Intratumoral microbiome signatures in a North Central Indian colorectal cancer cohort: identification of novel prognostic biomarkers and functional pathways

Colorectal cancer (CRC) remains a major global health burden, with emerging evidence implicating gut and oral microbiome dysbiosis in its pathogenesis. This comparative observational study aimed to investigate intratumoral microbial signatures in early-onset CRC (EOCRC) and their association with clinical outcomes. In fact, till date there is no comprehensive study yet that directly compares the microbiome of EOCRC patients in North Central India to other EOCRC groups globally. We analysed 50 matched tumor and adjacent normal tissues (obtained from the same patient) using 16S rRNA amplicon sequencing. Taxonomic and functional analyses were conducted using DESeq2, LEfSe, and KEGG pathway prediction (via PICRUSt2). Our findings revealed distinct intratumoral enrichment of oral pathobionts such as Leptotrichia buccalis and Filifactor alocis, which showed significant correlation with mortality risk. Caldilinea aerophila was detected for the first time in human tumor tissue and was strongly associated with advanced TNM stages (p = 0.01; 83% specificity) in North Central Indian population. LEfSe analysis identified an overrepresentation of Actinomycetales. KEGG pathway analysis revealed enrichment of MAPK signaling, styrene, and aminobenzoate degradation pathways. Depletion of Lactobacillus plantarum and presence of dietary-linked microbes suggest microbial modulation by lifestyle. These findings highlight novel microbial biomarkers and immune-related pathways with potential prognostic implications in this regional CRC cohort.