Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer/Experiment 1

From BugSigDB


Needs review

Curated date: 2022/01/03

Curator: Itslanapark

Revision editor(s): WikiWorks, Itslanapark, Scholastica, Aleru Divine

Subjects

Location of subjects
United States of America
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 , Feces Colorectal mucosa,colorectal mucosa,Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
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 tumor-adjacent biopsy
Group 1 name Corresponds to the case (exposed) group for case-control studies
CRC tumor biopsy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Colorectal tumor tissues
Group 0 sample size Number of subjects in the control (unexposed) group
294
Group 1 sample size Number of subjects in the case (exposed) group
294
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Cases with previous chemotherapy and antibiotic use were excluded as well as patients with antibiotic use within 1 - 3 months prior to sample collection.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina, 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


Signature 1

Needs review

Curated date: 2024/03/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 2A, Result text

Description: Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)

Abundance in Group 1: increased abundance in CRC tumor biopsy

NCBI Quality ControlLinks
Fusobacterium
Leptotrichia
Parvimonas
Peptostreptococcus
Streptococcus
Actinomycetota

Revision editor(s): Scholastica

Signature 2

Needs review

Curated date: 2024/03/11

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 2A, Result text

Description: Description: Pairwise differences in CRC tumor vs. healthy adjacent tissue. Boxplots indicate the distribution of the relative abundances of various taxa and corresponding lines connect paired samples, depicting the direction of change in relative abundance of statistically significantly different families between CRC tumor biopsy samples and adjacent non-affected tissue microbiome(n = 294 pairs, 588 samples)

Abundance in Group 1: decreased abundance in CRC tumor biopsy

NCBI Quality ControlLinks
Dorea
Faecalibacterium
Parabacteroides
unclassified Rikenellaceae
Oscillospiraceae

Revision editor(s): Scholastica