Inflammatory bowel disease (IBD) is a chronic intestinal disorder threatening human health. Di-
peptide alanyl-glutamine (
Ala-Gln) has various beneficial effects on gut health. However, its role and functional mechanism in treating IBD are still not clear. Therefore, the protective effects of
Ala-Gln and
glutamine (Gln) on
dextran sulfate sodium- (DSS-) induced colitic mice were investigated in this study. The results showed that oral supplementation of
Ala-Gln or Gln significantly attenuated the
colitis symptoms in mice, including
body weight loss, colon length, disease activity index, histological scores, and tissue apoptosis. The concentrations of
interleukin- (IL-) 1β,
IL-6,
tumor necrosis factor-α, and
myeloperoxidase were significantly decreased, while the concentrations of
immunoglobulins (
IgA,
IgG, and
IgM) and
superoxide dismutase were significantly increased by
Ala-Gln or Gln supplementation. The expression of
occludin and
peptide transporter 1 (PepT1) was significantly increased by
Ala-Gln or Gln. Interestingly,
Ala-Gln had better beneficial effects than Gln in alleviating
colitis. In addition, 16S
rDNA sequencing showed that the DSS-induced shifts of the microbiome (community diversity, evenness, richness, and composition) in the mouse colon were restored by Gln and
Ala-Gln, including Lactobacillus, Bacteroides_acidifaciens, Bacteroidales, Firmicutes, Clostridia, Helicobacter, and Bacteroides. Correspondingly, the functions of the microflora metabolism pathways were also rescued by
Ala-Gln, including
fatty acid metabolism,
membrane transporters,
infectious diseases, and immune system. In conclusion, the results revealed that
Ala-Gln can prevent
colitis through PepT1, enhancing the intestinal barrier and modulating gut microbiota and microflora metabolites.