Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues

Aisyah, Yunus and Norfilza, Mohd Mokhtar and Raja Affendi, Raja Ali * and Siti Maryam, Ahmad Kendong and Hajar, Fauzan Ahmad (2024) Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues. MethodsX, 12. ISSN 2215-0161

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Abstract

Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a putative biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To characterize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis revealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Expanding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer. •Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing. •Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening. •Contribution to the advancement of innovative colorectal cancer diagnostic methods and targeted therapies by applying gut mycobiome knowledge.

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