The microbiota plays a key role in fish health, influencing nutrient assimilation, immunity, and resistance to pathogens. In aquaculture, maintaining a stable microbiota is critical to prevent disease outbreaks. Phage therapy and phage-derived enzymes, such as endolysins (Lys), are promising antibiotic alternatives for controlling bacterial pathogens like Vibrio spp., major agents of mortality in fish and mollusks. This study evaluated the antibacterial efficacy of phage and Lys against Vibrio spp. and their impact on rotifer, water, and fish larvae microbiota.
Both phage and Lys exhibited potent activity against multiple Vibrio species (V. alginolyticus, V. parahaemolyticus, V. splendidus). In seawater, both treatments reduced Vibrio counts by >2 logs (>100-fold) within 20 min. In vivo, Vibrio loads decreased significantly in rotifers (~200 to ~3 CFU/individual) and fish larvae (zebrafish and amberjack), achieving ~3-log reductions (~1000-fold), confirming their efficacy across hosts and application contexts.
Microbiota analyses (rotifers, water, fish larvae) identified ASVs with sufficient sequencing depth. Alpha diversity remained unchanged. Beta diversity showed treatment-specific effects: rotifer microbiota clustered separately after Lys treatment, while water microbiota revealed significant shifts. Communities were dominated by Proteobacteria, Actinobacteriota, Firmicutes, and Bacteroidota. Rotifer and fish larvae microbiota remained largely stable, while water samples showed genus-level shifts (Glutamicibacter enriched by phage; Escherichia-Shigella enriched by Lys).
Overall, phage and Lys effectively controlled Vibrio in seawater, live feed, and fish larvae without major microbiota disruption, supporting their potential as targeted biocontrol tools for sustainable aquaculture.