Gut mucosal microbiome across stages of colorectal carcinogenesis

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J, Sung JJ
Journal
Nature communications
Year
2015
Gut microbial dysbiosis contributes to the development of colorectal cancer (CRC). Here we catalogue the microbial communities in human gut mucosae at different stages of colorectal tumorigenesis. We analyse the gut mucosal microbiome of 47 paired samples of adenoma and adenoma-adjacent mucosae, 52 paired samples of carcinoma and carcinoma-adjacent mucosae and 61 healthy controls. Probabilistic partitioning of relative abundance profiles reveals that a metacommunity predominated by members of the oral microbiome is primarily associated with CRC. Analysis of paired samples shows differences in community configurations between lesions and the adjacent mucosae. Correlations of bacterial taxa indicate early signs of dysbiosis in adenoma, and co-exclusive relationships are subsequently more common in cancer. We validate these alterations in CRC-associated microbiome by comparison with two previously published data sets. Our results suggest that a taxonomically defined microbial consortium is implicated in the development of CRC.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/24

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Peace Sandy

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
Intestine Bowel,Intestinal tract,Intestine,intestine
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
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 adenoma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
histology-proven adenoma
Group 0 sample size Number of subjects in the control (unexposed) group
61
Group 1 sample size Number of subjects in the case (exposed) group
47

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V4
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
Mann-Whitney (Wilcoxon)
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)?
Yes

Alpha Diversity

Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/24

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between patients with colorectal adenoma and controls

Abundance in Group 1: increased abundance in colorectal adenoma

NCBI Quality ControlLinks
Bacillales
Bacteroides uniformis
Blautia sp.
Enhydrobacter sp.
Escherichia coli
Gemella sp.
Parvimonas sp.
Peptostreptococcus sp.
Prevotella intermedia

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between patients with colorectal adenoma and controls

Abundance in Group 1: decreased abundance in colorectal adenoma

NCBI Quality ControlLinks
Bacillales
Bacteroides sp.
Bacteroides uniformis
Blautia obeum
Blautia sp.
Coprococcus sp.
Faecalibacterium prausnitzii
Prevotella sp.

Revision editor(s): Jeshudy, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/24

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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 1 name Corresponds to the case (exposed) group for case-control studies
colorectal cancer (adenocarcinoma)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
subjects with invasive adenocarcinoma
Group 1 sample size Number of subjects in the case (exposed) group
52

Lab analysis

Statistical Analysis

Alpha Diversity

Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between patients with colorectal adenocarcinoma and controls

Abundance in Group 1: increased abundance in colorectal cancer (adenocarcinoma)

NCBI Quality ControlLinks
Aggregatibacter segnis
Bacteroides fragilis
Bacteroides ovatus
Campylobacter sp.
Fusobacterium sp.
Gemella sp.
Granulicatella sp.
Oscillospira
Parvimonas sp.
Peptostreptococcus sp.
Porphyromonas endodontalis
Prevotella intermedia
Prevotella sp.
Pseudomonas veronii

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/26

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between patients with colorectal adenocarcinoma and controls

Abundance in Group 1: decreased abundance in colorectal cancer (adenocarcinoma)

NCBI Quality ControlLinks
Bacteroides sp.
Blautia sp.
Escherichia coli
Faecalibacterium prausnitzii
Pseudomonas veronii

Revision editor(s): Jeshudy, Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/27

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
colorectal adenoma
Group 1 name Corresponds to the case (exposed) group for case-control studies
colorectal cancer
Group 0 sample size Number of subjects in the control (unexposed) group
47

Lab analysis

Statistical Analysis

Alpha Diversity

Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/27

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma

Abundance in Group 1: increased abundance in colorectal cancer

NCBI Quality ControlLinks
Alistipes putredinis
Bacteroides fragilis
Bacteroides ovatus
Bacteroides sp.
Blautia sp.
Clostridiales bacterium
Fusobacterium sp.
Gemella sp.
Oscillospira
Parabacteroides sp.
Parvimonas sp.
Pedobacter cryoconitis
Peptostreptococcus sp.
Porphyromonas endodontalis
Prevotella intermedia
Prevotella sp.
Leyella stercorea
Ruminococcus sp.

