Integrated metagenomic-proteomic bioinformatic analysis of gut microbiota associated with colorectal cancer

Abstract

Colorectal cancer (CRC) is a major cause of cancer-related morbidity and mortality worldwide, and growing evidence links gut microbiota dysbiosis to its development. In this study, an integrative bioinformatic analysis was performed using publicly available shotgun metagenomic datasets from the European Nucleotide Archive. A total of eight fecal samples were analyzed, including four healthy controls and four CRC patients. Taxonomic profiling revealed clear microbial alterations between groups. Healthy controls were dominated by Prevotella copri (≈40%), Bacteroides spp. (≈21%), and butyrate￾producing Roseburia species (R. intestinalis 4%, R. inulinivorans 3%, R. faecis 2%). In CRC samples, Prevotella copri decreased to ≈4%, while Butyrivibrio crossotus increased to ≈17%, Bacteroides spp. reached ≈14%, and Enterobacteriaceae expanded to ≈2%. Functional analysis using HUMAnN3 and KEGG identified 47 significantly enriched and 32 depleted pathways in CRC (p < 0.05; p < 0.001). Lipopolysaccharide (LPS) biosynthesis increased from 3.18% to 8.52% (+2.68-fold; p < 0.001), bacterial invasion of epithelial cells from 2.82% to 7.21% (+2.56-fold; p < 0.001), and DNA replication/repair pathways from 3.14% to 6.84% (+2.18-fold; p < 0.001). Conversely, butanoate metabolism decreased from 8.52% to 3.24% (−2.63-fold; p < 0.001), propanoate metabolism from 7.82% to 3.48% (−2.25-fold; p < 0.001), and vitamin B12 biosynthesis from 7.18% to 2.85% (−2.52-fold; p < 0.001). Overall, CRC was associated with both taxonomic dysbiosis and functional reprogramming of the gut microbiome, characterized by increased inflammatory and virulence-related pathways alongside reduced metabolic and protective functions. These findings support the potential role of microbial signatures as biomarkers for CRC detection and therapeutic targeting.