium served as a significant biomarker distinguishing hawksbills from the other two species. Within the constraints of sample size, this study establishes critical foundational data on the mucosal microbiomes of these three sea turtle species in a controlled rescue environment. Based on these profiles, we propose that the nasal microbiota serves as a sentinel for monitoring environmental stress, while the cloacal microbiota acts as a cornerstone for maintaining physiological homeostasis, thereby providing a critical scientific basis for health assessment, the optimization of rescue environments, and the development of species-specific conservation strategies.