Integrated microbiome and metabolomic profiling reveals alterations across the adenoma–colorectal cancer sequence

ABSTRACT The incidence of colorectal cancer (CRC) has been increasing in Taiwan and is associated with multiple risk factors. Increasing evidence suggests that gut microbiota dysbiosis contributes to CRC development. This study aimed to characterize microbial and metabolic alterations across premalignant and malignant colorectal lesions and to identify potential microbiome-associated biomarkers. Individuals undergoing colonoscopy for screening or surveillance at Taipei Veterans General Hospital were enrolled. Gut microbial composition was analyzed using full-length 16S rRNA gene sequencing to achieve high-resolution taxonomic profiling. Predicted functional pathways were inferred from microbial communities, and targeted metabolomic profiling was performed to evaluate microbial metabolic outputs. A total of 122 individuals were included, comprising 62 healthy controls, 15 adenoma cases, and 45 CRC cases. Change in microbial composition and predicted functional pathways were observed across the control, adenoma, and CRC groups. Control-associated taxa were linked to carbohydrate fermentation and amino acid metabolism pathways, whereas CRC-associated taxa, particularly Fusobacterium, showed broad negative correlations with multiple biosynthetic pathways. Metabolomic analysis showed increased tauro-ursocholanic acid and reduced short-chain fatty acids (SCFAs) in CRC. CRC-associated bacteria were negatively correlated with SCFAs and positively correlated with several bile acid metabolites, including lithocholic acid, murocholic acid, tauro-ursocholanic acid, and taurohyocholic acid. Integrative analysis of full-length 16S rRNA sequencing, predicted functional pathways, and metabolomic profiling identified microbial and metabolic differences across the control, adenoma, and CRC groups. These findings are consistent with an association between gut microbial alterations and colorectal neoplasia and may inform future studies of microbial and metabolic biomarkers for CRC. IMPORTANCE Colorectal cancer (CRC) develops through an adenoma–carcinoma sequence, yet the microbial and metabolic alterations accompanying this progression remain incompletely understood. In this study, we integrated full-length 16S rRNA gene sequencing with metabolomic profiling to characterize taxonomic, functional, and metabolic changes across healthy controls, adenoma, and CRC. Our results showed coordinated changes in microbial taxa, predicted metabolic pathways, and fecal metabolites across the control, adenoma, and CRC groups. Control-associated taxa were linked to pathways related to carbohydrate fermentation and amino acid metabolism, whereas CRC-associated taxa, particularly Fusobacterium, showed negative correlations with several biosynthetic pathways. In addition, CRC-associated taxa were associated with reduced short-chain fatty acids (SCFAs) and increased levels of certain bile acid-related metabolites. These findings suggest an association between microbiome-associated metabolic alterations and colorectal neoplasia and support further investigation of microbial and metabolic biomarkers.