Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Subjects
- Location of subjects
- Italy
- 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
- Vaginal fluid Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HPV+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HPV+ determined through HR-HC2 assay
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 days
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
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
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 6a
Description: Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women
Abundance in Group 1: increased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Sneathia | ||
| Megasphaera | ||
| Pediococcus | ||
| Brevibacterium | ||
| Pseudomonas |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: figure 6a
Description: Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women
Abundance in Group 1: decreased abundance in HPV+
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudoxanthomonas | ||
| Actinomyces | ||
| Vampirovibrio | ||
| Alkanindiges |
Revision editor(s): WikiWorks
