Predictive modeling of colorectal cancer using exhaustive analysis of microbiome information layers available from public metagenomic data

Murovec, Boštjan (author), Deutsch, Leon (author), Stres, Blaž (author)

This study aimed to compare the microbiome profiles of patients with colorectal cancer (CRC, n = 380) and colorectal adenomas (CRA, n = 110) against generally healthy participants (n = 2,461) from various studies. The overarching objective was to conduct a real-life experiment and develop a robust machine learning model applicable to the general population. A total of 2,951 stool samples underwent a comprehensive analysis using the in-house MetaBakery pipeline. This included various data matrices such as microbial taxonomy, functional genes, enzymatic reactions, metabolic pathways, and predicted metabolites. The study found no statistically significant difference in microbial diversity among individuals. However, distinct clusters were identified for healthy, CRC, and CRA groups through linear discriminant analysis (LDA). Machine learning analysis demonstrated consistent model performance, indicating the potential of microbiome layers (microbial taxa, functional genes, enzymatic reactions, and metabolic pathways) as prediagnostic indicators for CRC and CRA. Notable biomarkers on the taxonomy level and microbial functionality (gene families, enzymatic reactions, and metabolic pathways) associated with CRC were identified. The research presents promising avenues for practical clinical applications, with potential validation on external clinical datasets in future studies.

• Language: English
• Keywords: gut microbiome, machine learning, colorectal cancer, colorectal adenoma, metagenomics, functional microbiome
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FE - Faculty of Electrical Engineering; BF - Biotechnical Faculty; FGG - Faculty of Civil and Geodetic Engineering
• Publication status: Published
• Publication version: Version of Record
• Publisher: Frontiers Research Foundation
• Year: 2024
• Number of pages: 10 str.
• Numbering: Vol. 15
• PID: 20.500.12556/RUL-161601
• UDC: 579:004.85
• ISSN on article: 1664-302X
• DOI: 10.3389/fmicb.2024.1426407
• COBISS.SI-ID: 207308547
• Publication date in RUL: 12.09.2024

Record is a part of a journal

• Title: Frontiers in microbiology
• Shortened title: Front. microbiol.
• Publisher: Frontiers Research Foundation
• ISSN: 1664-302X
• COBISS.SI-ID: 4146296

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: črevesni mikrobi, strojno učenje, rak debelega črevesja, črevesni adenom, metagenomika, funkcionalni mikrobiom