Several beneficial effects of poly-γ-glutamic acid (γ-PGA) have been reported. To test whether natto, a fermented soy food rich in γ-PGA, can improve intestinal microbiota content and lipid metabolism in a high-fat diet, we compared the intestinal microbiota content, plasma, liver, and fecal contents, and changes in gene expression in the livers and large intestines of a group of mice fed a high-fat diet supplemented with cooked soybeans (SC group) and a group fed a high-fat diet supplemented with natto (NA group) for 42 days; high-fat diet-fed mice were used as a control (Con group). Hepatic lipid levels were significantly lower, the fecal bile acid and lipid levels were significantly greater, and the
Bacteroidetes
/
Firmicutes
ratio was significantly higher in the SC and NA groups as compared to Con group. Additionally, plasma glucose and triglyceride levels, the expression of liver fatty acid synthase, and the relative abundance of
Lactobacillaceae
was significantly higher in the NA group than in the Con group. Although both natto and cooked soybeans impacted the metabolic response to a high-fat diet, the addition of natto had a greater effect on glucose and lipid metabolism. γ-PGA may play an important role in natto functionality.