Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer

Frontiers in Oncology

Oncology

Xudong Wu¹  Xianshu Wang¹  Zhimin Tang¹  Rongsong Zhao¹  Hongzhi Zou²  Side Liu³  Yusi Wang³ 

[1] Creative Biosciences (Guangzhou) CO., Ltd, Guangzhou, Guangdong, China;Creative Biosciences (Guangzhou) CO., Ltd, Guangzhou, Guangdong, China;Department of Colorectal Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China;Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China;

关键词: metagenomic sequencing;    fecal microbiota;    bacterial biomarker;    microbial taxonomy;    functional pathways;   

DOI  :  10.3389/fonc.2023.1218056

 received in 2023-05-06, accepted in 2023-07-10,  发布年份 2023

来源: Frontiers

【 摘 要 】

ObjectivesThis study aimed to identify colorectal cancer (CRC)-associated phylogenetic and functional bacterial features by a large-scale metagenomic sequencing and develop a binomial classifier to accurately distinguish between CRC patients and healthy individuals.MethodsWe conducted shotgun metagenomic analyses of fecal samples from a ZhongShanMed discovery cohort of 121 CRC and 52 controls and SouthernMed validation cohort of 67 CRC and 44 controls. Taxonomic profiling and quantification were performed by direct sequence alignment against genome taxonomy database (GTDB). High-quality reads were also aligned to IGC datasets to obtain functional profiles defined by Kyoto Encyclopedia of Genes and Genomes (KEGG). A least absolute shrinkage and selection operator (LASSO) classifier was constructed to quantify risk scores of probability of disease and to discriminate CRC from normal for discovery, validation, Fudan, GloriousMed, and HongKong cohorts.ResultsA diverse spectrum of bacterial and fungi species were found to be either enriched (368) or reduced (113) in CRC patients (q<0.05). Similarly, metabolic functions associated with biosynthesis and metabolism of amino acids and fatty acids were significantly altered (q<0.05). The LASSO regression analysis of significant changes in the abundance of microbial species in CRC achieved areas under the receiver operating characteristic curve (AUROCs) of 0.94 and 0.91 in the ZhongShanMed and SouthernMed cohorts, respectively. A further analysis of Fudan, GloriousMed, and HK cohorts using the same classification model also demonstrated AUROC of 0.80, 0.78, and 0.91, respectively. Moreover, major CRC-associated bacterial biomarkers identified in this study were found to be coherently enriched or depleted across 10 metagenomic sequencing studies of gut microbiota.ConclusionA coherent signature of CRC-associated bacterial biomarkers modeled on LASSO binomial classifier maybe used accurately for early detection of CRC.

【 授权许可】

Unknown   
Copyright © 2023 Wu, Tang, Zhao, Wang, Wang, Liu and Zou