Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study

Rana H. Abo-Hammam; Mohammed Salah; Sarah Shabayek; Amro Hanora; Samira Zakeer; Randa H. Khattab; Rana H. Abo-Hammam; Mohammed Salah; Sarah Shabayek; Amro Hanora; Samira Zakeer; Randa H. Khattab

doi:10.3934/microbiol.2024008

AIMS Microbiology

2024, Volume 10, Issue 1: 148-160. doi: 10.3934/microbiol.2024008

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Research article

Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study

1.
Forensic toxicologist and narcotics expert, Ministry of Justice, Tanta, Egypt
2.
Department of Microbiology and Immunology, Faculty of pharmacy, Port-Said University, Port-Said, Egypt
3.
Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
4.
Department of Microbiology and Immunology, Al-Salam University, Tanta, Egypt
† These Authors are equally contributed to this manuscript.

Received: 30 September 2023 Revised: 17 December 2023 Accepted: 29 December 2023 Published: 20 February 2024

One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.
- CRC,
- gut microbiota,
- metagenomic,
- dysbiosis,
- tumor biomarker
Citation: Rana H. Abo-Hammam, Mohammed Salah, Sarah Shabayek, Amro Hanora, Samira Zakeer, Randa H. Khattab. Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study[J]. AIMS Microbiology, 2024, 10(1): 148-160. doi: 10.3934/microbiol.2024008

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Abstract

One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.

Acknowledgments

The participants who made this study feasible have our sincere gratitude on behalf of all authors.

Authors contribution

Rana H. Abo-Hammam wrote the manuscript and analyzed the data. All authors read and approved the final manuscript.

Conflict of interests

The authors declare that they have no conflict of interests.

Funding

None.

Availability of data and materials

The datasets supporting the conclusions of this article are included within the article. The metagenomic shotgun data raw sequences of this study have been deposited in NCBI bioproject under accession number PRJNA895360. http://www.ncbi.nlm.nih.gov/bioproject/895360.

Ethics statement

The research was carried out in conformity with the rules established by the Faculty of Pharmacy, Suez Canal University, Egypt's Research Ethics Committee (Reference Code, 2020MH1). It was conducted according to the principle of the Declaration of Helsinki. Thirteen Tanta City Oncology Center patients, aged between 55 and 60, who had been diagnosed with cancer, participated in the study after giving their informed consent.

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