Abstract
BACKGROUND: Previous studies have established a strong link between intestinal microbiota and metabolism. However, no research has examined the relationship between the gastric microbiome and metabolism status. This study characterizes the gastric microbiome in patients with metabolically healthy obesity (MHO) and compares it with that of patients with metabolically unhealthy obesity (MUO). METHODS: Gastric microbiota composition was analyzed using deep sequencing of the 5-region (5R) 16 S ribosomal RNA (16 S rRNA) gene. RESULTS: The gastric microbiota profiles of MHO differed significantly from those of MUO. PICRUSt functional inference revealed distinct microbial metabolic pathways between the groups. PICRUSt analysis identified 30 differentially regulated pathways, with arginine, proline, tryptophan, and phenylalanine metabolism upregulated in MUO. By contrast, DNA repair and recombination proteins, ribosomes, amino acid-related enzymes, and ribosome biogenesis (KEGG Level 3) were upregulated in MHO. CONCLUSION: This study reveals significant differences in the gastric microbiome between MHO and MUO, highlighting the intricate relationship between microbiota composition and metabolic health. These findings suggest potential microbiome-based therapeutic targets for metabolic disorders. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13098-025-02075-y.