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Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues

Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a puta- tive biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyze...

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Main Authors:	Aisyah, Yunus, Norfilza, Mohd Mokhtar, Raja Affendi, Raja Ali, Siti Maryam, Ahmad Kendong, Hajar Fauzan, Ahmad
Format:	Article
Language:	English
Published:	Elsevier B.V. 2024
Subjects:	HD Industries. Land use. Labor Q Science (General)
Online Access:	http://umpir.ump.edu.my/id/eprint/40517/1/Methods%20for%20identification%20of%20the%20opportunistic%20gut%20mycobiome%20from%20colorectal%20adenocarcinoma%20biopsy%20tissues.pdf http://umpir.ump.edu.my/id/eprint/40517/ https://doi.org/10.1016/j.mex.2024.102623
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spelling	my.ump.umpir.405172024-02-27T01:24:40Z http://umpir.ump.edu.my/id/eprint/40517/ Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues Aisyah, Yunus Norfilza, Mohd Mokhtar Raja Affendi, Raja Ali Siti Maryam, Ahmad Kendong Hajar Fauzan, Ahmad HD Industries. Land use. Labor Q Science (General) Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a puta- tive biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To character- ize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis re- vealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Ex- panding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer. • Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing. • Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening. • Contribution to the advancement of innovative colorectal cancer diagnostic methods and tar- geted therapies by applying gut mycobiome knowledge. Elsevier B.V. 2024 Article PeerReviewed pdf en cc_by_4 http://umpir.ump.edu.my/id/eprint/40517/1/Methods%20for%20identification%20of%20the%20opportunistic%20gut%20mycobiome%20from%20colorectal%20adenocarcinoma%20biopsy%20tissues.pdf Aisyah, Yunus and Norfilza, Mohd Mokhtar and Raja Affendi, Raja Ali and Siti Maryam, Ahmad Kendong and Hajar Fauzan, Ahmad (2024) Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues. MethodsX, 12 (102623). ISSN 2215-0161. (Published) https://doi.org/10.1016/j.mex.2024.102623 10.1016/j.mex.2024.102623
institution	Universiti Malaysia Pahang Al-Sultan Abdullah
building	UMPSA Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Pahang Al-Sultan Abdullah
content_source	UMPSA Institutional Repository
url_provider	http://umpir.ump.edu.my/
language	English
topic	HD Industries. Land use. Labor Q Science (General)
spellingShingle	HD Industries. Land use. Labor Q Science (General) Aisyah, Yunus Norfilza, Mohd Mokhtar Raja Affendi, Raja Ali Siti Maryam, Ahmad Kendong Hajar Fauzan, Ahmad Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
description	Colorectal cancer poses a significant threat to global health, necessitating the development of effective early detection techniques. However, the potential of the fungal microbiome as a puta- tive biomarker for the detection of colorectal adenocarcinoma has not been extensively explored. We analyzed the viability of implementing the fungal mycobiome for this purpose. Biopsies were collected from cancer and polyp patients. The total genomic DNA was extracted from the biopsy samples by utilizing a comprehensive kit to ensure optimal microbial DNA recovery. To character- ize the composition and diversity of the fungal mycobiome, high-throughput amplicon sequencing targeting the internal transcribed spacer 1 (ITS1) region was proposed. A comparative analysis re- vealed discrete fungal profiles among the diseased groups. Here, we also proposed pipelines based on a predictive model using statistical and machine learning algorithms to accurately differentiate colorectal adenocarcinoma and polyp patients from normal individuals. These findings suggest the utility of gut mycobiome as biomarkers for the detection of colorectal adenocarcinoma. Ex- panding our understanding of the role of the gut mycobiome in disease detection creates novel opportunities for early intervention and personalized therapeutic strategies for colorectal cancer. • Detailed method to identify the gut mycobiome in colorectal cancer patients using ITS-specific amplicon sequencing. • Application of machine learning algorithms to the identification of potential mycobiome biomarkers for non-invasive colorectal cancer screening. • Contribution to the advancement of innovative colorectal cancer diagnostic methods and tar- geted therapies by applying gut mycobiome knowledge.
format	Article
author	Aisyah, Yunus Norfilza, Mohd Mokhtar Raja Affendi, Raja Ali Siti Maryam, Ahmad Kendong Hajar Fauzan, Ahmad
author_facet	Aisyah, Yunus Norfilza, Mohd Mokhtar Raja Affendi, Raja Ali Siti Maryam, Ahmad Kendong Hajar Fauzan, Ahmad
author_sort	Aisyah, Yunus
title	Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
title_short	Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
title_full	Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
title_fullStr	Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
title_full_unstemmed	Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
title_sort	methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues
publisher	Elsevier B.V.
publishDate	2024
url	http://umpir.ump.edu.my/id/eprint/40517/1/Methods%20for%20identification%20of%20the%20opportunistic%20gut%20mycobiome%20from%20colorectal%20adenocarcinoma%20biopsy%20tissues.pdf http://umpir.ump.edu.my/id/eprint/40517/ https://doi.org/10.1016/j.mex.2024.102623
_version_	1822924162760441856
score	13.244413

Methods for identification of the opportunistic gut mycobiome from colorectal adenocarcinoma biopsy tissues

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