Cervicovaginal microbiome and natural history of Chlamydia trachomatis in adolescents and young women/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- United States of America
- 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
- Uterine cervix Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bacterial vaginosis BACT VAGINITIDES,BACT VAGINITIS,BACT VAGINOSES,BACT VAGINOSIS,Bacterial Vaginitides,Bacterial Vaginitis,Bacterial Vaginoses,bacterial vaginosis,BV,Nonspecific Vaginitis,VAGINITIDES BACT,Vaginitides, Bacterial,VAGINITIS BACT,Vaginitis, Bacterial,Vaginitis, Nonspecific,VAGINOSES BACT,Vaginoses, Bacterial,VAGINOSIS BACT,Vaginosis, Bacterial,Bacterial vaginosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Chlamydia trichomonas Controls (t0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chlamydia trichomonas Cases (t0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cervicovaginal samples were collected approximately at time of the incident detection of CT infection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 187
- Group 1 sample size Number of subjects in the case (exposed) group
- 373
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, ethnic group, Matched on: "year of enrollment" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.year of enrollment, Matched on: "past history" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.past history, Matched on: "duration of illness" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.duration of illness
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 4E
Description: Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Controls (t0).
Abundance in Group 1: increased abundance in Chlamydia trichomonas Cases (t0)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Anaerococcus | ||
| Arcanobacterium | ||
| Atopobium | ||
| Chlamydia | ||
| Gardnerella | ||
| Gemella | ||
| Mobiluncus | ||
| Mycoplasma | ||
| Parvimonas | ||
| Prevotella | ||
| Sneathia |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 4E
Description: Results of ANCOM analysis of differentially abundant genera associated with Chlamydia trichomonas Cases (t0) vs Chlamydia trichomonas Controls (t0).
Abundance in Group 1: decreased abundance in Chlamydia trichomonas Cases (t0)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Lactobacillus |
Revision editor(s): MyleeeA
