Objective The study aimed to investigate the composition, diversity, and potential functions of the skin and gill mucosal microbiota of Nile tilapia (Oreochromis niloticus), providing a foundation for screening of fish-derived probiotics.

Method Skin and gill samples were collected from Nile tilapia cultured in earthen ponds across three sampling sites in southern China: Ding'an County (Hainan Province), and Gaoyao District (Zhaoqing City) and Boluo County (Huizhou City) in Guangdong Province. The microbiota was analyzed using high-throughput sequencing of the 16S rRNA gene.

Result A total of 1 236 OTUs (accounting for 79.75% of the total OTUs) were shared among skin samples, and 1 270 OTUs (78.97% of the total OTUs) were shared among gill samples across the three sites. No significant differences in alpha diversity were observed among all microbiota samples. At the phylum level, the dominant taxa in both skin and gill microbiota included Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes and Actinobacteria. At the class level, the major groups were Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Bacteroidia, Actinobacteria, Bacilli, and Deltaproteobacteria. Seven core genera were observed across all the skin and gill samples, including Sphingomonas, Methylobacterium, Janthinobacterium, Pseudomonas, Lactobacillus, Ramlibacter, and Acinetobacter. Massilia and Lysobacter also dominated in the gill samples. Functional comparative analysis revealed that the skin microbiota is significantly enriched in pathways related to infectious disease response and immunity, indicating its important role in host immune defense; whereas the gill microbiota is more involved in energy metabolism, glycerolipid metabolism, and membrane transport processes, potentially supporting gas exchange and osmoregulation in the gills through metabolic assistance.

Conclusion This study characterized the structure and function of the skin and gill mucosal microbiota of Nile tilapia cultured in earthen ponds in southern China using high-throughput sequencing, and provided information on the skin and gill microbiota of tilapia for understanding mucosal immune mechanisms and screening fish-derived probiotics.