High-Throughput Sequencing-Based Assessment of Intestinal Parasitic Infections in Economically and Medicinally Valuable Captive Tokay Gecko (Gekko gecko) and Chinese Blue-Tailed Skink (Plestiodon chinensis)

Captive reptiles bred for economic and medicinal purposes are often susceptible to intestinal parasites that undermine their health and overall farm productivity. In many regions, their economic value largely derives from medicinal use; accordingly, they are described as reptiles with medicinally driven economic value. In this study, we applied high-throughput sequencing to characterize gut eukaryotic communities and assess parasite prevalence in tokay geckos (<i>Gekko gecko</i>) and Chinese blue-tailed skinks (<i>Plestiodon chinensis</i>). Across both host species, six pathogenic genera were identified: <i>Cryptosporidium</i> (<i>P. chinensis</i>: 57.1%, 12/21; <i>G. gecko</i>: 0%), <i>Eimeria</i> (<i>P. chinensis</i>: 14.3%, 3/21; <i>G. gecko</i>: 0%), <i>Oswaldofilaria</i> (<i>P. chinensis</i>: 0%, <i>G. gecko</i>: 4.8%, 1/21), <i>Strongyloides</i> (<i>P. chinensis</i>: 14.3%, 3/21; <i>G. gecko</i>: 19.1%, 4/21), <i>Spironucleus</i> (<i>P. chinensis</i>: 14.3%, 3/21; <i>G. gecko</i>: 9.5%, 2/21), <i>Spauligodon</i> (<i>P. chinensis</i>: 0%, <i>G. gecko:</i> 14.3%, 3/21). Among these, <i>Cryptosporidium</i> exhibited a striking host-specific pattern, occurring exclusively in Chinese blue-tailed skinks (Fisher's exact test, <i>p</i> = 5.32 × 10^-5). Principal component analysis (PCA) demonstrated clear host-associated segregation along PC1, which accounted for 58.2% of total variance. Furthermore, co-occurrence network analysis revealed significant positive associations (all <i>p</i> < 0.01) between parasites and other eukaryotes, particularly fungi and protozoa. Collectively, these findings underscore the value of high-throughput sequencing for parasite surveillance in reptile farming and point to the importance of integrated diagnostic approaches and enhanced biosecurity measures for maintaining animal health.