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Probiotics have attracted considerable attention as potential antibiotic substitutes in aquaculture. However, their functional genomic characterisation remains incomplete. Therefore, this study aimed to evaluate the probiotic characteristics of Bacillus cereus G1-11 isolated from the gut of the hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂) by integrating genomics and phenotypic characteristics. Genome mining revealed gene clusters that are responsible for acid and bile tolerance as well as host intestinal adhesion and colonisation. Moreover, the G1-11 genome encodes proteins that associated with the bacterial antioxidant system and antimicrobial substances. Additionally, it contains gene clusters related to nutrient absorption, essential amino acids, and vitamin synthesis. The results showed that the G1-11 strain has the ability improved the intestinal barrier function of the host and enhanced the nutritional value of the feed. The genome analysis of G1-11 was complemented by in vitro experiments, which showed its ability to survive during gastrointestinal transit, as well as its antioxidant and antibacterial capabilities. The results indicate that B. cereus G1-11, as a probiotic, has the potential to enhance the growth and immunity of hybrid groupers. • Bacillus cereus G1-11 isolated from hybrid grouper gut was tested as a probiotic. • G1-11 has gene clusters for gut adhesion, colonisation, and immune functions. • G1-11 contains molecular markers associated with amino acid and vitamin synthesis. • Genes encoding secondary metabolites and bacteriocins were found in G1-11 genome. • G1-11 is resilient to gut transport and has antioxidant and antibacterial effects. [ABSTRACT FROM AUTHOR]