Langgeng, A.; Sigaud, M.; Prameswari, W.; Priambada, N. P.; Rianti, P.; Sanchez, K. L.; Moore, R.; Lee, W.; MacIntosh, A. J. J.; Matsuda, I.

Illegal wildlife trade and habitat degradation displace thousands of animals annually in Southeast Asia, placing confiscated primates into rehabilitation centers that increasingly function as long-term ecological holding environments. In slow lorises, dental extraction associated with the pet trade is common and may generate persistent disruption along the oral-gut axis, potentially undermining physiological readiness for release in ways not captured by conventional veterinary screening or behavioral assessment. Here, we evaluated whether microbiome structure provides an integrative ecological component of release readiness in rehabilitating Javan slow lorises (Nycticebus javanicus). From June to October 2024, we collected fecal (n = 26) and saliva (n = 18) samples from 19 adult individuals housed at Yayasan Inisiasi Alam Rehabilitasi Indonesia, including 10 release candidates and 9 non-candidates primarily unreleasable due to tooth loss. Bacterial communities were characterized using 16S rRNA (V3-V4) amplicon sequencing, with alpha diversity, beta diversity (weighted and unweighted UniFrac), taxonomic enrichment (LEfSe), and predicted functional profiles (PICRUSt2) assessed. Microbiome composition was strongly compartmentalized by body site, with higher alpha diversity in the gut than in the oral cavity. Release candidacy was associated with modest gut compositional differences driven by presence-absence patterns, whereas oral microbiomes showed pronounced divergence between candidates and non-candidates across both UniFrac metrics. Non-candidates were enriched in opportunistic or dysbiosis-associated taxa and degradation-oriented functional pathways, while candidate microbiomes showed enrichment of biosynthetic and central energy metabolism pathways. Gut microbiome structure did not differ between pre-release and soft-release phases, indicating short-term stability during early translocation. These findings indicate that oral and gut microbiomes represent distinct physiological niches and that persistent oral microbiome alteration is a sensitive marker of long-term dental perturbation. Integrating microbiome-informed metrics with behavioral frameworks may improve multidimensional assessment of release readiness.