Extending colonic mucosal microbiome analysis-assessment of colonic lavage as a proxy for endoscopic colonic biopsies/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- United Kingdom
- 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
- Sigmoid colon Colon sigmoideum,Pelvic colon,Sigmoid colon,Sigmoid flexure,sigmoid colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colonic Biopsy sample
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colonic Lavage Sample
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colonic lavage from sigmoid colon
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- increased
Signature 1
Needs review
Source: Table S2
Description: Table showing differential abundance between the two samples (Biopsy and Lavage)
Abundance in Group 1: increased abundance in Colonic Lavage Sample
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Holdemania | ||
| unclassified Lachnospiraceae |
Revision editor(s): Ifeanyisam
Signature 2
Needs review
Source: Table S2
Description: Table showing differential abundance between the two samples (Biopsy and Lavage)
Abundance in Group 1: decreased abundance in Colonic Lavage Sample
Revision editor(s): Ifeanyisam
