Risk of Secondary Bacterial Infections Revealed by Changes in Trachinotus ovatus Skin and Gill Microbiota During a Cryptocaryon irritans Infection Cycle

This study aims to investigate the response of surface bacterial communities in <i>Trachinotus ovatus</i> to <i>Cryptocaryon irritans</i> infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction in the richness and diversity of skin microbiota during infection, with partial recovery post-detachment. Beta diversity analysis revealed distinct structural shifts in skin microbiota at early (24 h) and post-detachment (168 h) stages compared to other phases, while gill microbiota remained stable except during detachment. At the phylum level, Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes were dominant on the skin at different stages, whereas the gill microbiota was predominantly Proteobacteria (>90%). At the genus level, opportunistic pathogens, such as <i>Vibrio</i> and <i>Nautella</i>, increased in relative abundance on the skin with the infection progression, while gill microbiota composition barely changed. The hepatic bacterial load continued to increase with infection duration. These findings indicate that <i>C. irritans</i> alters microbiota composition on skin, facilitating pathogen invasion, thereby elevating the risk of secondary bacterial infections in <i>T. ovatus</i>.