Fecal and Salivary Microbial Gene Markers for the Non-invasive Detection of Colorectal Cancer Progression

Aims: To evaluate the diagnostic potential of previously reported (5ar, nan) and novel microbial gene markers in fecal and salivary microbiomes for the non-invasive detection of colorectal cancer (CRC) progression. Study Design: Cross-sectional study. Place and Duration of Study: Department of Gastroenterology and Hepatology, Fujita Health University, Toyoake, Japan, between June 2024 and July 2025. Methodology: Fecal samples were collected from healthy controls (n = 65) and patients with colorectal adenoma (n = 38) or carcinoma (n = 27). Salivary samples were collected from healthy controls (n = 34) and the same patient cohorts. Microbial gene abundances were quantified via quantitative PCR, and microbiome composition was assessed using 16S rRNA gene sequencing. Group comparisons used the Kruskal-Wallis and Dunn’s tests. Beta diversity differences were evaluated by PERMANOVA. Results: In fecal samples, the abundances of 5ar, nan, and the Fusicatenibacter saccharivorans 16S rRNA gene (fsr) showed a stepwise decline from the adenoma stage onward, with significantly lower levels in carcinoma versus controls (5ar, P = 0.0023; nan, P = 0.0012; fsr, P = 0.0004). Conversely, in saliva, the Fusobacterium periodonticum tyrosine phenol lyase gene (tpl) was significantly reduced only in the carcinoma group (P = 0.0180). Fecal beta diversity differed significantly between controls and both colorectal neoplasia groups (both P ≤ 0.001), whereas salivary beta diversity differed only between controls and carcinoma patients (P = 0.014). Conclusion: Fecal and salivary microbial gene markers may serve as non-invasive, rapid, and cost-effective biomarkers for colorectal neoplasia. Fecal markers captured microbiota disruption at the adenoma stage (representing the early phase of CRC progression), whereas salivary markers predominantly reflected alterations specific to carcinoma (representing the later phase). Integrating these multi-niche biomarkers provides a promising clinical platform for early detection, monitoring of precursor lesions, and postoperative surveillance; however, validation in larger, independent cohorts is warranted.