Multi-omics analysis reveals stage-associated differences in the gut microbiome ecosystem across stages of colorectal cancer in a cross-sectional cohort

The etiology of colorectal cancer (CRC) involves complex interactions among gut microbiota alterations, metabolic dysregulation, and disturbances in essential ions. The study aims to compare stage-associated differences in the gut microbiome ecosystem across CRC stages in a cross-sectional design, with no within-individual longitudinal sampling and therefore no direct observation of in-host progression. In this study, we performed comprehensive metagenomic, metabolomic, and ionomic analyses on 984 samples in a cross-sectional design to characterize gut microbiome‑associated signatures across different colorectal cancer (CRC) disease‑stage groups. Samples were categorized into six groups: low‑risk (individuals under 45 years of age with no intestinal lesions detected by colonoscopy), high‑risk (individuals ≥ 45 years of age with no intestinal lesions detected by colonoscopy), advanced adenoma (AA), stages I&II CRC, stage III CRC, and stage IV CRC. Metagenomic results showed that dominant genera including UBA7182 , Lachnoclostridium B. , Faecalibacillus , Fusicatenibacter , and Anaerobutyricum showed progressively lower relative abundance across more advanced CRC stage groups, whereas Intestinimonas and Bacteroides showed higher relative abundance. The comparison between high-risk and advanced-adenoma groups showed a marked decline in the detection rate of low-abundance taxa at the sequencing depth used in this study and reduced microbial diversity. Metabolomic analysis revealed age- and risk-group-associated differences between the low- and high-risk groups (< 45 vs. ≥ 45 years) that may largely reflect age and age-associated factors rather than early-disease biology, while putatively annotated metabolite features (MSI Level 2/3) mapped to eight candidate KEGG pathway modules. Elemental analysis indicated highest levels of strontium, iron, and phosphorus in CRC III, whereas beryllium predominated in low-risk individuals and sulfur was enriched in both low- and high-risk groups. Integrated multi-omics evidence indicates that microbiota, metabolites, and ionic profiles differ across CRC stage groups, including the earliest disease-stage groups. These cross-sectional, correlation-level findings are hypothesis-generating for further studies of CRC-stage-associated changes in the gut microbiome ecosystem and of its interplay with senescence; before any diagnostic application, the patterns described here would need to be validated in independent prospective cohorts. Two limitations warrant particular caution against over-interpretation: the low-risk and high-risk groups differ by age (< 45 vs. ≥ 45 years), so differences between them are confounded by age and cannot be fully adjusted; and no microbiome positive or negative controls (mock community, extraction blank, no-template) were included, so reagent and background contamination cannot be fully excluded and the low-abundance findings are exploratory.