Gut mucosal microbiome across stages of colorectal carcinogenesis/Experiment 3

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

Curated date: 2022/06/25

Curator: Jeshudy

Revision editor(s): Jeshudy, Claregrieve1, WikiWorks

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 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 adenoma
Group 1 name Corresponds to the case (exposed) group for case-control studies
colorectal cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
subjects with invasive adenocarcinoma
Group 0 sample size Number of subjects in the control (unexposed) group
47
Group 1 sample size Number of subjects in the case (exposed) group
52

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

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 2023/01/27

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