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/27

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between patients with colorectal adenocarcinoma and colorectal adenoma

Abundance in Group 1: decreased abundance in colorectal cancer

NCBI Quality ControlLinks
Enhydrobacter sp.
Escherichia coli
Pedobacter cryoconitis
Pseudomonas veronii
Rothia terrae

Revision editor(s): Jeshudy, Claregrieve1

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/30

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
carcinoma-adjacent mucosae
Group 1 name Corresponds to the case (exposed) group for case-control studies
carcinoma mucosae
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
specimens collected from adenocarcinoma tissue
Group 0 sample size Number of subjects in the control (unexposed) group
52

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study
Matched on: "subject" 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.subject


Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae

Abundance in Group 1: decreased abundance in carcinoma mucosae

NCBI Quality ControlLinks
Blautia sp.
Pseudomonas veronii

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between carcinoma-adjacent mucosae and carcinoma mucosae

Abundance in Group 1: increased abundance in carcinoma mucosae

NCBI Quality ControlLinks
Fusobacterium sp.

Revision editor(s): Jeshudy, Claregrieve1

Experiment 5


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
adenoma-adjacent
Group 1 name Corresponds to the case (exposed) group for case-control studies
adenocarcinoma mucosae
Group 0 sample size Number of subjects in the control (unexposed) group
47

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples

Abundance in Group 1: decreased abundance in adenocarcinoma mucosae

NCBI Quality ControlLinks
Bacillus sp. (in: firmicutes)
Enhydrobacter sp.
Escherichia coli
Pedobacter cryoconitis
Pseudomonas veronii
Rothia terrae

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between adenoma-adjacent samples and adenocarcinoma samples

Abundance in Group 1: increased abundance in adenocarcinoma mucosae

NCBI Quality ControlLinks
Bacteroides fragilis
Blautia sp.
Campylobacter sp.
Clostridiales bacterium
Fusobacterium sp.
Gemella sp.
Granulicatella sp.
Oscillospira
Parabacteroides sp.
Parvimonas sp.
Peptostreptococcus sp.
Porphyromonas endodontalis
Prevotella intermedia
Prevotella sp.
Leyella stercorea

Revision editor(s): Jeshudy, Claregrieve1

Experiment 7


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
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
adenoma-adjacent
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
specimen collected adjacent to histology-proven adenoma
Group 0 sample size Number of subjects in the control (unexposed) group
61
Group 1 sample size Number of subjects in the case (exposed) group
47

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study
Not specified


Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue

Abundance in Group 1: decreased abundance in adenoma-adjacent

NCBI Quality ControlLinks
Blautia sp.
Coprococcus sp.
Enterocloster clostridioformis
Faecalibacterium prausnitzii

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between healthy control tissue and adenoma-adjacent tissue

Abundance in Group 1: increased abundance in adenoma-adjacent

NCBI Quality ControlLinks
Enhydrobacter sp.
Fusobacterium sp.
Pedobacter cryoconitis

Revision editor(s): Jeshudy, Claregrieve1

Experiment 8


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

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 1 name Corresponds to the case (exposed) group for case-control studies
carcinoma-adjacent
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
specimen collected from tissue adjacent to adenocarcinoma site
Group 1 sample size Number of subjects in the case (exposed) group
52

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplemental Figure 9

Description: Differential microbial abundance between healthy control tissue and adenocarcinoma-adjacent tissue

Abundance in Group 1: increased abundance in carcinoma-adjacent

NCBI Quality ControlLinks
Bacteroides fragilis
Bacteroides ovatus
Fusobacterium sp.
Gemella sp.
Granulicatella sp.
Peptostreptococcus sp.
Porphyromonas endodontalis
Prevotella sp.

Revision editor(s): Jeshudy, Claregrieve1

Experiment 9


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
colorectal adenoma tissue
Group 1 name Corresponds to the case (exposed) group for case-control studies
carcinoma-adjacent tissue
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
specimens collected from tissue adjacent to adenocarcinoma
Group 0 sample size Number of subjects in the control (unexposed) group
47
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Not specified

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples

Abundance in Group 1: increased abundance in carcinoma-adjacent tissue

NCBI Quality ControlLinks
Alistipes putredinis
Bacteroides fragilis
Bacteroides ovatus
Bacteroides sp.
Bacteroides uniformis
Blautia obeum
Blautia sp.
Clostridiales bacterium
Coprococcus sp.
Faecalibacterium prausnitzii
Fusobacterium sp.
Gemella sp.
Oscillospira
Parvimonas sp.
Peptostreptococcus sp.
Porphyromonas endodontalis
Prevotella intermedia
Prevotella sp.
Leyella stercorea
Ruminococcus sp.

Revision editor(s): Jeshudy, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/31

Curated date: 2022/07/05

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1

Source: Supplementary Figure 9

Description: Differential microbial abundance between adenoma samples and adenocarcinoma-adjacent samples

Abundance in Group 1: decreased abundance in carcinoma-adjacent tissue

NCBI Quality ControlLinks
Enhydrobacter sp.

Revision editor(s): Jeshudy, Claregrieve1