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Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset



Najla Kharrat1*, Mourad Assidi2,3, Muhammad Abu-Elmagd2,3,4, Peter N. Pushparaj2,3, AreejAlkhaldy5, Leila Arfaoui5, Muhammad Imran Naseer2,3, Abdelfatteh El Omri6, Safia Messaoudi7, Abdelbaset Buhmeida2,3, Ahmed Rebai1



1Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnologyof Sfax, Bioinformatics Group, P.O. Box: 1177, Sfax, 3018 Tunisia; 2Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia; 3Medical Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; 4School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK; 5Clinical Nutrition Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; 6Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; 7Forensic Biology Department, College of Forensic Sciences, Naf Arab University for Security Sciences, Riyadh, Saudi Arabia



Dr. Najla Kharrat Phone: +216 74 871 816; E-mail -; *Corresponding author


Article Type

Research Article



Received May 7, 2019; Accepted May 9, 2019; Published May 30, 2019



Gut microbiota and their metabolites play a vital role in colon health and disease. Accumulating evidence suggests that the gut microbiota contributes to the risk of colorectal cancer (CRC). However, the role of a specific microbial community together with their metabolites contributing to the risk, initiation and progression of CRC is still unknown. Hence, we used a Bayesian Networks in combination with the IDA (Intervention calculus when the DAG is absent) to generate a graphical model that allows causal relationships to be inferred from observational data. Results from the analysis of publically available datasets showed that four species: Fusobacteium, Citrobacter, Microbacterium and Slaxkia have estimated non-null lower bounds of causal effects of CRC. These findings support the hypothesis that specific bacterial species (microbial markers) act in concert with locally modified microbiota to cause or influence CRC progression. Additional comprehensive studies are required to validate the potential use of F. nucleatum, Citrobacter as well as Slackia as microbial
biomarkers in CRC for prevention, diagnosis, prognosis and/or therapeutics.



Colorectal cancer, microbiome, bacteria, Fusobacterium spp., IDA method, biomarker



Kharrat et al. Bioinformation 15(6): 372-379 (2019)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.