Background: Increasing the utilization efficiency of high-carbohydrate diet has the potential to promote “protein sparing effects” in farmed fish; however, many fish utilize carbohydrates poorly. The intestinal microbiota plays an important role in carbohydrate degradation. Whether the addition of functional bacteria could increase the carbohydrate utilization efficiency and alleviate high-carbohydrate diet-induced adverse effects is unknown.Results: A bacterial strain that could degrade starch in vitro was isolated from the intestines of Nile tilapia (Oreochromis niloticus). The bacterium was affiliated to Bacillus amyloliquefaciens (designated as B. amy SS1) based on 16S rRNA gene sequencing. Three diets, including control diet (CON), high-carbohydrate diet (HCD), and high-carbohydrate diet supplemented with B. amy SS1 (HCB), were used to feed Nile tilapia for 10 weeks. The beneficial effects of B. amy SS1 on weight gain and protein accumulation were observed. The HCB decreased blood glucose levels and reduced lipid deposition compared with the HCD group. To detect the possible mechanism, the intestinal microbiota composition was characterized using high-throughput sequencing. The HCB increased the abundance of short-chain fatty acid-producing bacteria. Gas chromatographic analysis indicated that theconcentration of acetate increased dramatically in the HCB group compared with that in the HCD group. Glucagon-like peptide-1 (GLP-1) levels increased in the intestine and serum of the HCB group. Different concentrations of sodium acetate (low (HLA), 900 mg/kg; medium (HMA), 1800 mg/kg, and high (HHA), 3600 mg/kg) were added to the HCD to feed the fish for eight weeks. The HMA and HHA groups mirrored the effects of the HCD supplemented with B. amy SS1 by increasing serum GLP-1 levels. Increased acetate concentrations stimulated GLP-1 production, which might account for the effects caused by the addition of B. amy SS1 to the HCD.Conclusions: This study systematically analyzed the influence of B. amy SS1 on fish metabolism, suggesting that B. amy SS1 treatment alleviates the metabolic syndrome caused by HCD by enriching acetate-producing bacteria in fish intestines. Regulating the intestinal microbiota and their metabolites might represent a powerful strategy for fish nutrition modulation and health maintenance in future.