Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
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
- Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low grade squamus intraepithelial lesion
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high grade squamus intraepithelial lesion
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- high grade squamus intraepithelial lesion confirmed by histology or cytology
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 92
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 14 days
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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 5
Description: Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis
Abundance in Group 1: increased abundance in high grade squamus intraepithelial lesion
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcus anaerobius | ||
| Anaerococcus | ||
| Anaerococcus tetradius | ||
| Sneathia | ||
| Fusobacteriales | ||
| Sneathia sanguinegens | ||
| Fusobacteriota | ||
| Leptotrichiaceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 5
Description: Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis
Abundance in Group 1: decreased abundance in high grade squamus intraepithelial lesion
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus jensenii | ||
| Limosilactobacillus coleohominis |
Revision editor(s): WikiWorks
