ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microorganisms in Vertebrate Digestive Systems
Metagenomic Profiling of Gut Microbiome Signatures Across Liver Disease Stages and HCV-Related Hepatocellular Carcinoma in Egyptian Patients
American University in Cairo, Cairo, Egypt
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Abstract
INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt. METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients. RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis. DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, 3 are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.
Summary
Keywords
Egypt, gut, HCV, Hepatocellular Carcinoma, Metagenomics, microbiome, whole-metagenome sequencing
Received
01 December 2025
Accepted
17 February 2026
Copyright
© 2026 Zahra, Ouf, Azzazy and Moustafa. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Marwa Atef Zahra; Ahmed Moustafa
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