Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Fatima, Claregrieve1, ChiomaBlessing
Subjects
- Location of subjects
- Sweden
- 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
- Mucosa of ascending colon Ascending colon mucosa,Ascending colon mucosa of organ,Ascending colon mucous membrane,Ascending colon organ mucosa,Mucosa of organ of ascending colon,Mucous membrane of ascending colon,Organ mucosa of ascending colon,Mucosa of ascending colon,mucosa of ascending 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
- control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colon cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with stage I-III colon cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- recent
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 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
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
Source: Table 2, supplemental table S1
Description: Microbiota alterations in colon cancer mucosa samples compared with non cancer control mucosa at colonoscopy
Abundance in Group 1: increased abundance in colon cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Bilophila | ||
| Clostridium | ||
| Dialister | ||
| Methanobacteriota | ||
| Fusobacteriota | ||
| Fusobacterium | ||
| Methanobrevibacter | ||
| Oscillospira | ||
| Peptostreptococcus | ||
| Mycoplasmatota |
Revision editor(s): Fatima, Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/10/29
Source: Table 2, supplemental table S1
Description: Microbiota alterations in colon cancer mucosa compared with non cancer control mucosa at colonoscopy
Abundance in Group 1: decreased abundance in colon cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Fatima, Claregrieve1, WikiWorks
