Background objectivesThe purpose of this study is to investigate changes in gut microbiota related to metabolic diseases after moderate and high-intensity exercise. A total of 24 participants were divided into three groups: Non-Exercise Group (NEG, n = 8, 28.6 ± 5.3 years, 176.0 ± 7.8 cm, 81.3 ± 14.6 kg), Moderate Intensity Exercise Group (MIEG, n = 8, 26.5 ± 3.3 years, 176.9 ± 5.0 cm, 75.4 ± 9.5 kg), and Vigorous Intensity Exercise Group (VIEG, n = 8, 30.6 ± 5.9 years, 174.2 ± 3.5 cm, 77.8 ± 12.2 kg). MethodsThe participants were selected by assessing physical activity, gut health status, presence of diseases, recent disease diagnoses, and dietary disorders. Those who reported any presence disease or recent disease diagnosis were excluded from the current study. Stool samples were collected after a 10-h fast for gut microbiome analysis. MIEG participants trained at 40–59 % heart rate reserve (HRR) for at least 150 min per week, while VIEG participants trained at ≥ 60 % HRR for at least 90 min per week. After 4 weeks, all participants provided stool samples for gut microbiome analysis.Data analysis was conducted using the Wilcoxon test, with statistical significance set at ≤ 0.05. ResultsThe results indicated an increase in Prevotella in MIEG, while Veillonella, Dorea_formicigenerans, and Dorea_longicatena exhibited a decrease (p < 0.05). In VIEG, there was an increase in Bacteroides, Butyricimonas, Odoribacter, and Alistipes (p < 0.05). ConclusionThese modified microbial groups were associated with factors related to metabolic diseases, including inflammatory bowel disease, obesity, colorectal cancer, diabetes, hypertension, metabolic liver diseases, and ischemic heart diseases. Additional research is essential to delve into the relationship between exercise and these alterations in the microbiome.