Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues

Abstract

Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized. Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth. Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing. Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing. Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities. Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.

Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota

“…Within our cohort, community-wide microbiota dissimilarity between paired on- and off-tumor samples varied substantially among patients. This is broadly consistent with previous observations, with some studies reporting differences ( Marchesi et al., 2011 ; Kostic et al., 2013 ; Boleij et al., 2015 ; Gao et al., 2015 ; Loke et al., 2018 ; Sheng et al., 2020 ; Zhu et al., 2022 ), whereas in other studies ( Chen et al., 2012 ; Kostic et al., 2012 ; Flemer et al., 2017 ; Murphy et al., 2021 ) on- and off-tumor microbiota were highly similar. These observations suggest that patients may be grouped according to whether they harbor distinct tumor-associated microbiota compared with adjacent normal tissues.…”

Effects of Long Non-Coding RNAs Induced by the Gut Microbiome on Regulating the Development of Colorectal Cancer

“…Enrichment of pathogenic bacteria in the gut can cause DNA damage, promote inflammation, induce tumor cell proliferation, and shield the tumor from immune attack [ 29 ]. Intestinal ecological dysregulation has been identified in several macrogenomic studies on CRC as a crucial risk factor for the development of colorectal malignancies [ 30 , 31 , 32 ]. The Alpha-bugs and the bacterial driver-passenger models are widely accepted theories for how dysregulated gut microbiota triggers the development and progression of CRC [ 33 , 34 ].…”