Colorectal cancer biofilm composition reveals distinct bacterial species signature

Human colon hosts a highly organized protective microbial ecosystem in the form of biofilms, increasingly recognized as key contributors to colorectal cancer (CRC) progression through microbial dysbiosis and complex host-microbiota interactions. In India, CRC ranks among the top ten cancers, with an age-standardized incidence rate of approximately 6.3 per 100,000 in males and 3.7 per 100,000 in females highlighting a higher risk in men, late-stage diagnosis, inadequate screening, and treatment limitations, particularly in urban populations. This study aims to explore the microbial composition of colonic biofilms from the Indian cohort of colorectal cancer patients from New Delhi, which is witnessing a rise in the incidence of CRC. Colorectal biopsies were taken from tumors (n = 15) and adjacent non-tumor tissues (n = 15) at the Gastrointestinal Department of AIIMS, New Delhi, India. Fluorescence in situ hybridization (FISH) was employed to determine the bacterial population in the biofilm. The workflow included microtomy, deparaffinization, tissue permeabilization, and hybridization with bacterial 16S rDNA probes, and the detected signals were visualized by confocal microscopy. The results showed quite different microbial patterns and tumor-associated biofilms were found to have an increased density of Escherichia coli, Klebsiella pneumoniae, and Bacteroides fragilis, while Fusobacterium nucleatum and E. coli (pks⁺) with a pks⁺ genomic island encoding the genotoxin colibactin were seen less often. These results confirm significant dysbiosis and the formation of invasive biofilms in CRC tissues. Understanding the composition of these biofilms may facilitate the development of targeted strategies to restore microbial balance and reduce CRC risk both in the Indian and global population. KEY POINTS: • Tumor-associated biofilms show distinct microbial dysbiosis in Indian CRC patients. • Enrichment of Escherichia coli, Klebsiella pneumoniae, and Bacteroides fragilis was observed at tumor site. • Insights into biofilm composition may aid to targeted interventions for CRC risk reduction.