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An acute infectious disease of northern sheatfish (Silurus soldatovi) was found in a commercial aquaculture pond in Tianjin, China. Herein, two dominant bacterial strains were isolated from naturally diseased northern sheatfish and identified as Aeromonas veronii and Vibrio cholerae. Seven healthy and seven naturally diseased fish that were collected from the pond were used for the gut microbiota analysis by high‐throughput 16S rRNA gene sequencing. The α‐diversity indices (ACE, Chao 1, and Shannon) did not differ significantly between diseased and healthy fish (p > 0.05), but a significant separation was observed between them when β‐diversity analysis of the bacterial population was performed. The diseased fish demonstrated a significant elevation in the relative abundances of Aeromonas, Vibrio, Blautia, and Megamonas and a decrease in Cetobacterium, Bacteroides, Chryseolinea, Ralstonia, and Pseudomonas compared with healthy fish (p < 0.05). Linear discriminant analysis effect size showed that microbial marker species in the diseased fish were in the order Aeromonadales, the family Aeromonadaceae, and the genus Aeromonas. The functional profiles of the microbial community that were predicted using the PICRUSt2 indicated that the disturbance of gut microbiota caused the alteration of its functional profiles in the diseased fish.

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