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Updated: Aug 15, 2025

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied

Han Shuwen^1,2, Wu Yinhang², Zhao Xingming³

¹Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, 88 Jiefang Road, Building 6 Room 2018, Hangzhou, 310009, Zhejiang, China.

|December 28, 2022

Abstract

Background:

Colorectal cancer (CRC) is a multifactorial disease with genetic and environmental factors. Regional differences in risk factors are an important reason for the different incidences of CRC in different regions.

Objective:

The goal was to clarify the intestinal microbial composition and structure of CRC patients in different regions and construct CRC risk prediction models based on regional differences.

Methods:

A metagenomic dataset of 601 samples from 6 countries in the GMrepo and NCBI databases was collected. All whole-genome sequencing (WGS) data were annotated for species by MetaPhlAn2. We obtained the relative abundance of species composition at the species level and genus level. The MicrobiotaProcess package was used to visualize species composition and PCA. LEfSe analysis was used to analyze the differences in the datasets in each region. Spearman correlation analysis was performed for CRC differential species. Finally, the CRC risk prediction model was constructed and verified in each regional dataset.

Results:

The composition of the intestinal bacterial community varied in different regions. Differential intestinal bacteria of CRC in different regions are inconsistent. There was a common diversity of bacteria in all six countries, such as Peptostreptococcus stomatis and Fusobacterium nucleatum at the species level. Peptostreptococcus stomatis (species level) and Peptostreptococcus (genus level) are important CRC-related bacteria that are related to other bacteria in different regions. Region has little influence on the accuracy of the CRC risk prediction model. Peptostreptococcus stomatis is an important variable in CRC risk prediction models in all regions.

Conclusion:

Peptostreptococcus stomatis is a common high-risk pathogen of CRC worldwide, and it is an important variable in CRC risk prediction models in all regions. However, regional differences in intestinal bacteria had no significant impact on the accuracy of the CRC risk prediction model.

Keywords:

Colorectal cancer Intestinal bacteria Regional difference

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