Research Article
Metagenomic Study of the Liver Microbiota in Liver Cancer-Metagenomic and Metatranscriptomic Analyses of the Hepatocellular Carcinoma- Associated Microbial Communities and the Potential Role of Microbial Communities in Liver Cancer
Asmaa Ezzat1, Mohd Noor Mat Isa2, Irni Suhayu Sapian2, Zeinat Kamel3, Abd ElHady Abd ElWahab4,Ekram Hamed5 and Mahmoud ElHefnawi1,6*1Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), National Research centre, Ciro, Egypt
2Malaysia Genome Institute, Malaysia
3Microbiology Department, Faculty of Science, Cairo University, Egypt
4Cancer Biology Department, National Cancer Institute, Cairo, Egypt
5Radiotherapy Department, National Cancer Institute, Cairo, Egypt
6Informatics and Systems Department, Engineering Division, National Research Centre, Cairo, Egypt
- *Corresponding Author:
- Mahmoud ElHefnawi
Informatics and Systems Department
Engineering division, National Research Centre
Cairo, Egypt
Tel: (02) 01111177817
Fax: (+202) 33370931C E-mail: mahef111@gmail.com
Received date: June 21, 2014; Accepted date: October 09, 2014; Published date: October 15, 2014
Citation: Ezzat A, Mat Isa MN, Sapian IS, Kamel Z, ElHady Abd ElWahab A, et al. (2014) Metagenomic Study of the Liver Microbiota in Liver Cancer-Metagenomic and Metatranscriptomic Analyses of the Hepatocellular Carcinoma-Associated Microbial Communities and the Potential Role of Microbial Communities in Liver Cancer. J Gastroint Dig Syst 4:228. doi:10.4172/2161-069X.1000228
Copyright: © 2014 Ezzat A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Objective: Metagenomics is a new science that revolutionized microbiology for its ability to study the microbiota of a given environment without the need of culture. Human microbiota is the collection of microbes that inhabit different sites of the human body and recently its alterations were related to different human diseases especially cancers. Liver cancer incidence is continually increasing in Egypt with a high mortality rate. This study aimed to identify the abundant microbial communities that inhabit the liver of the hepatocellular carcinoma patient and may be associated with disease incidence or at least disease progression.
Methods: Fresh liver biopsy samples of two hepatocellular carcinoma Egyptian patients were obtained. DNA from one sample and RNA from other sample were extracted followed by Illumina sequencing. Taxonomic and functional analyses were performed using the MG-RAST server.
Results: Proteobacteria was the dominant phylum followed by Firmicutes and Actinobacteria in both DNA and RNA samples. Some other phyla as Chlorobi, Bacteria and Cyanobacteria had the same abundance in the two dataset. But it was noted that the bacterial diversity and presence of useful bacteria in sample 2 of grade 1 disease (RNA sample) were more than it in sample 1 of grade 2 disease (DNA sample). Also, some other phyla are found in the cDNA dataset annotations. On the other hand, infectious diseases pathways analysis showed the enrichment of infectious diseases pathways of Staphylococcus aureus infection, Vibrio cholera infection, pathogenic Escherichia coli infection, Hepatitis c, Tuberculosis, Epithelial cell signalling in Helicobacter pylori infection, Bacterial invasion of epithelial cells, and salmonella infection.
Conclusions: There is a potential link between some definite microbial communities and liver cancer that need some attention for improving early diagnosis and preventing disease progression. Further studies are required to support this
