Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Cao Y, Shang F, Jin M, Deng S, Gu J, Mao F, Qin L, Wang J, Xue Y, Jiang Z, Cheng D, Liu L, Nie X, Liu T, Liu H, Cai K
Journal
BJS open
Year
2023
BACKGROUND: The relationship between intestinal obstruction due to colorectal cancer (CRC) and the gut microbiota remains largely unknown. The aim of this study was to investigate the potential association between alterations in gut microbiota and CRC in the presence of intestinal obstruction. METHODS: Patients with CRC with or without obstruction were recruited and compared using 1:1 propensity score matching (PSM). Total DNA from tumours and adjacent normal tissues of 84 patients and 36 frozen tumour tissues was extracted and amplified. 16S RNA sequencing was used to uncover differences in microbiota composition between the two groups. RESULTS: A total of 313 patients with CRC were recruited. Survival analysis demonstrated that patients in the obstruction group had shorter overall survival time and disease-free survival (DFS) time than those in the non-obstruction group. Microbial richness and diversity in tumour tissues of patients with obstruction were significantly higher than those of patients with no obstruction. The alpha diversity indices and beta diversity exhibited were different between the two groups (P < 0.05). At the phylum and genus levels, Bacteroidetes were significantly enriched in the tumour tissues of patients with obstruction. Alpha diversity in tumour tissues was closely related to specific microbiota. These findings were replicated in the 16S rRNA analyses from frozen samples. There were more Bacteroidetes in CRC patients with obstruction. CONCLUSIONS: Patients with obstructed CRC have worse prognosis and have differences in their microbiota. Higher levels of Bacteroides were observed in patients with obstructed CRC.

Experiment 1


incomplete

Curated date: 2024/01/31

Curator: Andre

Revision editor(s): Andre

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Colorectal cancer without intestinal obstruction
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colorectal cancer with intestinal obstruction

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Kruskall-Wallis
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
Confounders controlled for: "Age at diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age at diagnosis, sex, Confounders controlled for: "TNM stage" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.TNM stage, Confounders controlled for: "histological grade" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.histological grade, Confounders controlled for: "tumour size" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumour size, Confounders controlled for: "tumour site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumour site, chemotherapy, body mass index

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

incomplete

Curated date: 2024/01/31

Curator: Andre

Revision editor(s): Andre

Source: Fig. 5e & 5f

Description: Phyllum and genus level differences in microbial taxa between the CRC with intestinal obstruction and CRC without intestinal obstruction.

Abundance in Group 1: increased abundance in Colorectal cancer with intestinal obstruction

NCBI Quality ControlLinks
Bacillota
Deinococcota
Vulcanimicrobiota
Candidatus Saccharibacteria
Actinomycetota
Planctomycetales
Synergistota
Candidatus Parcubacteria
Nitrospirota
Chloroflexia
Bacteroidia
Verrucomicrobiota
Mycoplasmatota
Acidobacteriota
Gemmatimonadia
Ochrobactrum
Bacteroides
Thermus
Shigella
Flavobacterium
Sphingobium
Massilia
Brevundimonas
Arthrobacter
Herbaspirillum
Roseateles
Acinetobacter
Lactobacillus
Caulobacter
Ralstonia

Revision editor(s): Andre

Signature 2

incomplete

Curated date: 2024/01/31

Curator: Andre

Revision editor(s): Andre

Source: Fig. 5e & 5f

Description: Phyllum and genus level differences in microbial taxa between the CRC with intestinal obstruction and CRC without intestinal obstruction.

Abundance in Group 1: decreased abundance in Colorectal cancer with intestinal obstruction

NCBI Quality ControlLinks
Armatimonadota
Deferribacteres
Fusobacteriota
Pseudomonadota
Cyanobacteriota
Sphingomonas
Clostridium
Cupriavidus
Helicobacter
Leptotrichia

Revision editor(s): Andre

Experiment 2


incomplete

Curated date: 2024/01/31

Curator: Andre

Revision editor(s): Andre

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
Not specified
Statistical test
LEfSe
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2.45
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
body mass index, chemotherapy, sex, Confounders controlled for: "Age at diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age at diagnosis, Confounders controlled for: "TNM stage" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.TNM stage, Confounders controlled for: "histological grade" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.histological grade, Confounders controlled for: "tumour size" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumour size, Confounders controlled for: "tumour site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tumour site

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased