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Abstract The emulsification disease of swimming crab Portunus trituberculatus is mainly caused by Vibrio alginolyticus. Gut microbiota is involved in the immunity and diseases of crustaceans. In this study, we integrated 16S rRNA gene sequencing and 1H nuclear magnetic resonance metabolomics techniques to determine the effects of V. alginolyticus infection on bacterial composition and metabolic phenotype in the gut of P. trituberculatus. The results showed that V. alginolyticus infection induced marked changes in the gut bacterial composition of P. trituberculatus , which seems to drive the gut bacterial community into a kind of diseased status. The sums of the relative abundance of these indicator bacteria such as Vibrionaceae and Pseudoalteromonadaceae could be used to predict the increased risk of emulsification disease occurrence in swimming crab. V. alginolyticus infection also caused marked changes in the gut metabolic phenotype of P. trituberculatus , highlighted by the significantly changed levels of maltose, glucose, AMP, and amino acids. Importantly, the gut indicator bacteria showed comprehensive correlations with these significantly changed gut metabolites, which revealing the contributions of gut bacteria in pathogenesis of gut metabolic disorders of swimming crab after V. alginolyticus infection. Overall, this study provides solid evidence that gut bacteria are involved in the occurrence and development of crab vibriosis, which could be great important for gaining new insights into the pathogenesis mechanisms of emulsification disease and developing novel strategies for emulsification disease prevention of swimming crab. Highlights • V. alginolyticus infection caused marked changes in the bacterial composition and metabolic phenotype of crab gut. • Gut bacterial composition related to V. alginolyticus infection were analyzed by a 16S rRNA gene sequencing method. • Gut metabolites related to V. alginolyticus infection were analyzed by a NMR-based metabolomic method. • The gut indicator bacteria showed comprehensive correlations with the significantly changed gut metabolites. • The results revealed contributions of gut microbiota in pathogenesis of gut metabolic disorders of swimming crab. [ABSTRACT FROM AUTHOR]