Cargando…
Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer
Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8484797/ https://www.ncbi.nlm.nih.gov/pubmed/34604238 http://dx.doi.org/10.3389/fcell.2021.736994 |
_version_ | 1784577396602568704 |
---|---|
author | Yuan, Yumeng Chen, Yihuan Yao, Fen Zeng, Mi Xie, Qingdong Shafiq, Muhammad Noman, Sohail Muhammad Jiao, Xiaoyang |
author_facet | Yuan, Yumeng Chen, Yihuan Yao, Fen Zeng, Mi Xie, Qingdong Shafiq, Muhammad Noman, Sohail Muhammad Jiao, Xiaoyang |
author_sort | Yuan, Yumeng |
collection | PubMed |
description | Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF). Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software. Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue. Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method. |
format | Online Article Text |
id | pubmed-8484797 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-84847972021-10-02 Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer Yuan, Yumeng Chen, Yihuan Yao, Fen Zeng, Mi Xie, Qingdong Shafiq, Muhammad Noman, Sohail Muhammad Jiao, Xiaoyang Front Cell Dev Biol Cell and Developmental Biology Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF). Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software. Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue. Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method. Frontiers Media S.A. 2021-09-17 /pmc/articles/PMC8484797/ /pubmed/34604238 http://dx.doi.org/10.3389/fcell.2021.736994 Text en Copyright © 2021 Yuan, Chen, Yao, Zeng, Xie, Shafiq, Noman and Jiao. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cell and Developmental Biology Yuan, Yumeng Chen, Yihuan Yao, Fen Zeng, Mi Xie, Qingdong Shafiq, Muhammad Noman, Sohail Muhammad Jiao, Xiaoyang Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title | Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title_full | Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title_fullStr | Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title_full_unstemmed | Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title_short | Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer |
title_sort | microbiomes and resistomes in biopsy tissue and intestinal lavage fluid of colorectal cancer |
topic | Cell and Developmental Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8484797/ https://www.ncbi.nlm.nih.gov/pubmed/34604238 http://dx.doi.org/10.3389/fcell.2021.736994 |
work_keys_str_mv | AT yuanyumeng microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT chenyihuan microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT yaofen microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT zengmi microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT xieqingdong microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT shafiqmuhammad microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT nomansohailmuhammad microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer AT jiaoxiaoyang microbiomesandresistomesinbiopsytissueandintestinallavagefluidofcolorectalcancer |