Providencia vermicola Infection Alters Bacterial and Microeukaryotic Gut Community Composition in Nile Tilapia

Nile tilapia (Oreochromis niloticus) is a major aquaculture species worldwide, yet bacterial infections remain a critical constraint to production sustainability. Although pathogen-associated dysbiosis has been widely described, most studies have focused exclusively on bacterial communities, overlooking the multi-kingdom nature of the intestinal microbiota. This study evaluated the impact of experimental Providencia vermicola infection on both prokaryotic and microeukaryotic intestinal communities under controlled conditions. Using 16S (V3–V4) and 18S (V9) rRNA amplicon sequencing, we compared healthy and infected fish and assessed taxonomic, structural, and predicted functional changes. Infection was associated with significant compositional shifts, including increased relative abundances of Bacteroidota and Proteobacteria and decreased relative abundances of Fusobacteriota and Patescibacteria. Concomitantly, microeukaryotic groups such as Protalveolata, Nematozoa, and Phragmoplastophyta were significantly reduced. Functional prediction revealed metabolic pathway reconfiguration consistent with infection-associated ecological disturbance. Together, these results suggest that the pathogen challenge is associated with coordinated changes in the intestinal microbiota as an integrated system across multiple microbial kingdoms rather than as isolated bacterial shifts. This study supports ecosystem-level interpretations of dysbiosis and highlights the importance of incorporating cross-domain analyses into health assessment strategies in aquaculture species.