Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer/Experiment 1
From BugSigDB
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Reviewed Marked as Reviewed by Atrayees on 2023-8-18
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy volunteers (swc)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CRC patients (swp)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 37-88 years of age, diagnosed with colorectal cancer (swp = gut swab)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Sanger
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: decreased abundance in CRC patients (swp)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Catenibacterium | ||
| Faecalibacterium | ||
| Blautia | ||
| Gardnerella | ||
| Bifidobacterium | ||
| Lachnospira |
Signature 2
Source: Figure 4A
Description: Relative abundance of significantly different genera between CRC patients and healthy controls. (A) Genera different between swp and swc.
Abundance in Group 1: increased abundance in CRC patients (swp)
| NCBI | Quality Control | Links |
|---|---|---|
| Catonella | ||
| Fusobacterium | ||
| Gemella | ||
| Klebsiella | ||
| Mogibacterium | ||
| Peptostreptococcus | ||
| Porphyromonas | ||
| Selenomonas | ||
| Filifactor |
