Gut mucosal microbiome across stages of colorectal carcinogenesis/Experiment 9

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

Curated date: 2022/07/05

Curator: Jeshudy

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

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 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

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): Not specified

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

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

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 Control	Links
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.