Microbiota disbiosis is associated with colorectal cancer

From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-10-28
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Gao Z, Guo B, Gao R, Zhu Q, Qin H
Journal
Frontiers in microbiology
Year
2015
Keywords:
colorectal cancer, distal colon, gut dysbiosis, mucosa-associated microbiota, proximal colon
The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals differed significantly. Firmicutes and Fusobacteria were over-represented whereas Proteobacteria was under-represented in CRC patients. In addition, Lactococcus and Fusobacterium exhibited a relatively higher abundance while Pseudomonas and Escherichia-Shigella was reduced in cancerous tissues compared to adjacent non-cancerous tissues. Meanwhile, the overall microbial structures of proximal and distal colon cancerous tissues were similar; but certain potential pro-oncogenic pathogens were different. These results suggested that the mucosa-associated microbiota is dynamically associated with CRC, which may provide evidences for microbiota-associated diagnostic, prognostic, preventive, and therapeutic strategies for CRC.

Experiment 1


Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/25

Curator: Andre

Revision editor(s): Andre, Deacme, ChiomaBlessing

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
Colorectal mucosa Colorectal mucosa,colorectal mucosa
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
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Colorectal Cancer Patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals that have been diagnosed with cancer that originates in the colon, part of the digestive system.
Group 0 sample size Number of subjects in the control (unexposed) group
30
Group 1 sample size Number of subjects in the case (exposed) group
31
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Fisher's Exact Test
Chi-Square
T-Test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3
Matched on Factors on which subjects have been matched on in a case-control study
age, body mass index, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/25

Curator: Andre

Revision editor(s): Andre, Deacme, ChiomaBlessing

Source: Figure 2B, Figure 3

Description: Different structures of gut microbiota between healthy individuals and CRC patients

Abundance in Group 1: increased abundance in Colorectal Cancer Patients

NCBI Quality ControlLinks
Escherichia/Shigella sp.
Fusobacterium
Lactococcus
Peptostreptococcus
Prevotella
Fusobacteriaceae
Bacteroidia
Prevotellaceae
Gemella
Gemellaceae
Porphyromonadaceae
Shewanella
Shewanellaceae
Parvimonas
Dialister

Revision editor(s): Andre, Deacme, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/25

Curator: Andre

Revision editor(s): Andre, Deacme, ChiomaBlessing

Source: Figure 2, Figure 3

Description: Different structures of gut microbiota between healthy individuals and CRC patients

Abundance in Group 1: decreased abundance in Colorectal Cancer Patients

NCBI Quality ControlLinks
Acidovorax
Acinetobacter
Alphaproteobacteria
Brevundimonas
Buttiauxella
Caulobacter
Epilithonimonas
Flavobacterium
Janthinobacterium
Pedobacter
Propionibacterium
Pseudomonas
Psychrobacter
Rahnella
Sphingobacterium
Sphingomonas
Stenotrophomonas
Brochothrix
Moraxellaceae
Flavobacteriaceae
Flavobacteriales
Pseudomonadaceae
Pseudomonadota
Gammaproteobacteria
Pseudomonadales

Revision editor(s): Andre, Deacme, ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, Deacme, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
adjacent non-cancerous tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
cancerous tissues
Group 0 sample size Number of subjects in the control (unexposed) group
20

Lab analysis

Statistical Analysis

Statistical test
Fisher's Exact Test
Chi-Square
T-Test
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified
Matched on Factors on which subjects have been matched on in a case-control study
Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, Tolulopeo

Source: Figure 2D

Description: The dominant genera of group cancerous compared to non-cancerous mucosa

Abundance in Group 1: increased abundance in cancerous tissues

NCBI Quality ControlLinks
Bacteroides
Lactococcus
Fusobacterium
Prevotella
Streptococcus

Revision editor(s): Andre, Tolulopeo

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, Tolulopeo

Source: Figure 2D

Description: The dominant genera of group cancerous compared to non-cancerous mucosa.

Abundance in Group 1: decreased abundance in cancerous tissues

NCBI Quality ControlLinks
Pseudomonas

Revision editor(s): Andre, Tolulopeo

Experiment 3


Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, ChiomaBlessing

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Sigmoid neoplasm neoplasm of sigmoid colon,sigmoid colon neoplasm,sigmoid colon neoplasm (disease),sigmoid colon tumor,sigmoid neoplasm,tumor of sigmoid colon,Sigmoid neoplasm
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Proximal Colon Cancer
Group 1 name Corresponds to the case (exposed) group for case-control studies
Distal Colorectal Cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Distal colon cancer tissue samples obtained from patients diagnosed with colorectal cancer (CRC), located in the sigmoid colon (25–35 cm from anus)
Group 0 sample size Number of subjects in the control (unexposed) group
15
Group 1 sample size Number of subjects in the case (exposed) group
16

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, ChiomaBlessing

Source: FIGURE 4

Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)

Abundance in Group 1: increased abundance in Distal Colorectal Cancer

NCBI Quality ControlLinks
Escherichia/Shigella sp.
Fusobacterium
Leptotrichia

Revision editor(s): Andre, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Lwaldron on 2023-10-28

Curated date: 2023/07/26

Curator: Andre

Revision editor(s): Andre, ChiomaBlessing

Source: FIGURE 4

Description: Comparison of Gut Microbiota Between Proximal Colon Cancer and Distal Colorectal Cancer based on Principal component analysis (PCA) scores (97% similarity level)

Abundance in Group 1: decreased abundance in Distal Colorectal Cancer

NCBI Quality ControlLinks
Peptostreptococcus
Prevotella
Pyramidobacter sp.
Selenomonas

Revision editor(s): Andre, ChiomaBlessing