HPV/Chlamydia trachomatis co-infection: metagenomic analysis of cervical microbiota in asymptomatic women/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
- Endocervix Endocervix,endocervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chlamydia trachomatis infectious disease chlamydia,Chlamydia Infections,Chlamydia trachomatis caused disease or disorder,Chlamydia trachomatis disease or disorder,Chlamydia trachomatis infectious disease,chlamydia trachomatis infectious disease,chlamydial disease,Chlamydial Infection,Chlamydial infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- 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
- 7
- 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 |
|---|---|---|
| Aerococcus | ||
| Aerococcaceae | ||
| Aerococcus christensenii |
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 |
|---|---|---|
| Lactobacillales | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Bacillota | ||
| Bacilli |
Revision editor(s): WikiWorks
