HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women/Experiment 2
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
- Endocervix Endocervix,endocervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human papilloma virus infection , Chlamydophila infectious disease 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,Chlamydia caused disease or disorder,Chlamydia disease or disorder,Chlamydia infection,Chlamydia infectious disease,chlamydia infectious disease,Chlamydophila caused disease or disorder,Chlamydophila disease or disorder,Chlamydophila Infections,infection, Chlamydia,infections, Chlamydia,Chlamydophila infectious disease,chlamydophila infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HPV positive women
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patient with chlamydia infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient with Chlamydia infection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Current
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Figure 3
Description: LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.
Abundance in Group 1: increased abundance in patient with chlamydia infection
| NCBI | Quality Control | Links |
|---|---|---|
| Chlamydiota | ||
| Chlamydiaceae | ||
| Chlamydiia | ||
| Chlamydiales | ||
| Chlamydia | ||
| Chlamydia trachomatis |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09
Source: Figure 3
Description: LEfSe results on cervical microbiota in C. trachomatis-positive women compared to HPV-positive women or healthy controls.
Abundance in Group 1: decreased abundance in patient with chlamydia infection
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Lactobacillus | ||
| Bacilli | ||
| Lactobacillales | ||
| Bacillota |
Revision editor(s): WikiWorks
