Staphylococcus haemolyticus Infection Modifies Bacterial and Microeukaryotic Gut Communities in Nile Tilapia

The fish gut microbiota includes bacterial and microeukaryotic microorganisms that contribute to host nutrition, immune regulation, and intestinal homeostasis. However, the simultaneous responses of both microbial fractions to bacterial infection remain poorly explored in aquaculture species. This study evaluated intestinal microbiota differences associated with experimental Staphylococcus haemolyticus infection in Nile tilapia (Oreochromis niloticus). Juvenile female tilapia were randomly assigned to either a non-infected control group or a group experimentally infected with S. haemolyticus. Intestinal contents were collected seven days post-challenge, and microbial communities were characterized by amplicon sequencing targeting the V3–V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene. In the bacterial fraction, infected fish showed higher relative abundances of Proteobacteria and Firmicutes and lower relative abundances of Fusobacteriota, Patescibacteria, and Actinobacteriota. At the genus level, infected fish showed higher relative abundances of Staphylococcus, Mycobacterium, and other potentially opportunistic bacteria, along with lower relative abundances of Cetobacterium and Romboutsia. In the microeukaryotic fraction, infected fish showed higher relative abundances of Ciliophora and Ascomycota and a lower relative abundance of Nematozoa. Shannon and Simpson alpha diversity indices were significantly higher in infected fish in both microbial fractions. PICRUSt2-predicted MetaCyc profiles differed between treatments. Control fish showed higher predicted abundances of pathways related to fermentation and vitamin and cofactor metabolism, whereas infected fish showed higher predicted abundances of pathways related to bacterial cell wall metabolism, arginine and polyamine biosynthesis, lipid metabolism, and microbial adaptation. Overall, experimental S. haemolyticus infection was associated with taxon-specific differences in intestinal bacterial and microeukaryotic communities and in predicted bacterial functional potential.