Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection

<i>Ichthyophthirius multifiliis</i> poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of <i>Percocypris pingi</i>, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in <i>P. pingi</i> associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in <i>P. pingi</i>, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to <i>I. multifiliis</i> of <i>P. pingi</i>. Concurrently, skin microbiome analysis showed that <i>P. pingi</i> hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, <i>P. pingi</i> skin was significantly depleted of the parasitic bacteria <i>Candidatus_Megaira</i> and <i>Candidatus_Midichloria</i>, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that <i>P. pingi</i>'s microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of <i>P. pingi</i> to <i>I. multifiliis</i> is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish.