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, including aging, obesity, and dietary habits. 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. Progressive shifts in microbial composition and predicted functional pathways were observed along the adenoma–carcinoma sequence. Several bacterial taxa, including Phocaeicola dorei , Anaerotignum faecicola , Negativibacillus massiliensis , and Dysosmobacter segnis , were enriched in CRC. At the functional level, CRC samples showed enrichment of pathways associated with energy metabolism and bacterial stress responses. Metabolomic analysis further revealed increased levels of tauro-ursocholanic acid in CRC samples, whereas short-chain fatty acids (SCFAs) were reduced compared with controls. Integrative analysis combining full-length 16S sequencing, functional pathway prediction, and metabolomic profiling revealed coordinated microbial and metabolic alterations across the adenoma–carcinoma sequence. These findings provide insight into microbiome-associated processes in colorectal tumorigenesis and suggest potential microbial and metabolic biomarkers for CRC. Importance Colorectal cancer (CRC) develops through a 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 reveal synchronized shifts in specific microbial taxa, predicted metabolic pathways, and fecal metabolites along the adenoma–carcinoma sequence. Several bacterial species, including Phocaeicola dorei , Anaerotignum faecicola , and Dysosmobacter segnis, increased in CRC, whereas short-chain fatty acids decreased progressively from controls to adenoma and CRC. Functional pathway analysis further indicated alterations in microbial fermentation, amino acid metabolism, and energy-related pathways. Together, these findings highlight the potential role of microbiome-associated metabolic changes in colorectal tumorigenesis and suggest candidate microbial and metabolic markers that may aid in understanding disease development and improving risk stratification.