Abstract
INTRODUCTION: Regional differences in the gut microbiota and CRC incidence and mortality rates are well-documented. However, studies on the microbiota associated with CRC in Indonesia remain scarce. This study aimed to chracterize the gut microbiota profile of CRC in Indonesia. METHODS: We collected stool samples from 14 patients with CRC (CRC), 19 patients with non-CRC bowel diseases (non-CRC), and 16 healthy controls (HC). The gut microbiota profiles across the three groups were analyzed using 16 S rRNA gene amplicon sequencing. Data analysis was performed using several software packages: QIIME2, ANCOM-BC2, and PICRUSt2. RESULTS: In comparison to the non-CRC and HC groups, patients with CRC demonstrated significant differences in both alpha and beta diversity. The CRC group had lower evenness and richness than the HC group. Firmicutes and Bacteroidota were identified as the predominant phyla across all groups. The differential abundance analysis identified four beneficial genera that were substantially reduced in Indonesian CRC patients: Roseburia, Dialister, Agathobacter, and Muribaculaceae. No genera were found to be significantly enriched in CRC. Functional prediction analysis revealed multiple pathways such as mTOR, mRNA surveillance, basal transcription factors, phagosome, and proteasome, were reduced in CRC. Conversely, CRC demonstrated a significant upregulation of pathways related to lipid metabolism and the biosynthesis of flavonoids, stilbenoids, diarylheptanoids, and gingerols. CONCLUSION: Our study revealed distinct gut microbiota profiles in Indonesian CRC patients, highlighting the significance of decreased abundance of certain beneficial taxa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-026-00816-6.