Metagenomic insights into modulation of microbiota community composition, potential metabolic pathways and antimicrobial resistance mechanisms in cage-cultured hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) upon oral immuniz

Intensive grouper aquaculture plays a vital role in the economies of Southeast Asia but remains vulnerable to vibriosis outbreaks and the threat of antimicrobial resistance (AMR). This study evaluated the impact of a feed-based inactivated Vibrio vaccine on the hindgut microbiota of cage-cultured hybrid grouper ( E. fuscoguttatus ♀ × E. lanceolatus ♂) reared in an Indonesian fish farm. Fish in the vaccinated group received the feed-based vaccine at 4% body weight daily for five consecutive days during weeks 0, 2, and 6, while control fish were fed trash fish. Hindgut samples were collected for 16S rRNA amplicon sequencing on week 10 to assess microbial diversity and predicted functional profiles. Results revealed significant differences ( p < 0.05) in both alpha and beta diversity indices, indicating altered microbiota evenness. Notably, V. harveyi , an inactivated component of the vaccine, was detected and appeared to significantly suppress the abundance of opportunistic pathogens such as V. vulnificus and Photobacterium damselae . Additionally, the vaccine enhanced predicted metabolic pathways related to pyrimidine synthesis, L -glutamate metabolism, and vitamin K production. It also reduced the prevalence of genes associated with β-lactam and vancomycin resistance, while preserving potential immune-related microbial functions. Overall, the findings demonstrate that feed-based vaccination can modulate gut microbial ecology in hybrid grouper and contribute to microbiota-mediated mitigation of AMR, even under socially competitive feeding conditions. This approach offers a practical and scalable strategy for enhancing fish health and mitigating AMR risks in mariculture, particularly in low- and middle-income countries where injectable vaccine delivery remains challenging. • The feed-based Vibrio vaccine reduced V. vulnificus and P. damselae abundance in grouper hindgut microbiota. • The vaccine modulated potential metabolic pathways of grouper hindgut microbiota. • Predicted antibiotic resistance genes of grouper hindgut microbiota were reduced following vaccination.